chore: bump version to 0.8.16

.github/workflows/add-community-extension.lock.yml

@@ -1,4 +1,4 @@
-# gh-aw-metadata: {"schema_version":"v3","frontmatter_hash":"2ace61d3a4e86e81ce7ff110e118981b4d88a06aa351ecdc2c3b64e44b10690f","compiler_version":"v0.74.8","strict":true,"agent_id":"copilot"}
+# gh-aw-metadata: {"schema_version":"v3","frontmatter_hash":"1583d46477aa35f00e2c7ab97f06bacf4f6e21bdaa9d58b0ef704a588e588a7e","compiler_version":"v0.74.8","strict":true,"agent_id":"copilot"}
 # gh-aw-manifest: {"version":1,"secrets":["COPILOT_GITHUB_TOKEN","GH_AW_CI_TRIGGER_TOKEN","GH_AW_GITHUB_MCP_SERVER_TOKEN","GH_AW_GITHUB_TOKEN","GITHUB_TOKEN"],"actions":[{"repo":"actions/checkout","sha":"de0fac2e4500dabe0009e67214ff5f5447ce83dd","version":"v6.0.2"},{"repo":"actions/download-artifact","sha":"3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c","version":"v8.0.1"},{"repo":"actions/github-script","sha":"3a2844b7e9c422d3c10d287c895573f7108da1b3","version":"v9.0.0"},{"repo":"actions/setup-node","sha":"48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e","version":"v6.4.0"},{"repo":"actions/upload-artifact","sha":"043fb46d1a93c77aae656e7c1c64a875d1fc6a0a","version":"v7.0.1"},{"repo":"github/gh-aw-actions/setup","sha":"efa55847f72aadb03490d955263ff911bf758700","version":"v0.74.8"}],"containers":[{"image":"ghcr.io/github/gh-aw-firewall/agent:0.25.49"},{"image":"ghcr.io/github/gh-aw-firewall/api-proxy:0.25.49"},{"image":"ghcr.io/github/gh-aw-firewall/squid:0.25.49"},{"image":"ghcr.io/github/gh-aw-mcpg:v0.3.9","digest":"sha256:64828b42a4482f58fab16509d7f8f495a6d97c972a98a68aff20543531ac0388","pinned_image":"ghcr.io/github/gh-aw-mcpg:v0.3.9@sha256:64828b42a4482f58fab16509d7f8f495a6d97c972a98a68aff20543531ac0388"},{"image":"ghcr.io/github/github-mcp-server:v1.0.4"},{"image":"node:lts-alpine","digest":"sha256:d1b3b4da11eefd5941e7f0b9cf17783fc99d9c6fc34884a665f40a06dbdfc94f","pinned_image":"node:lts-alpine@sha256:d1b3b4da11eefd5941e7f0b9cf17783fc99d9c6fc34884a665f40a06dbdfc94f"}]}
 #    ___                   _   _      
 #   / _ \                 | | (_)     
@@ -38,7 +38,7 @@
 #   - actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9.0.0 (source v9)
 #   - actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
 #   - actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
-#   - github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+#   - github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
 #
 # Container images used:
 #   - ghcr.io/github/gh-aw-firewall/agent:0.25.49
@@ -52,6 +52,8 @@ name: "Add Community Extension from Issue Submission"
 on:
   issues:
     types:
+    - opened
+    - edited
     - labeled
   # skip-bots: # Skip-bots processed as bot check in pre-activation job
   # - github-actions # Skip-bots processed as bot check in pre-activation job
@@ -90,7 +92,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -204,23 +206,23 @@ jobs:
         run: |
           bash "${RUNNER_TEMP}/gh-aw/actions/create_prompt_first.sh"
           {
-          cat << 'GH_AW_PROMPT_767e1d181d9dae54_EOF'
+          cat << 'GH_AW_PROMPT_2b92c540a0b471a7_EOF'
           <system>
-          GH_AW_PROMPT_767e1d181d9dae54_EOF
+          GH_AW_PROMPT_2b92c540a0b471a7_EOF
           cat "${RUNNER_TEMP}/gh-aw/prompts/xpia.md"
           cat "${RUNNER_TEMP}/gh-aw/prompts/temp_folder_prompt.md"
           cat "${RUNNER_TEMP}/gh-aw/prompts/markdown.md"
           cat "${RUNNER_TEMP}/gh-aw/prompts/safe_outputs_prompt.md"
-          cat << 'GH_AW_PROMPT_767e1d181d9dae54_EOF'
+          cat << 'GH_AW_PROMPT_2b92c540a0b471a7_EOF'
           <safe-output-tools>
           Tools: add_comment(max:2), create_pull_request, add_labels(max:3), missing_tool, missing_data, noop
-          GH_AW_PROMPT_767e1d181d9dae54_EOF
+          GH_AW_PROMPT_2b92c540a0b471a7_EOF
           cat "${RUNNER_TEMP}/gh-aw/prompts/safe_outputs_create_pull_request.md"
-          cat << 'GH_AW_PROMPT_767e1d181d9dae54_EOF'
+          cat << 'GH_AW_PROMPT_2b92c540a0b471a7_EOF'
           </safe-output-tools>
-          GH_AW_PROMPT_767e1d181d9dae54_EOF
+          GH_AW_PROMPT_2b92c540a0b471a7_EOF
           cat "${RUNNER_TEMP}/gh-aw/prompts/mcp_cli_tools_prompt.md"
-          cat << 'GH_AW_PROMPT_767e1d181d9dae54_EOF'
+          cat << 'GH_AW_PROMPT_2b92c540a0b471a7_EOF'
           <github-context>
           The following GitHub context information is available for this workflow:
           {{#if github.actor}}
@@ -252,12 +254,12 @@ jobs:
             - **Note**: If a branch you need is not in the list above and is not listed as an additional fetched ref, it has NOT been checked out. For private repositories you cannot fetch it without proper authentication. If the branch is required and not available, exit with an error and ask the user to add it to the `fetch:` option of the `checkout:` configuration (e.g., `fetch: ["refs/pulls/open/*"]` for all open PR refs, or `fetch: ["main", "feature/my-branch"]` for specific branches).
           </github-context>
           
-          GH_AW_PROMPT_767e1d181d9dae54_EOF
+          GH_AW_PROMPT_2b92c540a0b471a7_EOF
           cat "${RUNNER_TEMP}/gh-aw/prompts/github_mcp_tools_with_safeoutputs_prompt.md"
-          cat << 'GH_AW_PROMPT_767e1d181d9dae54_EOF'
+          cat << 'GH_AW_PROMPT_2b92c540a0b471a7_EOF'
           </system>
           {{#runtime-import .github/workflows/add-community-extension.md}}
-          GH_AW_PROMPT_767e1d181d9dae54_EOF
+          GH_AW_PROMPT_2b92c540a0b471a7_EOF
           } > "$GH_AW_PROMPT"
       - name: Interpolate variables and render templates
         uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9.0.0
@@ -368,7 +370,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -464,9 +466,9 @@ jobs:
           mkdir -p "${RUNNER_TEMP}/gh-aw/safeoutputs"
           mkdir -p /tmp/gh-aw/safeoutputs
           mkdir -p /tmp/gh-aw/mcp-logs/safeoutputs
-          cat > "${RUNNER_TEMP}/gh-aw/safeoutputs/config.json" << 'GH_AW_SAFE_OUTPUTS_CONFIG_95f097d550e5bb4b_EOF'
-          {"add_comment":{"max":2},"add_labels":{"allowed":["extension-submission","validation-passed","validation-failed","needs-info"],"max":3},"create_pull_request":{"draft":true,"labels":["extension-submission","automated"],"max":1,"max_patch_files":100,"max_patch_size":1024,"protect_top_level_dot_folders":true,"protected_files":["package.json","bun.lockb","bunfig.toml","deno.json","deno.jsonc","deno.lock","global.json","NuGet.Config","Directory.Packages.props","mix.exs","mix.lock","go.mod","go.sum","stack.yaml","stack.yaml.lock","pom.xml","build.gradle","build.gradle.kts","settings.gradle","settings.gradle.kts","gradle.properties","package-lock.json","yarn.lock","pnpm-lock.yaml","npm-shrinkwrap.json","requirements.txt","Pipfile","Pipfile.lock","pyproject.toml","setup.py","setup.cfg","Gemfile","Gemfile.lock","uv.lock","CODEOWNERS","DESIGN.md","CONTRIBUTING.md","SECURITY.md","CODE_OF_CONDUCT.md","AGENTS.md","CLAUDE.md","GEMINI.md"],"protected_files_policy":"blocked","title_prefix":"[extension] "},"create_report_incomplete_issue":{},"missing_data":{},"missing_tool":{},"noop":{"max":1,"report-as-issue":"false"},"report_incomplete":{}}
-          GH_AW_SAFE_OUTPUTS_CONFIG_95f097d550e5bb4b_EOF
+          cat > "${RUNNER_TEMP}/gh-aw/safeoutputs/config.json" << 'GH_AW_SAFE_OUTPUTS_CONFIG_66c58b0f685caa27_EOF'
+          {"add_comment":{"max":2},"add_labels":{"allowed":["extension-submission","validation-passed","validation-failed","needs-info"],"max":3},"create_pull_request":{"draft":true,"labels":["extension-submission","automated"],"max":1,"max_patch_files":100,"max_patch_size":1024,"protect_top_level_dot_folders":true,"protected_files":["package.json","bun.lockb","bunfig.toml","deno.json","deno.jsonc","deno.lock","global.json","NuGet.Config","Directory.Packages.props","mix.exs","mix.lock","go.mod","go.sum","stack.yaml","stack.yaml.lock","pom.xml","build.gradle","build.gradle.kts","settings.gradle","settings.gradle.kts","gradle.properties","package-lock.json","yarn.lock","pnpm-lock.yaml","npm-shrinkwrap.json","requirements.txt","Pipfile","Pipfile.lock","pyproject.toml","setup.py","setup.cfg","Gemfile","Gemfile.lock","uv.lock","CODEOWNERS","DESIGN.md","CONTRIBUTING.md","SECURITY.md","CODE_OF_CONDUCT.md","AGENTS.md","CLAUDE.md","GEMINI.md"],"protected_files_policy":"blocked","title_prefix":"[extension] "},"create_report_incomplete_issue":{},"missing_data":{},"missing_tool":{},"noop":{"max":1,"report-as-issue":"true"},"report_incomplete":{}}
+          GH_AW_SAFE_OUTPUTS_CONFIG_66c58b0f685caa27_EOF
       - name: Generate Safe Outputs Tools
         env:
           GH_AW_TOOLS_META_JSON: |
@@ -722,7 +724,7 @@ jobs:
           
           mkdir -p /home/runner/.copilot
           GH_AW_NODE=$(which node 2>/dev/null || command -v node 2>/dev/null || echo node)
-          cat << GH_AW_MCP_CONFIG_9f16469ceb45c7f6_EOF | "$GH_AW_NODE" "${RUNNER_TEMP}/gh-aw/actions/start_mcp_gateway.cjs"
+          cat << GH_AW_MCP_CONFIG_881a93100a972629_EOF | "$GH_AW_NODE" "${RUNNER_TEMP}/gh-aw/actions/start_mcp_gateway.cjs"
           {
             "mcpServers": {
               "github": {
@@ -763,7 +765,7 @@ jobs:
               "payloadDir": "${MCP_GATEWAY_PAYLOAD_DIR}"
             }
           }
-          GH_AW_MCP_CONFIG_9f16469ceb45c7f6_EOF
+          GH_AW_MCP_CONFIG_881a93100a972629_EOF
       - name: Mount MCP servers as CLIs
         id: mount-mcp-clis
         continue-on-error: true
@@ -1045,7 +1047,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -1079,7 +1081,7 @@ jobs:
           GH_AW_WORKFLOW_NAME: "Add Community Extension from Issue Submission"
           GH_AW_RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
           GH_AW_AGENT_CONCLUSION: ${{ needs.agent.result }}
-          GH_AW_NOOP_REPORT_AS_ISSUE: "false"
+          GH_AW_NOOP_REPORT_AS_ISSUE: "true"
         with:
           github-token: ${{ secrets.GH_AW_GITHUB_TOKEN || secrets.GITHUB_TOKEN }}
           script: |
@@ -1186,7 +1188,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -1382,7 +1384,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -1454,7 +1456,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -1556,7 +1558,7 @@ jobs:
           GH_AW_ALLOWED_DOMAINS: "api.business.githubcopilot.com,api.enterprise.githubcopilot.com,api.github.com,api.githubcopilot.com,api.individual.githubcopilot.com,api.snapcraft.io,archive.ubuntu.com,azure.archive.ubuntu.com,crl.geotrust.com,crl.globalsign.com,crl.identrust.com,crl.sectigo.com,crl.thawte.com,crl.usertrust.com,crl.verisign.com,crl3.digicert.com,crl4.digicert.com,crls.ssl.com,github.com,host.docker.internal,json-schema.org,json.schemastore.org,keyserver.ubuntu.com,ocsp.digicert.com,ocsp.geotrust.com,ocsp.globalsign.com,ocsp.identrust.com,ocsp.sectigo.com,ocsp.ssl.com,ocsp.thawte.com,ocsp.usertrust.com,ocsp.verisign.com,packagecloud.io,packages.cloud.google.com,packages.microsoft.com,ppa.launchpad.net,raw.githubusercontent.com,registry.npmjs.org,s.symcb.com,s.symcd.com,security.ubuntu.com,telemetry.enterprise.githubcopilot.com,ts-crl.ws.symantec.com,ts-ocsp.ws.symantec.com,www.googleapis.com"
           GITHUB_SERVER_URL: ${{ github.server_url }}
           GITHUB_API_URL: ${{ github.api_url }}
-          GH_AW_SAFE_OUTPUTS_HANDLER_CONFIG: "{\"add_comment\":{\"max\":2},\"add_labels\":{\"allowed\":[\"extension-submission\",\"validation-passed\",\"validation-failed\",\"needs-info\"],\"max\":3},\"create_pull_request\":{\"draft\":true,\"labels\":[\"extension-submission\",\"automated\"],\"max\":1,\"max_patch_files\":100,\"max_patch_size\":1024,\"protect_top_level_dot_folders\":true,\"protected_files\":[\"package.json\",\"bun.lockb\",\"bunfig.toml\",\"deno.json\",\"deno.jsonc\",\"deno.lock\",\"global.json\",\"NuGet.Config\",\"Directory.Packages.props\",\"mix.exs\",\"mix.lock\",\"go.mod\",\"go.sum\",\"stack.yaml\",\"stack.yaml.lock\",\"pom.xml\",\"build.gradle\",\"build.gradle.kts\",\"settings.gradle\",\"settings.gradle.kts\",\"gradle.properties\",\"package-lock.json\",\"yarn.lock\",\"pnpm-lock.yaml\",\"npm-shrinkwrap.json\",\"requirements.txt\",\"Pipfile\",\"Pipfile.lock\",\"pyproject.toml\",\"setup.py\",\"setup.cfg\",\"Gemfile\",\"Gemfile.lock\",\"uv.lock\",\"CODEOWNERS\",\"DESIGN.md\",\"CONTRIBUTING.md\",\"SECURITY.md\",\"CODE_OF_CONDUCT.md\",\"AGENTS.md\",\"CLAUDE.md\",\"GEMINI.md\"],\"protected_files_policy\":\"blocked\",\"title_prefix\":\"[extension] \"},\"create_report_incomplete_issue\":{},\"missing_data\":{},\"missing_tool\":{},\"noop\":{\"max\":1,\"report-as-issue\":\"false\"},\"report_incomplete\":{}}"
+          GH_AW_SAFE_OUTPUTS_HANDLER_CONFIG: "{\"add_comment\":{\"max\":2},\"add_labels\":{\"allowed\":[\"extension-submission\",\"validation-passed\",\"validation-failed\",\"needs-info\"],\"max\":3},\"create_pull_request\":{\"draft\":true,\"labels\":[\"extension-submission\",\"automated\"],\"max\":1,\"max_patch_files\":100,\"max_patch_size\":1024,\"protect_top_level_dot_folders\":true,\"protected_files\":[\"package.json\",\"bun.lockb\",\"bunfig.toml\",\"deno.json\",\"deno.jsonc\",\"deno.lock\",\"global.json\",\"NuGet.Config\",\"Directory.Packages.props\",\"mix.exs\",\"mix.lock\",\"go.mod\",\"go.sum\",\"stack.yaml\",\"stack.yaml.lock\",\"pom.xml\",\"build.gradle\",\"build.gradle.kts\",\"settings.gradle\",\"settings.gradle.kts\",\"gradle.properties\",\"package-lock.json\",\"yarn.lock\",\"pnpm-lock.yaml\",\"npm-shrinkwrap.json\",\"requirements.txt\",\"Pipfile\",\"Pipfile.lock\",\"pyproject.toml\",\"setup.py\",\"setup.cfg\",\"Gemfile\",\"Gemfile.lock\",\"uv.lock\",\"CODEOWNERS\",\"DESIGN.md\",\"CONTRIBUTING.md\",\"SECURITY.md\",\"CODE_OF_CONDUCT.md\",\"AGENTS.md\",\"CLAUDE.md\",\"GEMINI.md\"],\"protected_files_policy\":\"blocked\",\"title_prefix\":\"[extension] \"},\"create_report_incomplete_issue\":{},\"missing_data\":{},\"missing_tool\":{},\"noop\":{\"max\":1,\"report-as-issue\":\"true\"},\"report_incomplete\":{}}"
           GH_AW_CI_TRIGGER_TOKEN: ${{ secrets.GH_AW_CI_TRIGGER_TOKEN }}
         with:
           github-token: ${{ secrets.GH_AW_GITHUB_TOKEN || secrets.GITHUB_TOKEN }}

.github/workflows/add-community-extension.md

@@ -4,7 +4,7 @@ emoji: "🧩"
 
 on:
   issues:
-    types: [labeled]
+    types: [opened, edited, labeled]
   skip-bots: [github-actions, copilot, dependabot]
 
 tools:
@@ -22,8 +22,6 @@ checkout:
   fetch-depth: 0
 
 safe-outputs:
-  noop:
-    report-as-issue: false
   create-pull-request:
     title-prefix: "[extension] "
     labels: [extension-submission, automated]
@@ -49,9 +47,14 @@ or update entries in the community extension catalog.
 
 ## Triggering Conditions
 
-This workflow only triggers when the `extension-submission` label is added to an
-issue. Before processing, verify that the issue title starts with `[Extension]:`.
-If it does not, stop without commenting.
+This workflow triggers on issue events. **Only process the issue if ALL of these
+conditions are met:**
+
+1. The issue has the `extension-submission` label
+2. The issue title starts with `[Extension]:`
+
+If the issue does not meet these conditions, add a brief comment explaining that
+this workflow only processes extension submission issues, then stop.
 
 ## Step 1 — Read and Parse the Issue
 

.github/workflows/add-community-preset.lock.yml

@@ -1,4 +1,4 @@
-# gh-aw-metadata: {"schema_version":"v3","frontmatter_hash":"f209d3fbcde6b25fd5099c7b1ea0d3dace8967b23d8049a92566c213ed9ccc5e","compiler_version":"v0.74.8","strict":true,"agent_id":"copilot"}
+# gh-aw-metadata: {"schema_version":"v3","frontmatter_hash":"6111bd4a1cd2c363f1f05f185164e08883d6df79da732a8c07b9aa602ed7dfe6","compiler_version":"v0.74.8","strict":true,"agent_id":"copilot"}
 # gh-aw-manifest: {"version":1,"secrets":["COPILOT_GITHUB_TOKEN","GH_AW_CI_TRIGGER_TOKEN","GH_AW_GITHUB_MCP_SERVER_TOKEN","GH_AW_GITHUB_TOKEN","GITHUB_TOKEN"],"actions":[{"repo":"actions/checkout","sha":"de0fac2e4500dabe0009e67214ff5f5447ce83dd","version":"v6.0.2"},{"repo":"actions/download-artifact","sha":"3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c","version":"v8.0.1"},{"repo":"actions/github-script","sha":"3a2844b7e9c422d3c10d287c895573f7108da1b3","version":"v9.0.0"},{"repo":"actions/setup-node","sha":"48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e","version":"v6.4.0"},{"repo":"actions/upload-artifact","sha":"043fb46d1a93c77aae656e7c1c64a875d1fc6a0a","version":"v7.0.1"},{"repo":"github/gh-aw-actions/setup","sha":"efa55847f72aadb03490d955263ff911bf758700","version":"v0.74.8"}],"containers":[{"image":"ghcr.io/github/gh-aw-firewall/agent:0.25.49"},{"image":"ghcr.io/github/gh-aw-firewall/api-proxy:0.25.49"},{"image":"ghcr.io/github/gh-aw-firewall/squid:0.25.49"},{"image":"ghcr.io/github/gh-aw-mcpg:v0.3.9","digest":"sha256:64828b42a4482f58fab16509d7f8f495a6d97c972a98a68aff20543531ac0388","pinned_image":"ghcr.io/github/gh-aw-mcpg:v0.3.9@sha256:64828b42a4482f58fab16509d7f8f495a6d97c972a98a68aff20543531ac0388"},{"image":"ghcr.io/github/github-mcp-server:v1.0.4"},{"image":"node:lts-alpine","digest":"sha256:d1b3b4da11eefd5941e7f0b9cf17783fc99d9c6fc34884a665f40a06dbdfc94f","pinned_image":"node:lts-alpine@sha256:d1b3b4da11eefd5941e7f0b9cf17783fc99d9c6fc34884a665f40a06dbdfc94f"}]}
 #    ___                   _   _      
 #   / _ \                 | | (_)     
@@ -38,7 +38,7 @@
 #   - actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9.0.0 (source v9)
 #   - actions/setup-node@48b55a011bda9f5d6aeb4c2d9c7362e8dae4041e # v6.4.0
 #   - actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
-#   - github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+#   - github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
 #
 # Container images used:
 #   - ghcr.io/github/gh-aw-firewall/agent:0.25.49
@@ -52,6 +52,8 @@ name: "Add Community Preset from Issue Submission"
 on:
   issues:
     types:
+    - opened
+    - edited
     - labeled
   # skip-bots: # Skip-bots processed as bot check in pre-activation job
   # - github-actions # Skip-bots processed as bot check in pre-activation job
@@ -90,7 +92,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -204,23 +206,23 @@ jobs:
         run: |
           bash "${RUNNER_TEMP}/gh-aw/actions/create_prompt_first.sh"
           {
-          cat << 'GH_AW_PROMPT_c25ce620b285c8e3_EOF'
+          cat << 'GH_AW_PROMPT_fc7609016a7d28af_EOF'
           <system>
-          GH_AW_PROMPT_c25ce620b285c8e3_EOF
+          GH_AW_PROMPT_fc7609016a7d28af_EOF
           cat "${RUNNER_TEMP}/gh-aw/prompts/xpia.md"
           cat "${RUNNER_TEMP}/gh-aw/prompts/temp_folder_prompt.md"
           cat "${RUNNER_TEMP}/gh-aw/prompts/markdown.md"
           cat "${RUNNER_TEMP}/gh-aw/prompts/safe_outputs_prompt.md"
-          cat << 'GH_AW_PROMPT_c25ce620b285c8e3_EOF'
+          cat << 'GH_AW_PROMPT_fc7609016a7d28af_EOF'
           <safe-output-tools>
           Tools: add_comment(max:2), create_pull_request, add_labels(max:3), missing_tool, missing_data, noop
-          GH_AW_PROMPT_c25ce620b285c8e3_EOF
+          GH_AW_PROMPT_fc7609016a7d28af_EOF
           cat "${RUNNER_TEMP}/gh-aw/prompts/safe_outputs_create_pull_request.md"
-          cat << 'GH_AW_PROMPT_c25ce620b285c8e3_EOF'
+          cat << 'GH_AW_PROMPT_fc7609016a7d28af_EOF'
           </safe-output-tools>
-          GH_AW_PROMPT_c25ce620b285c8e3_EOF
+          GH_AW_PROMPT_fc7609016a7d28af_EOF
           cat "${RUNNER_TEMP}/gh-aw/prompts/mcp_cli_tools_prompt.md"
-          cat << 'GH_AW_PROMPT_c25ce620b285c8e3_EOF'
+          cat << 'GH_AW_PROMPT_fc7609016a7d28af_EOF'
           <github-context>
           The following GitHub context information is available for this workflow:
           {{#if github.actor}}
@@ -252,12 +254,12 @@ jobs:
             - **Note**: If a branch you need is not in the list above and is not listed as an additional fetched ref, it has NOT been checked out. For private repositories you cannot fetch it without proper authentication. If the branch is required and not available, exit with an error and ask the user to add it to the `fetch:` option of the `checkout:` configuration (e.g., `fetch: ["refs/pulls/open/*"]` for all open PR refs, or `fetch: ["main", "feature/my-branch"]` for specific branches).
           </github-context>
           
-          GH_AW_PROMPT_c25ce620b285c8e3_EOF
+          GH_AW_PROMPT_fc7609016a7d28af_EOF
           cat "${RUNNER_TEMP}/gh-aw/prompts/github_mcp_tools_with_safeoutputs_prompt.md"
-          cat << 'GH_AW_PROMPT_c25ce620b285c8e3_EOF'
+          cat << 'GH_AW_PROMPT_fc7609016a7d28af_EOF'
           </system>
           {{#runtime-import .github/workflows/add-community-preset.md}}
-          GH_AW_PROMPT_c25ce620b285c8e3_EOF
+          GH_AW_PROMPT_fc7609016a7d28af_EOF
           } > "$GH_AW_PROMPT"
       - name: Interpolate variables and render templates
         uses: actions/github-script@3a2844b7e9c422d3c10d287c895573f7108da1b3 # v9.0.0
@@ -368,7 +370,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -464,9 +466,9 @@ jobs:
           mkdir -p "${RUNNER_TEMP}/gh-aw/safeoutputs"
           mkdir -p /tmp/gh-aw/safeoutputs
           mkdir -p /tmp/gh-aw/mcp-logs/safeoutputs
-          cat > "${RUNNER_TEMP}/gh-aw/safeoutputs/config.json" << 'GH_AW_SAFE_OUTPUTS_CONFIG_50dbf4670371d6f7_EOF'
-          {"add_comment":{"max":2},"add_labels":{"allowed":["preset-submission","validation-passed","validation-failed","needs-info"],"max":3},"create_pull_request":{"draft":true,"labels":["preset-submission","automated"],"max":1,"max_patch_files":100,"max_patch_size":1024,"protect_top_level_dot_folders":true,"protected_files":["package.json","bun.lockb","bunfig.toml","deno.json","deno.jsonc","deno.lock","global.json","NuGet.Config","Directory.Packages.props","mix.exs","mix.lock","go.mod","go.sum","stack.yaml","stack.yaml.lock","pom.xml","build.gradle","build.gradle.kts","settings.gradle","settings.gradle.kts","gradle.properties","package-lock.json","yarn.lock","pnpm-lock.yaml","npm-shrinkwrap.json","requirements.txt","Pipfile","Pipfile.lock","pyproject.toml","setup.py","setup.cfg","Gemfile","Gemfile.lock","uv.lock","CODEOWNERS","DESIGN.md","CONTRIBUTING.md","SECURITY.md","CODE_OF_CONDUCT.md","AGENTS.md","CLAUDE.md","GEMINI.md"],"protected_files_policy":"blocked","title_prefix":"[preset] "},"create_report_incomplete_issue":{},"missing_data":{},"missing_tool":{},"noop":{"max":1,"report-as-issue":"false"},"report_incomplete":{}}
-          GH_AW_SAFE_OUTPUTS_CONFIG_50dbf4670371d6f7_EOF
+          cat > "${RUNNER_TEMP}/gh-aw/safeoutputs/config.json" << 'GH_AW_SAFE_OUTPUTS_CONFIG_9e8dea0461236832_EOF'
+          {"add_comment":{"max":2},"add_labels":{"allowed":["preset-submission","validation-passed","validation-failed","needs-info"],"max":3},"create_pull_request":{"draft":true,"labels":["preset-submission","automated"],"max":1,"max_patch_files":100,"max_patch_size":1024,"protect_top_level_dot_folders":true,"protected_files":["package.json","bun.lockb","bunfig.toml","deno.json","deno.jsonc","deno.lock","global.json","NuGet.Config","Directory.Packages.props","mix.exs","mix.lock","go.mod","go.sum","stack.yaml","stack.yaml.lock","pom.xml","build.gradle","build.gradle.kts","settings.gradle","settings.gradle.kts","gradle.properties","package-lock.json","yarn.lock","pnpm-lock.yaml","npm-shrinkwrap.json","requirements.txt","Pipfile","Pipfile.lock","pyproject.toml","setup.py","setup.cfg","Gemfile","Gemfile.lock","uv.lock","CODEOWNERS","DESIGN.md","CONTRIBUTING.md","SECURITY.md","CODE_OF_CONDUCT.md","AGENTS.md","CLAUDE.md","GEMINI.md"],"protected_files_policy":"blocked","title_prefix":"[preset] "},"create_report_incomplete_issue":{},"missing_data":{},"missing_tool":{},"noop":{"max":1,"report-as-issue":"true"},"report_incomplete":{}}
+          GH_AW_SAFE_OUTPUTS_CONFIG_9e8dea0461236832_EOF
       - name: Generate Safe Outputs Tools
         env:
           GH_AW_TOOLS_META_JSON: |
@@ -722,7 +724,7 @@ jobs:
           
           mkdir -p /home/runner/.copilot
           GH_AW_NODE=$(which node 2>/dev/null || command -v node 2>/dev/null || echo node)
-          cat << GH_AW_MCP_CONFIG_04e1e53849e8d680_EOF | "$GH_AW_NODE" "${RUNNER_TEMP}/gh-aw/actions/start_mcp_gateway.cjs"
+          cat << GH_AW_MCP_CONFIG_c8953ff00c8ee9ee_EOF | "$GH_AW_NODE" "${RUNNER_TEMP}/gh-aw/actions/start_mcp_gateway.cjs"
           {
             "mcpServers": {
               "github": {
@@ -763,7 +765,7 @@ jobs:
               "payloadDir": "${MCP_GATEWAY_PAYLOAD_DIR}"
             }
           }
-          GH_AW_MCP_CONFIG_04e1e53849e8d680_EOF
+          GH_AW_MCP_CONFIG_c8953ff00c8ee9ee_EOF
       - name: Mount MCP servers as CLIs
         id: mount-mcp-clis
         continue-on-error: true
@@ -1045,7 +1047,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -1079,7 +1081,7 @@ jobs:
           GH_AW_WORKFLOW_NAME: "Add Community Preset from Issue Submission"
           GH_AW_RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
           GH_AW_AGENT_CONCLUSION: ${{ needs.agent.result }}
-          GH_AW_NOOP_REPORT_AS_ISSUE: "false"
+          GH_AW_NOOP_REPORT_AS_ISSUE: "true"
         with:
           github-token: ${{ secrets.GH_AW_GITHUB_TOKEN || secrets.GITHUB_TOKEN }}
           script: |
@@ -1186,7 +1188,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -1382,7 +1384,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -1454,7 +1456,7 @@ jobs:
     steps:
       - name: Setup Scripts
         id: setup
-        uses: github/gh-aw-actions/setup@b11be78086764c43fa463398aed7ffdcf40549c1 # v0.77.0
+        uses: github/gh-aw-actions/setup@318d7f4901f78b85e25b91709cf0109ac9b425f6 # v0.74.9
         with:
           destination: ${{ runner.temp }}/gh-aw/actions
           job-name: ${{ github.job }}
@@ -1556,7 +1558,7 @@ jobs:
           GH_AW_ALLOWED_DOMAINS: "api.business.githubcopilot.com,api.enterprise.githubcopilot.com,api.github.com,api.githubcopilot.com,api.individual.githubcopilot.com,api.snapcraft.io,archive.ubuntu.com,azure.archive.ubuntu.com,crl.geotrust.com,crl.globalsign.com,crl.identrust.com,crl.sectigo.com,crl.thawte.com,crl.usertrust.com,crl.verisign.com,crl3.digicert.com,crl4.digicert.com,crls.ssl.com,github.com,host.docker.internal,json-schema.org,json.schemastore.org,keyserver.ubuntu.com,ocsp.digicert.com,ocsp.geotrust.com,ocsp.globalsign.com,ocsp.identrust.com,ocsp.sectigo.com,ocsp.ssl.com,ocsp.thawte.com,ocsp.usertrust.com,ocsp.verisign.com,packagecloud.io,packages.cloud.google.com,packages.microsoft.com,ppa.launchpad.net,raw.githubusercontent.com,registry.npmjs.org,s.symcb.com,s.symcd.com,security.ubuntu.com,telemetry.enterprise.githubcopilot.com,ts-crl.ws.symantec.com,ts-ocsp.ws.symantec.com,www.googleapis.com"
           GITHUB_SERVER_URL: ${{ github.server_url }}
           GITHUB_API_URL: ${{ github.api_url }}
-          GH_AW_SAFE_OUTPUTS_HANDLER_CONFIG: "{\"add_comment\":{\"max\":2},\"add_labels\":{\"allowed\":[\"preset-submission\",\"validation-passed\",\"validation-failed\",\"needs-info\"],\"max\":3},\"create_pull_request\":{\"draft\":true,\"labels\":[\"preset-submission\",\"automated\"],\"max\":1,\"max_patch_files\":100,\"max_patch_size\":1024,\"protect_top_level_dot_folders\":true,\"protected_files\":[\"package.json\",\"bun.lockb\",\"bunfig.toml\",\"deno.json\",\"deno.jsonc\",\"deno.lock\",\"global.json\",\"NuGet.Config\",\"Directory.Packages.props\",\"mix.exs\",\"mix.lock\",\"go.mod\",\"go.sum\",\"stack.yaml\",\"stack.yaml.lock\",\"pom.xml\",\"build.gradle\",\"build.gradle.kts\",\"settings.gradle\",\"settings.gradle.kts\",\"gradle.properties\",\"package-lock.json\",\"yarn.lock\",\"pnpm-lock.yaml\",\"npm-shrinkwrap.json\",\"requirements.txt\",\"Pipfile\",\"Pipfile.lock\",\"pyproject.toml\",\"setup.py\",\"setup.cfg\",\"Gemfile\",\"Gemfile.lock\",\"uv.lock\",\"CODEOWNERS\",\"DESIGN.md\",\"CONTRIBUTING.md\",\"SECURITY.md\",\"CODE_OF_CONDUCT.md\",\"AGENTS.md\",\"CLAUDE.md\",\"GEMINI.md\"],\"protected_files_policy\":\"blocked\",\"title_prefix\":\"[preset] \"},\"create_report_incomplete_issue\":{},\"missing_data\":{},\"missing_tool\":{},\"noop\":{\"max\":1,\"report-as-issue\":\"false\"},\"report_incomplete\":{}}"
+          GH_AW_SAFE_OUTPUTS_HANDLER_CONFIG: "{\"add_comment\":{\"max\":2},\"add_labels\":{\"allowed\":[\"preset-submission\",\"validation-passed\",\"validation-failed\",\"needs-info\"],\"max\":3},\"create_pull_request\":{\"draft\":true,\"labels\":[\"preset-submission\",\"automated\"],\"max\":1,\"max_patch_files\":100,\"max_patch_size\":1024,\"protect_top_level_dot_folders\":true,\"protected_files\":[\"package.json\",\"bun.lockb\",\"bunfig.toml\",\"deno.json\",\"deno.jsonc\",\"deno.lock\",\"global.json\",\"NuGet.Config\",\"Directory.Packages.props\",\"mix.exs\",\"mix.lock\",\"go.mod\",\"go.sum\",\"stack.yaml\",\"stack.yaml.lock\",\"pom.xml\",\"build.gradle\",\"build.gradle.kts\",\"settings.gradle\",\"settings.gradle.kts\",\"gradle.properties\",\"package-lock.json\",\"yarn.lock\",\"pnpm-lock.yaml\",\"npm-shrinkwrap.json\",\"requirements.txt\",\"Pipfile\",\"Pipfile.lock\",\"pyproject.toml\",\"setup.py\",\"setup.cfg\",\"Gemfile\",\"Gemfile.lock\",\"uv.lock\",\"CODEOWNERS\",\"DESIGN.md\",\"CONTRIBUTING.md\",\"SECURITY.md\",\"CODE_OF_CONDUCT.md\",\"AGENTS.md\",\"CLAUDE.md\",\"GEMINI.md\"],\"protected_files_policy\":\"blocked\",\"title_prefix\":\"[preset] \"},\"create_report_incomplete_issue\":{},\"missing_data\":{},\"missing_tool\":{},\"noop\":{\"max\":1,\"report-as-issue\":\"true\"},\"report_incomplete\":{}}"
           GH_AW_CI_TRIGGER_TOKEN: ${{ secrets.GH_AW_CI_TRIGGER_TOKEN }}
         with:
           github-token: ${{ secrets.GH_AW_GITHUB_TOKEN || secrets.GITHUB_TOKEN }}

.github/workflows/add-community-preset.md

@@ -4,7 +4,7 @@ emoji: "🎨"
 
 on:
   issues:
-    types: [labeled]
+    types: [opened, edited, labeled]
   skip-bots: [github-actions, copilot, dependabot]
 
 tools:
@@ -22,8 +22,6 @@ checkout:
   fetch-depth: 0
 
 safe-outputs:
-  noop:
-    report-as-issue: false
   create-pull-request:
     title-prefix: "[preset] "
     labels: [preset-submission, automated]
@@ -49,9 +47,14 @@ or update entries in the community preset catalog.
 
 ## Triggering Conditions
 
-This workflow only triggers when the `preset-submission` label is added to an
-issue. Before processing, verify that the issue title starts with `[Preset]:`.
-If it does not, stop without commenting.
+This workflow triggers on issue events. **Only process the issue if ALL of these
+conditions are met:**
+
+1. The issue has the `preset-submission` label
+2. The issue title starts with `[Preset]:`
+
+If the issue does not meet these conditions, add a brief comment explaining that
+this workflow only processes preset submission issues, then stop.
 
 ## Step 1 — Read and Parse the Issue
 

.github/workflows/codeql.yml

@@ -22,11 +22,11 @@ jobs:
         uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@7211b7c8077ea37d8641b6271f6a365a22a5fbfa # v4
+        uses: github/codeql-action/init@9e0d7b8d25671d64c341c19c0152d693099fb5ba # v4
         with:
           languages: ${{ matrix.language }}
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@7211b7c8077ea37d8641b6271f6a365a22a5fbfa # v4
+        uses: github/codeql-action/analyze@9e0d7b8d25671d64c341c19c0152d693099fb5ba # v4
         with:
           category: "/language:${{ matrix.language }}"

.github/workflows/docs.yml

@@ -35,7 +35,7 @@ jobs:
           fetch-depth: 0 # Fetch all history for git info
 
       - name: Setup .NET
-        uses: actions/setup-dotnet@9a946fdbd5fb07b82b2f5a4466058b876ab72bb2 # v5.3.0
+        uses: actions/setup-dotnet@c2fa09f4bde5ebb9d1777cf28262a3eb3db3ced7 # v5.2.0
         with:
           dotnet-version: '8.x'
 

AGENTS.md

@@ -177,24 +177,7 @@ def _register_builtins() -> None:
 
 Set `context_file` on the integration class. The base integration setup creates or updates the managed Spec Kit section in that file, and uninstall removes the managed section when appropriate.
 
-The managed section is owned by the bundled `agent-context` extension (`extensions/agent-context/`). All configuration flows through the extension's own config file at `.specify/extensions/agent-context/agent-context-config.yml`:
-
-```yaml
-# Path to the coding agent context file managed by this extension
-context_file: CLAUDE.md
-
-# Delimiters for the managed Spec Kit section
-context_markers:
-  start: "<!-- SPECKIT START -->"
-  end: "<!-- SPECKIT END -->"
-```
-
-- `context_file` is written automatically from the integration's class attribute when `specify init` or `specify integration use` is run.
-- `context_markers.{start,end}` defaults to `IntegrationBase.CONTEXT_MARKER_START` / `CONTEXT_MARKER_END`. Users who want custom markers edit `agent-context-config.yml` directly — both the Python layer (`upsert_context_section()` / `remove_context_section()`) and the bundled scripts (`extensions/agent-context/scripts/bash/update-agent-context.sh` and `.ps1`) read from this single source of truth.
-
-Users can opt out entirely with `specify extension disable agent-context`; while disabled, Spec Kit skips context-file creation, updates, and removal (the gates are inside `upsert_context_section()` and `remove_context_section()`).
-
-Only add custom setup logic when the agent needs non-standard behavior. Integrations no longer require per-agent thin wrapper scripts or shared context-update dispatcher scripts — the `agent-context` extension is fully generic.
+Only add custom setup logic when the agent needs non-standard behavior. Most integrations do not need wrapper scripts or separate context-update dispatch code.
 
 ### 5. Test it
 
@@ -426,7 +409,7 @@ When an issue exists, include its number immediately after the prefix — this i
 ## Common Pitfalls
 
 1. **Using shorthand keys for CLI-based integrations**: For CLI-based integrations (`requires_cli: True`), the `key` must match the executable name (e.g., `"cursor-agent"` not `"cursor"`). `shutil.which(key)` is used for CLI tool checks — mismatches require special-case mappings. IDE-based integrations (`requires_cli: False`) are not subject to this constraint.
-2. **Forgetting context configuration**: The bundled `agent-context` extension reads from `.specify/extensions/agent-context/agent-context-config.yml`. New integrations only need to set `context_file` on the class — markers and dispatcher scripts are managed centrally.
+2. **Forgetting update scripts**: Both bash and PowerShell thin wrappers and the shared context-update scripts must be updated.
 3. **Incorrect `requires_cli` value**: Set to `True` only for agents that have a CLI tool; set to `False` for IDE-based agents.
 4. **Wrong argument format**: Use `$ARGUMENTS` for Markdown agents, `{{args}}` for TOML agents.
 5. **Skipping registration**: The import and `_register()` call in `_register_builtins()` must both be added.

CHANGELOG.md

@@ -2,48 +2,6 @@
 
 <!-- insert new changelog below this comment -->
 
-## [0.9.0] - 2026-06-01
-
-### Changed
-
-- chore: recompile workflow lock files (#2774)
-- Add Multi-Sites Spec Kit extension to community catalog (#2791)
-- Update Product Spec Extension to v0.8.3 (#2790)
-- Publish May 2026 Newsletter (#2787)
-- fix: move URL install confirmation prompt before spinner (#2783) (#2784)
-- Update Reqnroll BDD extension to v1.1.0 (#2775)
-- Extract agent context updates into bundled agent-context extension (#2546)
-- chore(deps): bump actions/setup-dotnet from 5.2.0 to 5.3.0 (#2755)
-- chore: release 0.8.18, begin 0.8.19.dev0 development (#2766)
-
-## [0.8.18] - 2026-05-29
-
-### Changed
-
-- Add support for SPECKIT_WORKFLOW_RUN_ID override (#2742)
-- feat: support SPECKIT_INTEGRATION_<KEY>_EXECUTABLE env var (#2743)
-- chore(deps): bump github/gh-aw-actions from 0.74.8 to 0.77.0 (#2754)
-- chore(deps): bump github/codeql-action from 4.35.5 to 4.36.0 (#2753)
-- fix: disable no-op issue reporting for catalog submission workflows (#2748)
-- Add confirmation prompt for URL-based extension installs (#2745)
-- fix: restrict community submission workflows to labeled event only (#2741)
-- feat(integrations): support SPECIFY_<KEY>_EXTRA_ARGS env var for agent subprocess flags (#2596)
-- chore: release 0.8.17, begin 0.8.18.dev0 development (#2737)
-
-## [0.8.17] - 2026-05-28
-
-### Changed
-
-- docs: consolidate Community sections in README (#2736)
-- Fix shared script command hints for integration separators (#2627)
-- docs: update security-governance preset to v0.4.0 (#2703)
-- feat(agy): enhance Google Antigravity CLI integration (#2689)
-- Fix --dev extension agent symlinks (#2554)
-- Share skills hook note post-processing (#2679)
-- feat: add Hermes Agent integration (with review fixes) (#2651)
-- Update Superpowers Implementation Bridge to v0.7.0 (#2732)
-- chore: release 0.8.16, begin 0.8.17.dev0 development (#2729)
-
 ## [0.8.16] - 2026-05-27
 
 ### Changed

README.md

@@ -22,7 +22,10 @@
 - [🤔 What is Spec-Driven Development?](#-what-is-spec-driven-development)
 - [⚡ Get Started](#-get-started)
 - [📽️ Video Overview](#️-video-overview)
-- [🌍 Community](#-community)
+- [🧩 Community Extensions](#-community-extensions)
+- [🎨 Community Presets](#-community-presets)
+- [🚶 Community Walkthroughs](#-community-walkthroughs)
+- [🛠️ Community Friends](#️-community-friends)
 - [🤖 Supported AI Coding Agent Integrations](#-supported-ai-coding-agent-integrations)
 - [🔧 Specify CLI Reference](#-specify-cli-reference)
 - [🧩 Making Spec Kit Your Own: Extensions & Presets](#-making-spec-kit-your-own-extensions--presets)
@@ -109,19 +112,31 @@ Want to see Spec Kit in action? Watch our [video overview](https://www.youtube.c
 
 [![Spec Kit video header](/media/spec-kit-video-header.jpg)](https://www.youtube.com/watch?v=a9eR1xsfvHg&pp=0gcJCckJAYcqIYzv)
 
-## 🌍 Community
+## 🧩 Community Extensions
 
-Explore community-contributed resources on the [Spec Kit docs site](https://github.github.io/spec-kit/):
-
-- [Extensions](https://github.github.io/spec-kit/community/extensions.html) — commands, hooks, and capabilities
-- [Presets](https://github.github.io/spec-kit/community/presets.html) — template and terminology overrides
-- [Walkthroughs](https://github.github.io/spec-kit/community/walkthroughs.html) — end-to-end SDD scenarios
-- [Friends](https://github.github.io/spec-kit/community/friends.html) — projects that extend or build on Spec Kit
+Community-contributed extensions add new commands, hooks, and capabilities to Spec Kit. See the full list on the [Community Extensions](https://github.github.io/spec-kit/community/extensions.html) page.
 
 > [!NOTE]
-> Community contributions are independently created and maintained by their respective authors. Review source code before installation and use at your own discretion.
+> Community extensions are independently created and maintained by their respective authors. Maintainers only verify that catalog entries are complete and correctly formatted — they do **not review, audit, endorse, or support the extension code itself**. Review extension source code before installation and use at your own discretion.
 
-Want to contribute? See the [Extension Publishing Guide](extensions/EXTENSION-PUBLISHING-GUIDE.md) or the [Presets Publishing Guide](presets/PUBLISHING.md).
+To submit your own extension, see the [Extension Publishing Guide](extensions/EXTENSION-PUBLISHING-GUIDE.md).
+
+## 🎨 Community Presets
+
+Community-contributed presets customize how Spec Kit behaves — overriding templates, commands, and terminology without changing any tooling. See the full list on the [Community Presets](https://github.github.io/spec-kit/community/presets.html) page.
+
+> [!NOTE]
+> Community presets are third-party contributions and are not maintained by the Spec Kit team. Review them carefully before use, and see the docs page above for the full disclaimer.
+
+To submit your own preset, see the [Presets Publishing Guide](presets/PUBLISHING.md).
+
+## 🚶 Community Walkthroughs
+
+See Spec-Driven Development in action across different scenarios with community-contributed walkthroughs; find the full list on the [Community Walkthroughs](https://github.github.io/spec-kit/community/walkthroughs.html) page.
+
+## 🛠️ Community Friends
+
+Community projects that extend, visualize, or build on Spec Kit. See the full list on the [Community Friends](https://github.github.io/spec-kit/community/friends.html) page.
 
 ## 🤖 Supported AI Coding Agent Integrations
 
@@ -191,7 +206,7 @@ specify extension add <extension-name>
 
 For example, extensions could add Jira integration, post-implementation code review, V-Model test traceability, or project health diagnostics.
 
-See the [Extensions reference](https://github.github.io/spec-kit/reference/extensions.html) for the full command guide. Browse the [community extensions](https://github.github.io/spec-kit/community/extensions.html) for what's available.
+See the [Extensions reference](https://github.github.io/spec-kit/reference/extensions.html) for the full command guide. Browse the [community extensions](#-community-extensions) above for what's available.
 
 ### Presets — Customize Existing Workflows
 

docs/community/extensions.md

@@ -70,7 +70,6 @@ The following community-contributed extensions are available in [`catalog.commun
 | MemoryLint | Agent memory governance tool: Automatically audits and fixes boundary conflicts between AGENTS.md and the constitution. | `process` | Read+Write | [memorylint](https://github.com/RbBtSn0w/spec-kit-extensions/tree/main/memorylint) |
 | Microsoft 365 Integration | Fetch Teams messages, meeting transcripts, and SharePoint/OneDrive files as local Markdown for spec generation | `integration` | Read+Write | [spec-kit-m365](https://github.com/BenBtg/spec-kit-m365) |
 | Multi-Model Review | Cross-model Spec Kit handoffs for spec authoring, implementation routing, and review. | `process` | Read+Write | [multi-model-review](https://github.com/formin/multi-model-review) |
-| Multi-Sites Spec Kit | Multi-site aware specify command with per-site spec folders, auto-increment, and Drupal support | `process` | Read+Write | [spec-kit-multi-sites](https://github.com/teeyo/spec-kit-multi-sites) |
 | .NET Framework to Modern .NET Migration | Orchestrate end-to-end .NET Framework to modern .NET migration across 7 phases, with SDD lifecycle integration | `process` | Read+Write | [spec-kit-fx-to-net](https://github.com/RogerBestMsft/spec-kit-FxToNet) |
 | Onboard | Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step | `process` | Read+Write | [spec-kit-onboard](https://github.com/dmux/spec-kit-onboard) |
 | Optimize | Audit and optimize AI governance for context efficiency — token budgets, rule health, interpretability, compression, coherence, and echo detection | `process` | Read+Write | [spec-kit-optimize](https://github.com/sakitA/spec-kit-optimize) |

docs/community/presets.md

@@ -23,7 +23,7 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | Multi-Repo Branching | Coordinates feature branch creation across multiple git repositories (independent repos and submodules) during plan and tasks phases | 2 commands | — | [spec-kit-preset-multi-repo-branching](https://github.com/sakitA/spec-kit-preset-multi-repo-branching) |
 | Pirate Speak (Full) | Transforms all Spec Kit output into pirate speak — specs become "Voyage Manifests", plans become "Battle Plans", tasks become "Crew Assignments" | 6 templates, 9 commands | — | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
 | Screenwriting | Spec-Driven Development for screenwriting/scriptwriting/tutorials: feature films, television (pilot, episode, limited series), and stage plays. Adapts the Spec Kit workflow to screenplay craft — slug lines, action lines, act breaks, beat sheets, and industry-standard pitch documents. Supports three-act, Save the Cat, TV pilot, network episode, cable/streaming episode, and stage-play structural frameworks. Export to Fountain, FTX, PDF | 26 templates, 32 commands, 1 script | — | [speckit-preset-screenwriting](https://github.com/adaumann/speckit-preset-screenwriting) |
-| Security Governance | Adds secure development governance: memory-safe-language preference, language-specific secure-coding profiles, NIST SSDF, CWE Top 25, OWASP ASVS, SBOM/AI-SBOM, VEX/SLSA, OpenSSF Scorecard, G7/BSI AI-SBOM target evidence, and EU CRA applicability | 12 templates, 3 commands | — | [spec-kit-preset-security-governance](https://github.com/hindermath/spec-kit-preset-security-governance) |
+| Security Governance | Adds secure development governance: memory-safe-language preference, secure code generation, NIST SSDF, CWE Top 25, OWASP ASVS, SBOM/AI-SBOM, VEX/SLSA, OpenSSF Scorecard, G7/BSI AI-SBOM target evidence, and EU CRA applicability | 12 templates, 3 commands | — | [spec-kit-preset-security-governance](https://github.com/hindermath/spec-kit-preset-security-governance) |
 | Spec2Cloud | Spec-driven workflow tuned for shipping to Azure: spec → plan → tasks → implement → deploy | 5 templates, 8 commands | — | [spec2cloud](https://github.com/Azure-Samples/Spec2Cloud) |
 | Table of Contents Navigation | Adds a navigable Table of Contents to generated spec.md, plan.md, and tasks.md documents | 3 templates, 3 commands | — | [spec-kit-preset-toc-navigation](https://github.com/Quratulain-bilal/spec-kit-preset-toc-navigation) |
 | VS Code Ask Questions | Enhances the clarify command to use `vscode/askQuestions` for batched interactive questioning. | 1 command | — | [spec-kit-presets](https://github.com/fdcastel/spec-kit-presets) |

extensions/README.md

@@ -76,7 +76,7 @@ specify extension add <extension-name> --from https://github.com/org/spec-kit-ex
 
 🔍 **Browse and search community extensions on the [Community Extensions website](https://speckit-community.github.io/extensions/).**
 
-See the [Community Extensions](https://github.github.io/spec-kit/community/extensions.html) page for the full list of available community-contributed extensions.
+See the [Community Extensions](../README.md#-community-extensions) section in the main README for the full list of available community-contributed extensions.
 
 For the raw catalog data, see [`catalog.community.json`](catalog.community.json).
 

extensions/agent-context/README.md

@@ -1,57 +0,0 @@
-# Coding Agent Context Extension
-
-This bundled extension manages the **coding agent context/instruction file** (e.g. `CLAUDE.md`, `.github/copilot-instructions.md`, `AGENTS.md`, `GEMINI.md`, …) for the active integration.
-
-It owns the lifecycle of the managed section delimited by the configurable start/end markers (defaults: `<!-- SPECKIT START -->` / `<!-- SPECKIT END -->`).
-
-## Why an extension?
-
-Not every Spec Kit user wants Spec Kit to write into the coding agent's context file. Extracting this behavior into a dedicated extension lets users:
-
-- **Opt out** entirely with `specify extension disable agent-context` — Spec Kit will then never create or modify the agent context file.
-- **Customize the markers** by editing `.specify/extensions/agent-context/agent-context-config.yml` — both the Python layer and the bundled scripts honor the same `context_markers` value.
-- **Refresh on demand** with `/speckit.agent-context.update`, or automatically through the hooks declared in `extension.yml` (`after_specify`, `after_plan`).
-
-## Commands
-
-| Command | Description |
-|---------|-------------|
-| `speckit.agent-context.update` | Refresh the managed section in the agent context file with the current plan path. |
-
-## Configuration
-
-All configuration flows through the extension's own config file at
-`.specify/extensions/agent-context/agent-context-config.yml`:
-
-```yaml
-# Path to the coding agent context file managed by this extension
-context_file: CLAUDE.md
-
-# Delimiters for the managed Spec Kit section
-context_markers:
-  start: "<!-- SPECKIT START -->"
-  end: "<!-- SPECKIT END -->"
-```
-
-- `context_file` — the project-relative path to the coding agent context file, written by `specify init` and `specify integration install`.
-- `context_markers.start` / `.end` — the delimiters around the managed section. Edit these to use custom markers.
-
-## Requirements
-
-The bundled update scripts require **Python 3** with **PyYAML** for YAML/upsert processing (PowerShell can also use `ConvertFrom-Yaml` when available).
-
-PyYAML ships with the `specify` CLI and is normally available via the same `python3` interpreter. If a hook reports *"PyYAML is required … not available in the current Python environment"*, it means the system `python3` differs from the one used to install Spec Kit. To resolve, run:
-
-```bash
-pip install pyyaml
-# or target the specific interpreter Spec Kit uses:
-/path/to/speckit-python -m pip install pyyaml
-```
-
-## Disable
-
-```bash
-specify extension disable agent-context
-```
-
-When disabled, Spec Kit skips context file creation, updates, and removal (the gates are inside `upsert_context_section()` and `remove_context_section()`).

extensions/agent-context/agent-context-config.yml

@@ -1,15 +0,0 @@
-# Coding Agent Context Extension Configuration
-# These values are populated automatically by `specify init` and
-# `specify integration use` / `specify integration install`.
-
-# Path (relative to the project root) to the coding agent context file
-# managed by this extension (e.g. CLAUDE.md, AGENTS.md,
-# .github/copilot-instructions.md). Set automatically from the active
-# integration and regenerated during `specify init` or integration switches.
-context_file: ""
-
-# Delimiters for the managed Spec Kit section.
-# Edit these to use custom markers.
-context_markers:
-  start: "<!-- SPECKIT START -->"
-  end: "<!-- SPECKIT END -->"

extensions/agent-context/commands/speckit.agent-context.update.md

@@ -1,26 +0,0 @@
----
-description: "Refresh the managed Spec Kit section in the coding agent context file"
----
-
-# Update Coding Agent Context
-
-Refresh the managed Spec Kit section inside the active coding agent's context/instruction file (e.g. `CLAUDE.md`, `.github/copilot-instructions.md`, `AGENTS.md`).
-
-## Behavior
-
-The script reads the agent-context extension config at
-`.specify/extensions/agent-context/agent-context-config.yml` to discover:
-
-- `context_file` — the path of the coding agent context file to manage.
-- `context_markers.start` / `.end` — the delimiters surrounding the managed section. Defaults to `<!-- SPECKIT START -->` and `<!-- SPECKIT END -->` when the field is missing.
-
-It then creates, replaces, or appends the managed block so that the section points at the most recent plan path when one can be discovered (`specs/<feature>/plan.md`).
-
-If `context_file` is empty or the file cannot be located, the command reports nothing to do and exits successfully.
-
-## Execution
-
-- **Bash**: `.specify/extensions/agent-context/scripts/bash/update-agent-context.sh [plan_path]`
-- **PowerShell**: `.specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1 [plan_path]`
-
-When `plan_path` is omitted, the script auto-detects the most recently modified `specs/*/plan.md`.

extensions/agent-context/extension.yml

@@ -1,34 +0,0 @@
-schema_version: "1.0"
-
-extension:
-  id: agent-context
-  name: "Coding Agent Context"
-  version: "1.0.0"
-  description: "Manages coding agent context/instruction files (e.g., CLAUDE.md, copilot-instructions.md) with project-specific plan references and configurable markers"
-  author: spec-kit-core
-  repository: https://github.com/github/spec-kit
-  license: MIT
-
-requires:
-  speckit_version: ">=0.2.0"
-
-provides:
-  commands:
-    - name: speckit.agent-context.update
-      file: commands/speckit.agent-context.update.md
-      description: "Refresh the managed Spec Kit section in the coding agent context file"
-
-hooks:
-  after_specify:
-    command: speckit.agent-context.update
-    optional: true
-    description: "Refresh agent context after specification"
-  after_plan:
-    command: speckit.agent-context.update
-    optional: true
-    description: "Refresh agent context after planning"
-
-tags:
-  - "agent"
-  - "context"
-  - "core"

extensions/agent-context/scripts/bash/update-agent-context.sh

@@ -1,200 +0,0 @@
-#!/usr/bin/env bash
-# update-agent-context.sh
-#
-# Refresh the managed Spec Kit section in the coding agent's context file
-# (e.g. CLAUDE.md, .github/copilot-instructions.md, AGENTS.md).
-#
-# Reads `context_file` and `context_markers.{start,end}` from the
-# agent-context extension config:
-#   .specify/extensions/agent-context/agent-context-config.yml
-#
-# Usage: update-agent-context.sh [plan_path]
-#
-# When `plan_path` is omitted, the script picks the most recently modified
-# `specs/*/plan.md` if any exist, otherwise emits the section without a
-# concrete plan path.
-
-set -euo pipefail
-
-PROJECT_ROOT="$(pwd)"
-EXT_CONFIG="$PROJECT_ROOT/.specify/extensions/agent-context/agent-context-config.yml"
-DEFAULT_START="<!-- SPECKIT START -->"
-DEFAULT_END="<!-- SPECKIT END -->"
-
-if [[ ! -f "$EXT_CONFIG" ]]; then
-  echo "agent-context: $EXT_CONFIG not found; nothing to do." >&2
-  exit 0
-fi
-
-# Locate a suitable Python interpreter (python3, then python).
-_python=""
-if command -v python3 >/dev/null 2>&1; then
-  _python="python3"
-elif command -v python >/dev/null 2>&1 && python --version 2>&1 | grep -q "^Python 3"; then
-  _python="python"
-fi
-
-if [[ -z "$_python" ]]; then
-  echo "agent-context: Python 3 not found on PATH; skipping update." >&2
-  exit 0
-fi
-
-# Parse extension config once; emit three newline-separated fields:
-# context_file, context_markers.start, context_markers.end
-if ! _raw_opts="$("$_python" - "$EXT_CONFIG" <<'PY'
-import sys
-try:
-    import yaml
-except ImportError:
-    print(
-        "agent-context: PyYAML is required to parse extension config but is not available "
-        "in the current Python environment.\n"
-        "  To resolve: pip install pyyaml (or install it into the environment used by python3).\n"
-        "  Context file will not be updated until PyYAML is importable.",
-        file=sys.stderr,
-    )
-    sys.exit(2)
-try:
-    with open(sys.argv[1], "r", encoding="utf-8") as fh:
-        data = yaml.safe_load(fh)
-except Exception as exc:
-    print(
-        f"agent-context: unable to parse {sys.argv[1]} ({exc}); cannot update context.",
-        file=sys.stderr,
-    )
-    sys.exit(2)
-if not isinstance(data, dict):
-    data = {}
-def get_str(obj, *keys):
-    node = obj
-    for k in keys:
-        if isinstance(node, dict) and k in node:
-            node = node[k]
-        else:
-            return ""
-    return node if isinstance(node, str) else ""
-print(get_str(data, "context_file"))
-print(get_str(data, "context_markers", "start"))
-print(get_str(data, "context_markers", "end"))
-PY
-)"; then
-  echo "agent-context: skipping update (see above for details)." >&2
-  exit 0
-fi
-
-_opts_lines=()
-while IFS= read -r _line || [[ -n "$_line" ]]; do
-  _opts_lines+=("$_line")
-done < <(printf '%s\n' "$_raw_opts")
-if (( ${#_opts_lines[@]} < 3 )); then
-  echo "agent-context: malformed config parser output; expected 3 lines (context_file, marker_start, marker_end), got ${#_opts_lines[@]}; skipping update." >&2
-  exit 0
-fi
-CONTEXT_FILE="${_opts_lines[0]}"
-MARKER_START="${_opts_lines[1]}"
-MARKER_END="${_opts_lines[2]}"
-
-if [[ -z "$CONTEXT_FILE" ]]; then
-  echo "agent-context: context_file not set in extension config; nothing to do." >&2
-  exit 0
-fi
-
-# Reject absolute paths, backslash separators, and '..' path segments in context_file
-if [[ "$CONTEXT_FILE" == /* ]] || [[ "$CONTEXT_FILE" =~ ^[A-Za-z]: ]]; then
-  echo "agent-context: context_file must be a project-relative path; got '$CONTEXT_FILE'." >&2
-  exit 1
-fi
-if [[ "$CONTEXT_FILE" == *\\* ]]; then
-  echo "agent-context: context_file must not contain backslash separators; got '$CONTEXT_FILE'." >&2
-  exit 1
-fi
-IFS='/' read -ra _cf_parts <<< "$CONTEXT_FILE"
-for _seg in "${_cf_parts[@]}"; do
-  if [[ "$_seg" == ".." ]]; then
-    echo "agent-context: context_file must not contain '..' path segments; got '$CONTEXT_FILE'." >&2
-    exit 1
-  fi
-done
-unset _cf_parts _seg
-
-[[ -z "$MARKER_START" ]] && MARKER_START="$DEFAULT_START"
-[[ -z "$MARKER_END"   ]] && MARKER_END="$DEFAULT_END"
-
-PLAN_PATH="${1:-}"
-if [[ -z "$PLAN_PATH" ]]; then
-  # Pick the most recently modified plan.md one level deep (specs/<feature>/plan.md).
-  # Use find + sort by modification time to avoid ls/head fragility with
-  # spaces in paths or SIGPIPE from pipefail.
-  _plan_abs="$("$_python" - "$PROJECT_ROOT" <<'PY'
-import sys, os
-from pathlib import Path
-specs = Path(sys.argv[1]) / "specs"
-plans = sorted(
-    specs.glob("*/plan.md"),
-    key=lambda p: p.stat().st_mtime,
-    reverse=True,
-)
-print(plans[0] if plans else "")
-PY
-)"
-  if [[ -n "$_plan_abs" ]]; then
-    PLAN_PATH="${_plan_abs#"$PROJECT_ROOT/"}"
-  fi
-fi
-
-CTX_PATH="$PROJECT_ROOT/$CONTEXT_FILE"
-mkdir -p "$(dirname "$CTX_PATH")"
-
-# Build the managed section
-TMP_SECTION="$(mktemp)"
-trap 'rm -f "$TMP_SECTION"' EXIT
-{
-  echo "$MARKER_START"
-  echo "For additional context about technologies to be used, project structure,"
-  echo "shell commands, and other important information, read the current plan"
-  if [[ -n "$PLAN_PATH" ]]; then
-    echo "at $PLAN_PATH"
-  fi
-  echo "$MARKER_END"
-} > "$TMP_SECTION"
-
-"$_python" - "$CTX_PATH" "$MARKER_START" "$MARKER_END" "$TMP_SECTION" <<'PY'
-import sys, os
-ctx_path, start, end, section_path = sys.argv[1:5]
-with open(section_path, "r", encoding="utf-8") as fh:
-    section = fh.read().rstrip("\n") + "\n"
-
-if os.path.exists(ctx_path):
-    with open(ctx_path, "r", encoding="utf-8-sig") as fh:
-        content = fh.read()
-    s = content.find(start)
-    e = content.find(end, s if s != -1 else 0)
-    if s != -1 and e != -1 and e > s:
-        end_of_marker = e + len(end)
-        if end_of_marker < len(content) and content[end_of_marker] == "\r":
-            end_of_marker += 1
-        if end_of_marker < len(content) and content[end_of_marker] == "\n":
-            end_of_marker += 1
-        new_content = content[:s] + section + content[end_of_marker:]
-    elif s != -1:
-        new_content = content[:s] + section
-    elif e != -1:
-        end_of_marker = e + len(end)
-        if end_of_marker < len(content) and content[end_of_marker] == "\r":
-            end_of_marker += 1
-        if end_of_marker < len(content) and content[end_of_marker] == "\n":
-            end_of_marker += 1
-        new_content = section + content[end_of_marker:]
-    else:
-        if content and not content.endswith("\n"):
-            content += "\n"
-        new_content = (content + "\n" + section) if content else section
-else:
-    new_content = section
-
-new_content = new_content.replace("\r\n", "\n").replace("\r", "\n")
-with open(ctx_path, "wb") as fh:
-    fh.write(new_content.encode("utf-8"))
-PY
-
-echo "agent-context: updated $CONTEXT_FILE"

extensions/agent-context/scripts/powershell/update-agent-context.ps1

@@ -1,237 +0,0 @@
-#!/usr/bin/env pwsh
-# update-agent-context.ps1
-#
-# Refresh the managed Spec Kit section in the coding agent's context file
-# (e.g. CLAUDE.md, .github/copilot-instructions.md, AGENTS.md).
-#
-# Reads `context_file` and `context_markers.{start,end}` from the
-# agent-context extension config:
-#   .specify/extensions/agent-context/agent-context-config.yml
-#
-# Usage: update-agent-context.ps1 [plan_path]
-
-[CmdletBinding()]
-param(
-    [Parameter(Position = 0)]
-    [string]$PlanPath
-)
-
-function Get-ConfigValue {
-    param(
-        [AllowNull()][object]$Object,
-        [Parameter(Mandatory = $true)][string]$Key
-    )
-
-    if ($null -eq $Object) {
-        return $null
-    }
-    if ($Object -is [System.Collections.IDictionary]) {
-        return $Object[$Key]
-    }
-    $prop = $Object.PSObject.Properties[$Key]
-    if ($prop) {
-        return $prop.Value
-    }
-    return $null
-}
-
-function Test-ConfigObject {
-    param(
-        [AllowNull()][object]$Object
-    )
-
-    if ($null -eq $Object) {
-        return $false
-    }
-    if ($Object -is [System.Collections.IDictionary]) {
-        return $true
-    }
-    if ($Object -is [System.Management.Automation.PSCustomObject]) {
-        return $true
-    }
-    return $false
-}
-
-$ErrorActionPreference = 'Stop'
-$DefaultStart = '<!-- SPECKIT START -->'
-$DefaultEnd   = '<!-- SPECKIT END -->'
-$ProjectRoot  = (Get-Location).Path
-$ExtConfig    = Join-Path $ProjectRoot '.specify/extensions/agent-context/agent-context-config.yml'
-
-if (-not (Test-Path -LiteralPath $ExtConfig)) {
-    Write-Warning "agent-context: $ExtConfig not found; nothing to do."
-    exit 0
-}
-
-$Options = $null
-if (Get-Command ConvertFrom-Yaml -ErrorAction SilentlyContinue) {
-    try {
-        $Options = Get-Content -LiteralPath $ExtConfig -Raw | ConvertFrom-Yaml -ErrorAction Stop
-    } catch {
-        # fall through to Python fallback
-    }
-}
-
-if ($null -eq $Options) {
-    # ConvertFrom-Yaml unavailable or failed; fall back to Python+PyYAML.
-    $pythonCmd = $null
-    foreach ($candidate in @('python3', 'python')) {
-        if (Get-Command $candidate -ErrorAction SilentlyContinue) {
-            # Verify it is Python 3
-            $verOut = & $candidate --version 2>&1
-            if ($verOut -match 'Python 3') {
-                $pythonCmd = $candidate
-                break
-            }
-        }
-    }
-
-    if ($pythonCmd) {
-        try {
-            $jsonOut = & $pythonCmd -c @'
-import json
-import sys
-try:
-    import yaml
-except ImportError:
-    print(
-        "agent-context: PyYAML is required to parse extension config; cannot update context.",
-        file=sys.stderr,
-    )
-    sys.exit(2)
-
-try:
-    with open(sys.argv[1], "r", encoding="utf-8") as fh:
-        data = yaml.safe_load(fh)
-except Exception as exc:
-    print(
-        f"agent-context: unable to parse {sys.argv[1]} ({exc}); cannot update context.",
-        file=sys.stderr,
-    )
-    sys.exit(2)
-
-if not isinstance(data, dict):
-    data = {}
-
-print(json.dumps(data))
-'@ $ExtConfig
-            if ($LASTEXITCODE -eq 0 -and $jsonOut) {
-                $Options = $jsonOut | ConvertFrom-Json -ErrorAction Stop
-            }
-        } catch {
-            $Options = $null
-        }
-    }
-
-    if (-not $Options) {
-        Write-Warning "agent-context: unable to parse $ExtConfig; skipping update."
-        exit 0
-    }
-}
-
-if (-not (Test-ConfigObject -Object $Options)) {
-    Write-Warning "agent-context: $ExtConfig must contain a YAML mapping; skipping update."
-    exit 0
-}
-
-$ContextFile = Get-ConfigValue -Object $Options -Key 'context_file'
-if (-not $ContextFile) {
-    Write-Warning 'agent-context: context_file not set in extension config; nothing to do.'
-    exit 0
-}
-
-# Reject absolute paths and '..' path segments in context_file
-if ([System.IO.Path]::IsPathRooted($ContextFile)) {
-    Write-Warning "agent-context: context_file must be a project-relative path; got '$ContextFile'."
-    exit 1
-}
-$cfSegments = $ContextFile -split '[/\\]'
-if ($cfSegments -contains '..') {
-    Write-Warning "agent-context: context_file must not contain '..' path segments; got '$ContextFile'."
-    exit 1
-}
-
-$MarkerStart = $DefaultStart
-$MarkerEnd   = $DefaultEnd
-$cm = Get-ConfigValue -Object $Options -Key 'context_markers'
-if ($cm) {
-    $cmStart = Get-ConfigValue -Object $cm -Key 'start'
-    if ($cmStart -is [string] -and $cmStart) {
-        $MarkerStart = $cmStart
-    }
-    $cmEnd = Get-ConfigValue -Object $cm -Key 'end'
-    if ($cmEnd -is [string] -and $cmEnd) {
-        $MarkerEnd = $cmEnd
-    }
-}
-
-if (-not $PlanPath) {
-    # Discover plan.md exactly one level deep (specs/<feature>/plan.md),
-    # matching the bash glob specs/*/plan.md. Wrap in try/catch so access errors under
-    # $ErrorActionPreference = 'Stop' don't abort the script.
-    try {
-        $specsDir = Join-Path $ProjectRoot 'specs'
-        $candidate = Get-ChildItem -Path $specsDir -Directory -ErrorAction SilentlyContinue |
-            ForEach-Object { Get-Item -LiteralPath (Join-Path $_.FullName 'plan.md') -ErrorAction SilentlyContinue } |
-            Where-Object { $_ } |
-            Sort-Object LastWriteTime -Descending |
-            Select-Object -First 1
-        if ($candidate) {
-            $PlanPath = [System.IO.Path]::GetRelativePath($ProjectRoot, $candidate.FullName).Replace('\','/')
-        }
-    } catch {
-        # Non-fatal: continue without a plan path.
-    }
-}
-
-$CtxPath = Join-Path $ProjectRoot $ContextFile
-$CtxDir  = Split-Path -Parent $CtxPath
-if ($CtxDir -and -not (Test-Path -LiteralPath $CtxDir)) {
-    New-Item -ItemType Directory -Path $CtxDir -Force | Out-Null
-}
-
-$lines = @($MarkerStart,
-           'For additional context about technologies to be used, project structure,',
-           'shell commands, and other important information, read the current plan')
-if ($PlanPath) {
-    $lines += "at $PlanPath"
-}
-$lines += $MarkerEnd
-$Section = ($lines -join "`n") + "`n"
-
-if (Test-Path -LiteralPath $CtxPath) {
-    $rawBytes = [System.IO.File]::ReadAllBytes($CtxPath)
-    # Strip UTF-8 BOM if present
-    if ($rawBytes.Length -ge 3 -and $rawBytes[0] -eq 0xEF -and $rawBytes[1] -eq 0xBB -and $rawBytes[2] -eq 0xBF) {
-        $content = [System.Text.Encoding]::UTF8.GetString($rawBytes, 3, $rawBytes.Length - 3)
-    } else {
-        $content = [System.Text.Encoding]::UTF8.GetString($rawBytes)
-    }
-
-    $s = $content.IndexOf($MarkerStart)
-    $e = if ($s -ge 0) { $content.IndexOf($MarkerEnd, $s) } else { $content.IndexOf($MarkerEnd) }
-
-    if ($s -ge 0 -and $e -ge 0 -and $e -gt $s) {
-        $endOfMarker = $e + $MarkerEnd.Length
-        if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`r") { $endOfMarker++ }
-        if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`n") { $endOfMarker++ }
-        $newContent = $content.Substring(0, $s) + $Section + $content.Substring($endOfMarker)
-    } elseif ($s -ge 0) {
-        $newContent = $content.Substring(0, $s) + $Section
-    } elseif ($e -ge 0) {
-        $endOfMarker = $e + $MarkerEnd.Length
-        if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`r") { $endOfMarker++ }
-        if ($endOfMarker -lt $content.Length -and $content[$endOfMarker] -eq "`n") { $endOfMarker++ }
-        $newContent = $Section + $content.Substring($endOfMarker)
-    } else {
-        if ($content -and -not $content.EndsWith("`n")) { $content += "`n" }
-        if ($content) { $newContent = $content + "`n" + $Section } else { $newContent = $Section }
-    }
-} else {
-    $newContent = $Section
-}
-
-$newContent = $newContent.Replace("`r`n", "`n").Replace("`r", "`n")
-[System.IO.File]::WriteAllText($CtxPath, $newContent, (New-Object System.Text.UTF8Encoding($false)))
-
-Write-Host "agent-context: updated $ContextFile"

extensions/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-06-01T00:00:00Z",
+  "updated_at": "2026-05-27T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "aide": {
@@ -1724,37 +1724,6 @@
       "created_at": "2026-05-04T02:51:52Z",
       "updated_at": "2026-05-04T02:51:52Z"
     },
-    "multi-sites": {
-      "name": "Multi-Sites Spec Kit",
-      "id": "multi-sites",
-      "description": "Multi-site aware specify command with per-site spec folders, auto-increment, and Drupal support",
-      "author": "teeyo",
-      "version": "1.0.0",
-      "download_url": "https://github.com/teeyo/spec-kit-multi-sites/archive/refs/tags/v1.0.0.zip",
-      "repository": "https://github.com/teeyo/spec-kit-multi-sites",
-      "homepage": "https://github.com/teeyo/spec-kit-multi-sites",
-      "documentation": "https://github.com/teeyo/spec-kit-multi-sites/blob/main/README.md",
-      "changelog": "https://github.com/teeyo/spec-kit-multi-sites/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.1.0"
-      },
-      "provides": {
-        "commands": 1,
-        "hooks": 0
-      },
-      "tags": [
-        "multi-site",
-        "drupal",
-        "workflow",
-        "process"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-06-01T00:00:00Z",
-      "updated_at": "2026-06-01T00:00:00Z"
-    },
     "onboard": {
       "name": "Onboard",
       "id": "onboard",
@@ -1981,12 +1950,12 @@
       "name": "Product Spec Extension",
       "id": "product",
       "description": "Generates PRFAQ, Lean PRD, stakeholder summaries, and technical designs from engineering specs.",
-      "author": "d0whc3r",
-      "version": "0.8.3",
-      "download_url": "https://github.com/d0whc3r/spec-kit-product/releases/download/v0.8.3/product-0.8.3.zip",
+      "author": "spec-kit-product contributors",
+      "version": "0.1.3",
+      "download_url": "https://github.com/d0whc3r/spec-kit-product/releases/download/v0.1.3/product-0.1.3.zip",
       "repository": "https://github.com/d0whc3r/spec-kit-product",
-      "homepage": "https://d0whc3r.github.io/spec-kit-product/",
-      "documentation": "https://github.com/d0whc3r/spec-kit-product/wiki",
+      "homepage": "https://github.com/d0whc3r/spec-kit-product",
+      "documentation": "https://github.com/d0whc3r/spec-kit-product/blob/main/README.md",
       "changelog": "https://github.com/d0whc3r/spec-kit-product/blob/main/CHANGELOG.md",
       "license": "MIT",
       "requires": {
@@ -1994,30 +1963,20 @@
       },
       "provides": {
         "commands": 4,
-        "hooks": 3
+        "hooks": 6
       },
       "tags": [
-        "design",
-        "documentation",
-        "jtbd",
-        "lean-prd",
-        "planning",
-        "prd",
-        "prfaq",
         "product",
-        "product-management",
-        "requirements",
         "spec",
-        "spec-kit",
-        "spec-kit-extension",
-        "stakeholder",
-        "technical-design"
+        "prd",
+        "design",
+        "documentation"
       ],
       "verified": false,
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-05-26T00:00:00Z",
-      "updated_at": "2026-06-01T00:00:00Z"
+      "updated_at": "2026-05-26T00:00:00Z"
     },
     "product-forge": {
       "name": "Product Forge",
@@ -2259,8 +2218,8 @@
       "id": "reqnroll-bdd",
       "description": "Adds Reqnroll BDD planning, Gherkin generation, traceability, safe task injection, handoff, and verification to Spec Kit.",
       "author": "LoogaCY Studio",
-      "version": "1.1.0",
-      "download_url": "https://github.com/LoogacyStudio/spec-kit-reqnroll-bdd/archive/refs/tags/v1.1.0.zip",
+      "version": "1.0.0",
+      "download_url": "https://github.com/LoogacyStudio/spec-kit-reqnroll-bdd/archive/refs/tags/v1.0.0.zip",
       "repository": "https://github.com/LoogacyStudio/spec-kit-reqnroll-bdd",
       "homepage": "https://github.com/LoogacyStudio/spec-kit-reqnroll-bdd",
       "documentation": "https://github.com/LoogacyStudio/spec-kit-reqnroll-bdd#readme",
@@ -2290,7 +2249,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-05-13T00:00:00Z",
-      "updated_at": "2026-05-30T00:00:00Z"
+      "updated_at": "2026-05-13T00:00:00Z"
     },
     "retro": {
       "name": "Retro Extension",
@@ -2691,8 +2650,8 @@
       "id": "speckit-superpowers-bridge",
       "description": "Thin orchestrator between Spec Kit (design) and Superpowers (implementation). Cross-agent.",
       "author": "lihan3238",
-      "version": "0.7.0",
-      "download_url": "https://github.com/lihan3238/speckit-superpowers-bridge/releases/download/v0.7.0/speckit-superpowers-bridge-v0.7.0.zip",
+      "version": "0.5.0",
+      "download_url": "https://github.com/lihan3238/speckit-superpowers-bridge/releases/download/v0.5.0/speckit-superpowers-bridge-v0.5.0.zip",
       "repository": "https://github.com/lihan3238/speckit-superpowers-bridge",
       "homepage": "https://github.com/lihan3238/speckit-superpowers-bridge",
       "documentation": "https://github.com/lihan3238/speckit-superpowers-bridge#readme",
@@ -2733,7 +2692,7 @@
       "downloads": 0,
       "stars": 0,
       "created_at": "2026-05-15T00:00:00Z",
-      "updated_at": "2026-05-28T00:00:00Z"
+      "updated_at": "2026-05-20T00:00:00Z"
     },
     "speckit-utils": {
       "name": "SDD Utilities",

extensions/catalog.json

@@ -3,20 +3,6 @@
   "updated_at": "2026-04-10T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.json",
   "extensions": {
-    "agent-context": {
-      "name": "Coding Agent Context",
-      "id": "agent-context",
-      "version": "1.0.0",
-      "description": "Manages coding agent context/instruction files (e.g., CLAUDE.md, copilot-instructions.md) with project-specific plan references and configurable markers",
-      "author": "spec-kit-core",
-      "repository": "https://github.com/github/spec-kit",
-      "bundled": true,
-      "tags": [
-        "agent",
-        "context",
-        "core"
-      ]
-    },
     "git": {
       "name": "Git Branching Workflow",
       "id": "git",

integrations/catalog.json

@@ -272,15 +272,6 @@
       "author": "spec-kit-core",
       "repository": "https://github.com/github/spec-kit",
       "tags": ["cli"]
-    },
-    "hermes": {
-      "id": "hermes",
-      "name": "Hermes Agent",
-      "version": "1.0.0",
-      "description": "Hermes Agent skills-based integration by Nous Research",
-      "author": "spec-kit-core",
-      "repository": "https://github.com/github/spec-kit",
-      "tags": ["cli", "skills"]
     }
   }
 }

newsletters/2026-May.md

@@ -1,138 +0,0 @@
-# Spec Kit - May 2026 Newsletter
-
-This edition covers Spec Kit activity in May 2026 — a month defined by three milestone 100s: **100,000+ stars**, **100+ community extensions**, and recognition as a **top-100 GitHub project**. Fourteen releases shipped (v0.8.4 through v0.8.17), delivering multi-agent install support, constitution governance enforcement, and continued architecture cleanup. The Open Source Friday livestream, a wave of multilingual coverage, and analyst recognition from The Futurum Group marked the project's transition from fast-moving experiment to established ecosystem. A summary is in the table below, followed by details.
-
-| **Spec Kit Core (May 2026)** | **Community & Content** | **SDD Ecosystem & Next** |
-| --- | --- | --- |
-| Fourteen releases shipped with key features: multi-install for concurrent agent integrations, constitution governance in implement, authentication provider registry, Hermes and Lingma agents, and a `__init__.py` decomposition series. The repo grew from ~92k to **106,951 stars**, crossing **100K** on May 21. [\[github.com\]](https://github.com/github/spec-kit/releases) | The community extension catalog crossed **100 entries** (now 105). Open Source Friday livestream drove a press wave: Visual Studio Magazine, DevOps.com, MarkTechPost, HackerNoon, and 25+ more articles — now tracked across multiple languages following an expanded discovery methodology. **217 contributors** now listed. | MarkTechPost called Spec Kit "the most community-adopted open-source option" for SDD. The Futurum Group's Mitch Ashley framed specs as "the unit of governance across agents and contributors." Truong Phung published a 61-min production playbook referencing Spec Kit. Competitors grew but differentiate on orchestration; Spec Kit leads in portability and community. |
-
-***
-
-> **A Month of 100s.** May 2026 was defined by three milestones that all share the same number. The community extension catalog crossed **100 entries** during the week of May 21, making Spec Kit a genuine platform with more capabilities in its ecosystem than in its core. The repository crossed **100,000 GitHub stars** on the same week. And with 107K stars at month's end, Spec Kit now ranks among the **top 100 most-starred projects on all of GitHub**. None of this would have happened without the community — the contributors, extension authors, preset builders, article writers, and practitioners who turned a spec-driven development experiment into an ecosystem. Thank you.
-
-## Spec Kit Project Updates
-
-### Releases Overview
-
-**v0.8.4–v0.8.7** (May 1–7) opened the month with four patch releases delivering the most-requested feature of the year: **multi-install support for concurrent AI agent integrations** (#2389), enabling multiple agents in a single project. This closed five long-standing issues dating back 228 days. The releases also added **constitution governance in `/speckit.implement`** (#2460), ensuring the implement phase now loads `constitution.md` to enforce governance during code generation. An **authentication provider registry** (#2393) added config-driven multi-platform auth. The **Lingma agent** joined the integration roster. Security hardening included pinning all remaining GitHub Actions to immutable SHAs (#2441) and URL scheme validation to prevent SSRF-style bugs (#2449). Seven new community extensions and six new governance-themed presets landed. [\[github.com\]](https://github.com/github/spec-kit/releases)
-
-**v0.8.8–v0.8.10** (May 8–14) shipped three releases focused on stability. **Version feature reporting** (#2548) improved upgrade visibility. Bug fixes addressed the Kiro CLI `$ARGUMENTS` placeholder (#1926, open 52 days), markdownlint-safe template metadata (#1343, open 147 days), and preset skill description precedence. The `__init__.py` decomposition series began with PRs 1–2/8, extracting `_console.py`, `_assets.py`, and `_utils.py`. Seven new extensions joined (Architecture Workflow, Agent Governance, BrownKit, Schedule, Reqnroll BDD, MDE, Changelog) along with two new presets (MDE, game-narrative-writing). The docs site received a major overhaul: the landing page was revamped with a four-pillar card layout, the install section was streamlined, and the community extensions table moved to the docs site. [\[github.com\]](https://github.com/github/spec-kit/releases)
-
-**v0.8.11–v0.8.13** (May 15–21) delivered three releases as the repo **crossed 100K stars**. **Agentic catalog submissions** (#2655) added AI-assisted workflows for community catalog contributions. A **high-assurance spec workflow** was documented (#2518). The while/do-while loop stale output bug (#2592) was caught and fixed same-day. **Integration auto mode** (#2421) now follows the project's initialized AI instead of hardcoding Copilot. The PowerShell UTF-8 BOM issue (#2280) was resolved. Four new extensions joined (Team Assign, Interactive HTML Preview, Time Machine, Superpowers Implementation Bridge), bringing the catalog to **103 entries** — crossing the 100 mark. [\[github.com\]](https://github.com/github/spec-kit/releases)
-
-**v0.8.14–v0.8.17** (May 22–28) closed the month with four releases. The **Hermes Agent** joined as a new integration target (#2651). Workflows gained a **`{{ context.run_id }}` template variable** (#2664). A new `SPECKIT_INTEGRATION_<KEY>_EXTRA_ARGS` environment variable (#2596) lets users pass extra flags to agent subprocesses. **Extension installs from URLs now prompt for confirmation** (#2745), a security improvement for URL-based installs. The spec quality checklist is now **re-validated after clarify updates the spec** (#2715). Token Budget, Product Spec, and Workflow Preset extensions joined the catalog, bringing it to **105 entries**. [\[github.com\]](https://github.com/github/spec-kit/releases)
-
-### Architecture & Refactoring
-
-The most significant internal effort in May was the **`__init__.py` decomposition series**, progressing through PRs 1–4 of 8. This systematic extraction moved `_console.py`, `_assets.py`, `_utils.py`, `_version.py`, and the `commands/` package out of the monolithic init module, improving maintainability and contributor onboarding. The **ExtensionCatalog was migrated to the shared catalog stack base** (#2437), reducing duplicated catalog handling across extension, preset, and integration catalogs. [\[github.com\]](https://github.com/github/spec-kit/releases)
-
-### Bug Fixes and Security
-
-Fourteen releases produced a strong cadence of fixes. Long-standing issues resolved include the Kiro CLI `$ARGUMENTS` placeholder (52 days), markdownlint template metadata line breaks (147 days), and the `--ai` flag for adding agent commands (136 days). The PowerShell UTF-8 BOM issue was fixed, preset skill rendering now correctly resolves `__SPECKIT_COMMAND_*__` refs (#2717), and a Windows gate-step crash was addressed (#2635).
-
-Security improvements included **URL-based extension install confirmation** (#2745), **pinning GitHub Actions to immutable SHAs** (#2441), **URL scheme validation** (#2449), and restricting community submission workflows to labeled events only (#2741). [\[github.com\]](https://github.com/github/spec-kit/releases)
-
-### The Extension & Preset Ecosystem
-
-The community extension catalog grew from 92 to **105 entries** during May, crossing the **100 mark** on May 21. Thirteen new extensions were added over the month. Community presets grew from 18 to **21 entries**, with three new presets added.
-
-Notable new extensions by category:
-
-- **Architecture & governance**: Architecture Workflow (bigsmartben), Agent Governance (bigben), Architecture Guard (DyanGalih), BrownKit (Maksim Shautsou)
-- **Cost & token management**: Cost Tracker (Quratulain-bilal), Token Analyzer (Chris Roberts), Token Budget (Tine Kondo)
-- **Agent orchestration**: Agent Orchestrator (pragya247), Multi-Model Review (formin)
-- **Project management**: Team Assign (tarunkumarbhati), Changelog (Quratulain-bilal)
-- **Cloud & enterprise**: Spec2Cloud for Azure (Azure Samples), .NET Framework to Modern .NET Migration (RogerBestMsft)
-- **API & lifecycle**: API Evolve (Quratulain-bilal), Product Spec (spec-kit-product contributors)
-- **Quality**: Schedule with CP-SAT solver (Julio César Franco Ardila), Reqnroll BDD (LoogaCY Studio), MDE (AI-MDE)
-- **Spec exploration**: Interactive HTML Preview (bigsmartben), Time Machine (te3yo)
-- **Cross-tool bridges**: Superpowers Implementation Bridge (lihan3238)
-
-New governance-themed presets dominated: a11y-governance, architecture-governance, security-governance, cross-platform-governance, agent-parity-governance, and Spec2Cloud preset. Creative presets included game-narrative-writing and MDE.
-
-The extension ecosystem also showed maturation through active maintenance. **Architecture Guard** progressed through four releases (v1.6.7 → v1.8.9), adding documentation quality improvements and governance features. **Memory MD** shipped multiple updates (v0.6.9 → v0.8.0), adding a `speckit.memory-md.log-finding` command. **Security Review** reached v1.4.5 with a new `speckit.security-review.log-finding` command. **Superpowers Implementation Bridge** evolved rapidly (v0.5.0 → v0.7.0). **Squad Bridge** updated to v1.3.0, **Fiction Book Writing** to v1.8.1, **Security Governance** to v0.4.0, and **MemoryLint** to v1.4.0. [\[github.com\]](https://github.github.io/spec-kit/community/extensions.html)
-
-### Documentation & Docs Site
-
-The docs site received its most significant update since launch. The **landing page was revamped** with a four-pillar card layout (#2531). The **install section was streamlined** (#2561). The **community extensions table** was moved from the README to the docs site (#2560), reducing README length while improving discoverability. **Community sections in the README** were consolidated (#2736). The **uv installation guide** was added with inline callouts (#2465). Landing page stats and branch naming conventions were updated (#2727). [\[github.com\]](https://github.com/github/spec-kit/releases)
-
-## Community & Content
-
-### The Open Source Friday Livestream
-
-On **May 8**, the **GitHub Open Source Friday livestream** featured Spec Kit, hosted by Andrea Griffiths with lead maintainer Manfred Riem. The livestream demonstrated a full SDD workflow building a time-zone-aware command-line utility with GitHub Copilot in VS Code. Riem described AI agents as "a very capable intern and a very quick intern but it's still an intern nonetheless." He emphasized that "the spec is always the source of truth" and highlighted the community ecosystem, noting the project was "nearing the 100 mark" for extensions. The livestream drove significant press attention in the following days. [\[youtube.com\]](https://www.youtube.com/watch?v=2IArMAhkJcE)
-
-### Press and Industry Coverage
-
-May produced the broadest press coverage to date, with publications from the mainstream developer media covering Spec Kit for the first time.
-
-**Visual Studio Magazine** (David Ramel, May 12) published *"GitHub Spec Kit Takes Off as Antidote to Piecemeal 'Vibe Coding'"*, reporting on the Open Source Friday livestream and the growing ecosystem. The article noted Spec Kit's story is "no longer just that GitHub open sourced a spec-driven development toolkit last fall" but that "the toolkit is becoming a fast-moving ecosystem for teams trying to make AI-assisted development more structured, repeatable and traceable." [\[visualstudiomagazine.com\]](https://visualstudiomagazine.com/articles/2026/05/12/github-spec-kit-takes-off-as-antidote-to-piecemeal-vibe-coding.aspx)
-
-**DevOps.com** (Tom Smith, May 11) published *"GitHub's Spec Kit Puts the Spec Back in Software Development"*, featuring analyst commentary from The Futurum Group (see The Analyst View below). [\[devops.com\]](https://devops.com/githubs-spec-kit-puts-the-spec-back-in-software-development/)
-
-**MarkTechPost** (Asif Razzaq, May 8) published two articles: a comprehensive step-by-step tutorial calling Spec Kit an open-source toolkit with "90k+ stars" and "one of the faster-growing developer tooling repositories," and a 9-tool SDD comparison calling Spec Kit **"the most community-adopted open-source option"** and "the default starting point for teams new to SDD." [\[marktechpost.com\]](https://www.marktechpost.com/2026/05/08/meet-github-spec-kit-an-open-source-toolkit-for-spec-driven-development-with-ai-coding-agents/)
-
-**HackerNoon** (Andrey Kucherenko, May 6) published *"The Spec-First Development Showdown"*, a hands-on comparison of Spec Kit, OpenSpec, BMAD, and Gangsta Agents. [\[hackernoon.com\]](https://hackernoon.com/the-spec-first-development-showdown-spec-kit-openspec-bmad-and-gangsta-agents-compared)
-
-### Developer Articles and Blog Posts
-
-May produced a wave of independent coverage — well beyond any previous month. Starting this month, article discovery was expanded beyond English-centric search engines to include language-appropriate engines for 25+ languages, so the broader coverage partly reflects wider discovery rather than a sudden spike.
-
-Notable non-English coverage:
-
-- **Japanese**: テックオーシャン published a detailed experience report on *"Claude Code × Spec Kit"* on note.com, praising task decomposition accuracy while noting spec sync requires manual workarounds. [\[note.com\]](https://note.com/techocean_corp/n/nd2bd63106c16)
-- **Portuguese**: Jady Sobjak de Mello Godoi published *"GitHub Spec Kit: Revolucionando o Desenvolvimento com SDD"* on DEV Community. [\[dev.to\]](https://dev.to/jadysmgodoi/github-speckit-revolucionando-o-desenvolvimento-com-sdd-l66)
-- **Italian**: Cosmonet published a comprehensive guide, *"GitHub Spec Kit: la guida completa allo Spec-Driven Development."* [\[cosmonet.info\]](https://www.cosmonet.info/github-spec-kit-guida-spec-driven-development/)
-- **French**: InnoSpira covered Spec Kit's rapid growth past 100K stars. [\[innospira.fr\]](https://www.innospira.fr/index.php/2026/05/12/github-spec-kit-place-au-developpement-pilote-par-la-spec/)
-- **Spanish**: Q2B Studio published an overview for Spanish-speaking developers. [\[q2bstudio.com\]](https://www.q2bstudio.com/nuestro-blog/1727819/github-spec-kit-desarrollo-especificaciones-ia)
-
-Notable English-language articles:
-
-- **Truong Phung** (DEV Community, May 29) published a comprehensive production playbook for AI-assisted development, referencing Spec Kit (see The Production Playbook Pattern below). [\[dev.to\]](https://dev.to/truongpx396/building-production-grade-fullstack-products-with-ai-coding-agents-a-practical-playbook-2idd)
-- **Mehul Gupta** (Medium, May 17) called Spec Kit "an operating system for AI-assisted software engineering." [\[medium.com\]](https://medium.com/data-science-in-your-pocket/what-is-github-spec-kit-bye-bye-vibe-coding-37efbaa32880)
-- **Kento IKEDA** (DEV Community / AWS Builders, May 2) examined the emerging three-layer pattern for AI agent instructions (AGENTS.md, SKILL.md, DESIGN.md), referencing Spec Kit's approach. [\[dev.to\]](https://dev.to/aws-builders/agentsmd-skillmd-designmd-how-ai-instructions-split-into-three-layers-d0g)
-- **PyShine** (May 13) published a detailed guide covering the 6-step workflow, 30+ integrations, and 60+ extensions. [\[pyshine.com\]](https://pyshine.com/GitHub-Spec-Kit-Spec-Driven-Development/)
-- **DeployHQ** (Alex M, May 13) examined the "deployment gap" — Spec Kit ends at code, Workspaces ends at PR — and showed how to wire DeployHQ into the post-merge step. [\[deployhq.com\]](https://www.deployhq.com/blog/spec-kit-copilot-workspaces-deployment)
-- **spec-coding.dev** (May 11) examined five practical SDD patterns shared by OpenSpec, Superpowers, and Spec Kit. [\[spec-coding.dev\]](https://spec-coding.dev/blog/spec-driven-development-tools-openspec-spec-kit-superpowers)
-- **kiadev.net** (Ignaty Kashnitsky, May 9) published two articles: a detailed technical protocol and a 9-tool comparison recommending Spec Kit as a "portable, community-driven starting point." [\[kiadev.net\]](https://www.kiadev.net/news/2026-05-09-github-spec-kit-sdd-toolkit)
-
-Coverage also appeared on WinBuzzer, Let's Data Science, Openflows, AI in Plain English (Medium), Artiverse, KnightLi Blog (multilingual EN/CN/JP/ES), and fundesk.io.
-
-### Community Growth by the Numbers
-
-| Metric | Start of May | End of May | Change |
-| --- | --- | --- | --- |
-| GitHub stars | 92,038 | 106,951 | +14,913 (+16%) |
-| Forks | ~8,000 | 9,464 | +~1,500 |
-| Contributors | — | 217 | — |
-| Releases (total) | 135 | 152 | +17 (incl. 3 late-April) |
-| Community extensions | 92 | 105 | +13 |
-| Community presets | 18 | 21 | +3 |
-| Discussions (open) | ~400 | 422 | +~22 |
-
-## SDD Ecosystem & Industry Trends
-
-### The Analyst View
-
-The Futurum Group's **Mitch Ashley** provided the most significant analyst framing of SDD to date on DevOps.com: "GitHub's Spec Kit signals AI-assisted coding is shifting from prompts to durable, versioned specifications. Vendors are competing to own the artifact that governs intent across Copilot, Claude Code, and Gemini CLI." He warned that "verification at each checkpoint cannot be deferred to the agent producing it" — echoing the project's own emphasis on human oversight at phase boundaries. [\[devops.com\]](https://devops.com/githubs-spec-kit-puts-the-spec-back-in-software-development/)
-
-### The Production Playbook Pattern
-
-**Truong Phung's** 61-minute production playbook represented a new level of depth in community content. Rather than reviewing Spec Kit as a tool, Phung treated SDD as a given and built a comprehensive guide around the **Spec → Plan → Code → Verify loop**, with Spec Kit and Superpowers as the reference implementations. His seven opening truths — "the bottleneck moved from typing to thinking," "context engineering > prompt engineering," and "the PR is the unit of work, not the ticket" — capture the emerging practitioner consensus around structured AI development. [\[dev.to\]](https://dev.to/truongpx396/building-production-grade-fullstack-products-with-ai-coding-agents-a-practical-playbook-2idd)
-
-### Competitive Landscape
-
-The **MarkTechPost comparison** of nine SDD tools called Spec Kit "the most community-adopted open-source option," while positioning competitors along distinct axes: **Kiro** (integrated IDE with EARS-based specs and agent hooks), **BMAD-METHOD** (~48K stars, 12+ specialized agents), **GSD** (~64K stars, lean meta-prompting), **Augment Code** (context engine for 400K+ files, not a spec authoring tool), **OpenSpec** (~52K stars, change accountability and audit trails), and **Tessl** (spec registry with 10K+ library specs). [\[marktechpost.com\]](https://www.marktechpost.com/2026/05/08/9-best-ai-tools-for-spec-driven-development-in-2026-kiro-bmad-gsd-and-more-compare/)
-
-With 107K stars at month's end, Spec Kit is the **only spec-driven development tool in the top 100 most-starred repositories on GitHub** — none of the competitors above are close to the 100K threshold. The broader top-100 list includes AI-adjacent projects like agentic skills frameworks (obra/superpowers at 212K, anthropics/skills at 143K), agent harness tools, and LLM inference engines, but Spec Kit is the only one built around a spec-first development workflow. [\[github.com\]](https://github.com/search?q=stars%3A%3E100000&type=repositories&s=stars&o=desc)
-
-## Roadmap
-
-Areas under discussion or in progress for future development:
-
-- **CLI architecture cleanup** — the `__init__.py` decomposition (4/8 complete) continues toward a modular command structure. This internal cleanup improves contributor onboarding and test isolation. [\[github.com\]](https://github.com/github/spec-kit/releases)
-- **Spec lifecycle management** — spec drift and context rot remain the most cited concern across articles (DevOps.com, DeployHQ, テックオーシャン). The clarify re-validation (#2715) and reconcile extensions are incremental steps; a more comprehensive solution is expected. [\[devops.com\]](https://devops.com/githubs-spec-kit-puts-the-spec-back-in-software-development/)
-- **Multi-agent workflows** — multi-install support (#2389) was the most-requested feature. The next frontier is orchestrating multiple agents across phases, a pattern the community's MAQA, Fleet, and Conduct extensions already explore. [\[github.com\]](https://github.com/github/spec-kit/releases)
-- **Catalog maturity** — catalog discovery CLI (v0.8.3), agentic submissions (v0.8.13), and GITHUB_TOKEN auth (v0.8.2) are building toward a package-manager experience. As the catalog grows past 100 entries, curation and quality signals become critical. [\[github.com\]](https://github.com/github/spec-kit/releases)
-- **Experience simplification** — the deployment gap (DeployHQ), ceremony overhead for small tasks (テックオーシャン, spec-coding.dev), and verbose output (Thoughtworks Radar) continue as open concerns. The lean preset, TinySpec extension, and workflow engine provide answers; discoverability of these options remains an opportunity. [\[deployhq.com\]](https://www.deployhq.com/blog/spec-kit-copilot-workspaces-deployment)
-- **Toward a stable release** — fourteen releases in one month reflects pre-1.0 momentum. The git extension default-off notice (#2432, gated at v0.10.0) and the `--no-git` deprecation (removal at v0.10.0) signal a path toward API stabilization. [\[github.com\]](https://github.com/github/spec-kit/releases)

presets/catalog.community.json

@@ -472,11 +472,11 @@
     "security-governance": {
       "name": "Security Governance",
       "id": "security-governance",
-      "version": "0.4.0",
-      "description": "Adds memory-safe-language preference, language-specific secure coding profiles, ASVS verification, SBOM/AI-SBOM supply-chain transparency, and EU Cyber Resilience Act awareness.",
+      "version": "0.3.0",
+      "description": "Adds memory-safe-language preference, secure code generation, ASVS verification, SBOM/AI-SBOM supply-chain transparency, and EU Cyber Resilience Act awareness.",
       "author": "Thorsten Hindermann",
       "repository": "https://github.com/hindermath/spec-kit-preset-security-governance",
-      "download_url": "https://github.com/hindermath/spec-kit-preset-security-governance/archive/refs/tags/v0.4.0.zip",
+      "download_url": "https://github.com/hindermath/spec-kit-preset-security-governance/archive/refs/tags/v0.3.0.zip",
       "homepage": "https://github.com/hindermath/spec-kit-preset-security-governance",
       "documentation": "https://github.com/hindermath/spec-kit-preset-security-governance/blob/main/README.md",
       "license": "MIT",
@@ -499,20 +499,12 @@
         "vex",
         "slsa",
         "cwe-top-25",
-        "secure-coding",
-        "rust",
-        "go",
-        "swift",
-        "java",
-        "kotlin",
-        "python",
-        "typescript",
         "g7",
         "bsi",
         "cra"
       ],
       "created_at": "2026-04-27T00:00:00Z",
-      "updated_at": "2026-05-26T00:00:00Z"
+      "updated_at": "2026-05-22T00:00:00Z"
     },
     "spec2cloud": {
       "name": "Spec2Cloud",

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.9.0"
+version = "0.8.16"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [
@@ -40,7 +40,6 @@ packages = ["src/specify_cli"]
 "scripts/powershell" = "specify_cli/core_pack/scripts/powershell"
 # Bundled extensions (installable via `specify extension add <name>`)
 "extensions/git" = "specify_cli/core_pack/extensions/git"
-"extensions/agent-context" = "specify_cli/core_pack/extensions/agent-context"
 # Bundled workflows (auto-installed during `specify init`)
 "workflows/speckit" = "specify_cli/core_pack/workflows/speckit"
 # Bundled presets (installable via `specify preset add <name>` or `specify init --preset <name>`)

scripts/bash/check-prerequisites.sh

@@ -117,20 +117,20 @@ check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
 # Validate required directories and files
 if [[ ! -d "$FEATURE_DIR" ]]; then
     echo "ERROR: Feature directory not found: $FEATURE_DIR" >&2
-    echo "Run __SPECKIT_COMMAND_SPECIFY__ first to create the feature structure." >&2
+    echo "Run /speckit.specify first to create the feature structure." >&2
     exit 1
 fi
 
 if [[ ! -f "$IMPL_PLAN" ]]; then
     echo "ERROR: plan.md not found in $FEATURE_DIR" >&2
-    echo "Run __SPECKIT_COMMAND_PLAN__ first to create the implementation plan." >&2
+    echo "Run /speckit.plan first to create the implementation plan." >&2
     exit 1
 fi
 
 # Check for tasks.md if required
 if $REQUIRE_TASKS && [[ ! -f "$TASKS" ]]; then
     echo "ERROR: tasks.md not found in $FEATURE_DIR" >&2
-    echo "Run __SPECKIT_COMMAND_TASKS__ first to create the task list." >&2
+    echo "Run /speckit.tasks first to create the task list." >&2
     exit 1
 fi
 

scripts/bash/common.sh

@@ -186,7 +186,7 @@ read_feature_json_feature_directory() {
 }
 
 # Returns 0 when .specify/feature.json lists feature_directory that exists as a directory
-# and matches the resolved active FEATURE_DIR (so __SPECKIT_COMMAND_PLAN__ can skip git branch pattern checks).
+# and matches the resolved active FEATURE_DIR (so /speckit.plan can skip git branch pattern checks).
 # Delegates parsing to read_feature_json_feature_directory, which is safe under `set -e`.
 feature_json_matches_feature_dir() {
     local repo_root="$1"
@@ -262,7 +262,7 @@ get_feature_paths() {
 
     # Resolve feature directory.  Priority:
     #   1. SPECIFY_FEATURE_DIRECTORY env var (explicit override)
-    #   2. .specify/feature.json "feature_directory" key (persisted by __SPECKIT_COMMAND_SPECIFY__)
+    #   2. .specify/feature.json "feature_directory" key (persisted by /speckit.specify)
     #   3. Branch-name-based prefix lookup (legacy fallback)
     local feature_dir
     if [[ -n "${SPECIFY_FEATURE_DIRECTORY:-}" ]]; then
@@ -642,3 +642,4 @@ except Exception:
     printf '%s' "$content"
     return 0
 }
+

scripts/bash/setup-tasks.sh

@@ -35,13 +35,13 @@ fi
 
 if [[ ! -f "$IMPL_PLAN" ]]; then
     echo "ERROR: plan.md not found in $FEATURE_DIR" >&2
-    echo "Run __SPECKIT_COMMAND_PLAN__ first to create the implementation plan." >&2
+    echo "Run /speckit.plan first to create the implementation plan." >&2
     exit 1
 fi
 
 if [[ ! -f "$FEATURE_SPEC" ]]; then
     echo "ERROR: spec.md not found in $FEATURE_DIR" >&2
-    echo "Run __SPECKIT_COMMAND_SPECIFY__ first to create the feature structure." >&2
+    echo "Run /speckit.specify first to create the feature structure." >&2
     exit 1
 fi
 

scripts/powershell/check-prerequisites.ps1

@@ -89,20 +89,20 @@ if (-not (Test-FeatureBranch -Branch $paths.CURRENT_BRANCH -HasGit:$paths.HAS_GI
 # Validate required directories and files
 if (-not (Test-Path $paths.FEATURE_DIR -PathType Container)) {
     Write-Output "ERROR: Feature directory not found: $($paths.FEATURE_DIR)"
-    Write-Output "Run __SPECKIT_COMMAND_SPECIFY__ first to create the feature structure."
+    Write-Output "Run /speckit.specify first to create the feature structure."
     exit 1
 }
 
 if (-not (Test-Path $paths.IMPL_PLAN -PathType Leaf)) {
     Write-Output "ERROR: plan.md not found in $($paths.FEATURE_DIR)"
-    Write-Output "Run __SPECKIT_COMMAND_PLAN__ first to create the implementation plan."
+    Write-Output "Run /speckit.plan first to create the implementation plan."
     exit 1
 }
 
 # Check for tasks.md if required
 if ($RequireTasks -and -not (Test-Path $paths.TASKS -PathType Leaf)) {
     Write-Output "ERROR: tasks.md not found in $($paths.FEATURE_DIR)"
-    Write-Output "Run __SPECKIT_COMMAND_TASKS__ first to create the task list."
+    Write-Output "Run /speckit.tasks first to create the task list."
     exit 1
 }
 

scripts/powershell/common.ps1

@@ -165,7 +165,7 @@ function Test-FeatureBranch {
 }
 
 # True when .specify/feature.json pins an existing feature directory that matches the
-# active FEATURE_DIR from Get-FeaturePathsEnv (so __SPECKIT_COMMAND_PLAN__ can skip git branch pattern checks).
+# active FEATURE_DIR from Get-FeaturePathsEnv (so /speckit.plan can skip git branch pattern checks).
 function Test-FeatureJsonMatchesFeatureDir {
     param(
         [Parameter(Mandatory = $true)][string]$RepoRoot,
@@ -288,7 +288,7 @@ function Get-FeaturePathsEnv {
 
     # Resolve feature directory.  Priority:
     #   1. SPECIFY_FEATURE_DIRECTORY env var (explicit override)
-    #   2. .specify/feature.json "feature_directory" key (persisted by __SPECKIT_COMMAND_SPECIFY__)
+    #   2. .specify/feature.json "feature_directory" key (persisted by /speckit.specify)
     #   3. Branch-name-based prefix lookup (same as scripts/bash/common.sh)
     $featureJson = Join-Path $repoRoot '.specify/feature.json'
     if ($env:SPECIFY_FEATURE_DIRECTORY) {
@@ -640,4 +640,4 @@ except Exception:
     }
 
     return $content
-}
+}

scripts/powershell/setup-tasks.ps1

@@ -28,13 +28,13 @@ if (-not (Test-FeatureJsonMatchesFeatureDir -RepoRoot $paths.REPO_ROOT -ActiveFe
 
 if (-not (Test-Path $paths.IMPL_PLAN -PathType Leaf)) {
     [Console]::Error.WriteLine("ERROR: plan.md not found in $($paths.FEATURE_DIR)")
-    [Console]::Error.WriteLine("Run __SPECKIT_COMMAND_PLAN__ first to create the implementation plan.")
+    [Console]::Error.WriteLine("Run /speckit.plan first to create the implementation plan.")
     exit 1
 }
 
 if (-not (Test-Path $paths.FEATURE_SPEC -PathType Leaf)) {
     [Console]::Error.WriteLine("ERROR: spec.md not found in $($paths.FEATURE_DIR)")
-    [Console]::Error.WriteLine("Run __SPECKIT_COMMAND_SPECIFY__ first to create the feature structure.")
+    [Console]::Error.WriteLine("Run /speckit.specify first to create the feature structure.")
     exit 1
 }
 

src/specify_cli/__init__.py

@@ -161,9 +161,9 @@ def _install_shared_infra(
     ``bash`` when *script_type* is ``"sh"`` and ``powershell`` when it is
     ``"ps"``.  Tracks all installed files in ``speckit.manifest.json``.
 
-    Shared scripts and page templates are processed to resolve
-    ``__SPECKIT_COMMAND_<NAME>__`` placeholders using *invoke_separator*
-    (``"."`` for markdown agents, ``"-"`` for skills agents).
+    Page templates are processed to resolve ``__SPECKIT_COMMAND_<NAME>__``
+    placeholders using *invoke_separator* (``"."`` for markdown agents,
+    ``"-"`` for skills agents).
 
     Overwrite policy:
 
@@ -304,72 +304,6 @@ def load_init_options(project_path: Path) -> dict[str, Any]:
         return {}
 
 
-# ---------------------------------------------------------------------------
-# Agent-context extension config helpers
-# ---------------------------------------------------------------------------
-
-_AGENT_CTX_EXT_CONFIG = (
-    Path(".specify") / "extensions" / "agent-context" / "agent-context-config.yml"
-)
-
-
-def _load_agent_context_config(project_root: Path) -> dict[str, Any]:
-    """Load the agent-context extension config, returning defaults on failure."""
-    from .integrations.base import IntegrationBase
-
-    defaults: dict[str, Any] = {
-        "context_file": "",
-        "context_markers": {
-            "start": IntegrationBase.CONTEXT_MARKER_START,
-            "end": IntegrationBase.CONTEXT_MARKER_END,
-        },
-    }
-    path = project_root / _AGENT_CTX_EXT_CONFIG
-    if not path.exists():
-        return defaults
-    try:
-        raw = yaml.safe_load(path.read_text(encoding="utf-8"))
-    except (OSError, UnicodeError, yaml.YAMLError):
-        return defaults
-    if not isinstance(raw, dict):
-        return defaults
-    return raw
-
-
-def _save_agent_context_config(
-    project_root: Path, config: dict[str, Any]
-) -> None:
-    """Persist *config* to the agent-context extension config file."""
-    path = project_root / _AGENT_CTX_EXT_CONFIG
-    path.parent.mkdir(parents=True, exist_ok=True)
-    path.write_text(yaml.safe_dump(config, default_flow_style=False, sort_keys=False), encoding="utf-8")
-
-
-def _update_agent_context_config_file(
-    project_root: Path,
-    context_file: str | None,
-    *,
-    preserve_markers: bool = True,
-) -> None:
-    """Update the agent-context extension config with *context_file*.
-
-    When *preserve_markers* is True (default), any existing
-    ``context_markers`` values are kept unchanged so user customisations
-    survive integration changes and reinit.  When False, the default
-    markers are written unconditionally.
-    """
-    from .integrations.base import IntegrationBase
-
-    cfg = _load_agent_context_config(project_root)
-    cfg["context_file"] = context_file or ""
-    if not preserve_markers or not isinstance(cfg.get("context_markers"), dict):
-        cfg["context_markers"] = {
-            "start": IntegrationBase.CONTEXT_MARKER_START,
-            "end": IntegrationBase.CONTEXT_MARKER_END,
-        }
-    _save_agent_context_config(project_root, cfg)
-
-
 def _get_skills_dir(project_path: Path, selected_ai: str) -> Path:
     """Resolve the agent-specific skills directory.
 
@@ -715,31 +649,13 @@ def _refresh_init_options_speckit_version(project_root: Path) -> None:
 
 
 def _clear_init_options_for_integration(project_root: Path, integration_key: str) -> None:
-    """Clear active integration keys from init-options.json when they match.
-
-    Also clears ``context_file`` from the agent-context extension config so
-    no stale path is left behind when the integration is uninstalled.
-    """
+    """Clear active integration keys from init-options.json when they match."""
     opts = load_init_options(project_root)
-    has_legacy_context_keys = ("context_file" in opts) or ("context_markers" in opts)
-    # Remove legacy fields that older versions may have written.
-    opts.pop("context_file", None)
-    opts.pop("context_markers", None)
-
     if opts.get("integration") == integration_key or opts.get("ai") == integration_key:
         opts.pop("integration", None)
         opts.pop("ai", None)
         opts.pop("ai_skills", None)
-        save_init_options(project_root, opts)
-        # Clear context_file in the extension config if it already exists.
-        # Avoid creating the config (and parent dirs) in projects where the
-        # agent-context extension was never installed.
-        ext_cfg_path = project_root / _AGENT_CTX_EXT_CONFIG
-        if ext_cfg_path.exists():
-            _update_agent_context_config_file(
-                project_root, "", preserve_markers=True
-            )
-    elif has_legacy_context_keys:
+        opts.pop("context_file", None)
         save_init_options(project_root, opts)
 
 
@@ -825,7 +741,6 @@ def _set_default_integration(
     parsed_options: dict[str, Any] | None = None,
     refresh_templates: bool = True,
     refresh_templates_force: bool = False,
-    refresh_hint: str | None = None,
 ) -> None:
     """Persist *key* as default and align active runtime metadata."""
     resolved_script = _resolve_integration_script_type(project_root, state, key, script_type)
@@ -840,19 +755,16 @@ def _set_default_integration(
 
     if refresh_templates:
         try:
-            _install_shared_infra(
+            _refresh_shared_templates(
                 project_root,
-                resolved_script,
                 invoke_separator=_invoke_separator_for_integration(
                     integration, {"integration_settings": settings}, key, parsed_options
                 ),
                 force=refresh_templates_force,
-                refresh_managed=True,
-                refresh_hint=refresh_hint,
             )
         except (ValueError, OSError) as exc:
             raise _SharedTemplateRefreshError(
-                f"Failed to refresh shared infrastructure for '{key}': {exc}"
+                f"Failed to refresh shared templates for '{key}': {exc}"
             ) from exc
 
     _write_integration_json(project_root, key, installed_keys, settings)
@@ -1184,23 +1096,12 @@ def _update_init_options_for_integration(
     integration: Any,
     script_type: str | None = None,
 ) -> None:
-    """Update init-options.json and the agent-context extension config to
-    reflect *integration* as the active one.
-
-    ``context_file`` and ``context_markers`` are stored in the agent-context
-    extension config (``.specify/extensions/agent-context/agent-context-config.yml``),
-    not in ``init-options.json``.  Existing user-customised markers are
-    always preserved when the config already exists; invalid marker values
-    are silently ignored at runtime by ``_resolve_context_markers()`` which
-    falls back to the class-level defaults.
-    """
+    """Update ``init-options.json`` to reflect *integration* as the active one."""
     from .integrations.base import SkillsIntegration
     opts = load_init_options(project_root)
     opts["integration"] = integration.key
     opts["ai"] = integration.key
-    # Remove legacy fields if they were written by an older version.
-    opts.pop("context_file", None)
-    opts.pop("context_markers", None)
+    opts["context_file"] = integration.context_file
     opts["speckit_version"] = get_speckit_version()
     if script_type:
         opts["script"] = script_type
@@ -1208,32 +1109,13 @@ def _update_init_options_for_integration(
         opts["ai_skills"] = True
     else:
         opts.pop("ai_skills", None)
-
-    # Update the agent-context extension config BEFORE init-options.json
-    # so a failure here doesn't leave init-options partially updated.
-    ext_cfg_path = project_root / _AGENT_CTX_EXT_CONFIG
-    if ext_cfg_path.exists():
-        _update_agent_context_config_file(
-            project_root,
-            integration.context_file,
-            preserve_markers=True,
-        )
-    elif integration.context_file:
-        # Extension config doesn't exist yet (extension not installed).
-        # Write defaults so scripts have something to read.
-        _update_agent_context_config_file(
-            project_root,
-            integration.context_file,
-            preserve_markers=False,
-        )
-
     save_init_options(project_root, opts)
 
 
 @integration_app.command("use")
 def integration_use(
     key: str = typer.Argument(help="Installed integration key to make the default"),
-    force: bool = typer.Option(False, "--force", help="Overwrite existing shared infrastructure files, including customizations, while changing the default"),
+    force: bool = typer.Option(False, "--force", help="Overwrite managed shared templates while changing the default"),
 ):
     """Set the default integration without uninstalling other integrations."""
     from .integrations import get_integration
@@ -1264,10 +1146,6 @@ def integration_use(
         raw_options=raw_options,
         parsed_options=parsed_options,
         refresh_templates_force=force,
-        refresh_hint=(
-            "To overwrite customizations, re-run with "
-            f"[cyan]specify integration use {key} --force[/cyan]."
-        ),
     )
     console.print(f"[green]✓[/green] Default integration set to [bold]{key}[/bold].")
 
@@ -1340,14 +1218,11 @@ def integration_uninstall(
         console.print(f"[dim]Details:[/dim] {exc}")
         raise typer.Exit(1)
 
-    if not integration:
-        console.print(
-            f"[yellow]Warning:[/yellow] Integration '{key}' not found "
-            "in registry. Falling back to manifest-based cleanup."
-        )
-        removed, skipped = manifest.uninstall(project_root, force=force)
-    else:
-        removed, skipped = integration.teardown(project_root, manifest, force=force)
+    removed, skipped = manifest.uninstall(project_root, force=force)
+
+    # Remove managed context section from the agent context file
+    if integration:
+        integration.remove_context_section(project_root)
 
     remaining = [installed for installed in installed_keys if installed != key]
     new_default = default_key if default_key != key else (remaining[0] if remaining else None)
@@ -1437,7 +1312,7 @@ def integration_switch(
             )
             console.print(
                 f"\n[green]✓[/green] Default integration remains [bold]{target}[/bold]; "
-                "shared infrastructure refreshed."
+                "managed shared templates refreshed."
             )
             raise typer.Exit(0)
         console.print(f"[yellow]Integration '{target}' is already the default integration. Nothing to switch.[/yellow]")
@@ -1489,9 +1364,8 @@ def integration_switch(
                     f"run [cyan]specify integration uninstall {installed_key}[/cyan], then retry."
                 )
                 raise typer.Exit(1)
-            removed, skipped = current_integration.teardown(
-                project_root, old_manifest, force=force,
-            )
+            removed, skipped = old_manifest.uninstall(project_root, force=force)
+            current_integration.remove_context_section(project_root)
             if removed:
                 console.print(f"  Removed {len(removed)} file(s)")
             if skipped:
@@ -1793,18 +1667,16 @@ def integration_upgrade(
         )
         if installed_key == key:
             try:
-                _install_shared_infra(
+                _refresh_shared_templates(
                     project_root,
-                    selected_script,
                     invoke_separator=_invoke_separator_for_integration(
                         integration, {"integration_settings": settings}, key, parsed_options
                     ),
                     force=force,
-                    refresh_managed=True,
                 )
             except (ValueError, OSError) as exc:
                 raise _SharedTemplateRefreshError(
-                    f"Failed to refresh shared infrastructure for '{key}': {exc}"
+                    f"Failed to refresh shared templates for '{key}': {exc}"
                 ) from exc
         new_manifest.save()
         _write_integration_json(project_root, installed_key, installed_keys, settings)
@@ -3082,43 +2954,6 @@ def extension_add(
     manager = ExtensionManager(project_root)
     speckit_version = get_speckit_version()
 
-    # Prompt for URL-based installs BEFORE the spinner so the user can
-    # actually see and respond to the confirmation (the Rich status
-    # spinner overwrites the typer.confirm prompt line, making it appear
-    # as though the command is hung).
-    # Guard with ``not dev`` so that --dev + --from does not show a
-    # confusing confirmation for a URL that will be ignored.
-    if from_url and not dev:
-        from urllib.parse import urlparse
-        from rich.markup import escape as _escape_markup
-
-        parsed = urlparse(from_url)
-        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
-
-        if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
-            console.print("[red]Error:[/red] URL must use HTTPS for security.")
-            console.print("HTTP is only allowed for localhost URLs.")
-            raise typer.Exit(1)
-
-        safe_url = _escape_markup(from_url)
-
-        # Warn about untrusted sources — default-deny confirmation
-        console.print()
-        console.print(Panel(
-            f"[bold]You are installing an extension from an external URL that is not\n"
-            f"listed in any of your configured extension catalogs.[/bold]\n\n"
-            f"URL: {safe_url}\n\n"
-            f"Only install extensions from sources you trust.",
-            title="[bold yellow]⚠ Untrusted Source[/bold yellow]",
-            border_style="yellow",
-            padding=(1, 2),
-        ))
-        console.print()
-        confirm = typer.confirm("Continue with installation?", default=False)
-        if not confirm:
-            console.print("Cancelled")
-            raise typer.Exit(0)
-
     try:
         with console.status(f"[cyan]Installing extension: {extension}[/cyan]"):
             if dev:
@@ -3132,18 +2967,27 @@ def extension_add(
                     console.print(f"[red]Error:[/red] No extension.yml found in {source_path}")
                     raise typer.Exit(1)
 
-                manifest = manager.install_from_directory(
-                    source_path,
-                    speckit_version,
-                    priority=priority,
-                    link_commands=True,
-                )
+                manifest = manager.install_from_directory(source_path, speckit_version, priority=priority)
 
             elif from_url:
                 # Install from URL (ZIP file)
+                import urllib.request
                 import urllib.error
+                from urllib.parse import urlparse
 
-                console.print(f"Downloading from {safe_url}...")
+                # Validate URL
+                parsed = urlparse(from_url)
+                is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+
+                if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
+                    console.print("[red]Error:[/red] URL must use HTTPS for security.")
+                    console.print("HTTP is only allowed for localhost URLs.")
+                    raise typer.Exit(1)
+
+                # Warn about untrusted sources
+                console.print("[yellow]Warning:[/yellow] Installing from external URL.")
+                console.print("Only install extensions from sources you trust.\n")
+                console.print(f"Downloading from {from_url}...")
 
                 # Download ZIP to temp location
                 download_dir = project_root / ".specify" / "extensions" / ".cache" / "downloads"
@@ -3160,7 +3004,7 @@ def extension_add(
                     # Install from downloaded ZIP
                     manifest = manager.install_from_zip(zip_path, speckit_version, priority=priority)
                 except urllib.error.URLError as e:
-                    console.print(f"[red]Error:[/red] Failed to download from {safe_url}: {e}")
+                    console.print(f"[red]Error:[/red] Failed to download from {from_url}: {e}")
                     raise typer.Exit(1)
                 finally:
                     # Clean up downloaded ZIP
@@ -3757,9 +3601,7 @@ def extension_update(
                     if agent_name not in registrar.AGENT_CONFIGS:
                         continue
                     agent_config = registrar.AGENT_CONFIGS[agent_name]
-                    commands_dir = _AgentReg._resolve_agent_dir(
-                        agent_name, agent_config, project_root
-                    )
+                    commands_dir = project_root / agent_config["dir"]
 
                     for cmd_name in cmd_names:
                         output_name = _AgentReg._compute_output_name(agent_name, cmd_name, agent_config)
@@ -3920,9 +3762,7 @@ def extension_update(
                             if agent_name not in registrar.AGENT_CONFIGS:
                                 continue
                             agent_config = registrar.AGENT_CONFIGS[agent_name]
-                            commands_dir = _AgentReg._resolve_agent_dir(
-                                agent_name, agent_config, project_root
-                            )
+                            commands_dir = project_root / agent_config["dir"]
 
                             for cmd_name in cmd_names:
                                 output_name = _AgentReg._compute_output_name(agent_name, cmd_name, agent_config)

src/specify_cli/agents.py

@@ -374,15 +374,8 @@ class CommandRegistrar:
 
         body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
 
-        # Resolve __CONTEXT_FILE__ from the agent-context extension config.
-        # Fall back to init-options.json for projects that haven't migrated.
-        # Local import: _load_agent_context_config lives in __init__.py which
-        # imports agents.py, so a top-level import would be circular.
-        from . import _load_agent_context_config
-        ac_cfg = _load_agent_context_config(project_root)
-        context_file = ac_cfg.get("context_file") or ""
-        if not context_file:
-            context_file = init_opts.get("context_file") or ""
+        # Resolve __CONTEXT_FILE__ from init-options
+        context_file = init_opts.get("context_file") or ""
         body = body.replace("__CONTEXT_FILE__", context_file)
 
         return CommandRegistrar.rewrite_project_relative_paths(body)
@@ -446,7 +439,6 @@ class CommandRegistrar:
         project_root: Path,
         context_note: str = None,
         _resolved_dir: Path = None,
-        link_outputs: bool = False,
     ) -> List[str]:
         """Register commands for a specific agent.
 
@@ -461,9 +453,6 @@ class CommandRegistrar:
                 only — avoids a second ``_resolve_agent_dir`` call and
                 duplicate deprecation warnings when invoked from
                 ``register_commands_for_all_agents``).
-            link_outputs: If True, write rendered output to a source-local
-                dev cache and symlink the agent command file to it. Falls back
-                to a normal file write when symlinks are unavailable.
 
         Returns:
             List of registered command names
@@ -570,15 +559,7 @@ class CommandRegistrar:
             dest_file = commands_dir / f"{output_name}{agent_config['extension']}"
             self._ensure_inside(dest_file, commands_dir)
             dest_file.parent.mkdir(parents=True, exist_ok=True)
-            self._write_registered_output(
-                dest_file,
-                output,
-                source_dir,
-                agent_name,
-                output_name,
-                agent_config["extension"],
-                link_outputs,
-            )
+            dest_file.write_text(output, encoding="utf-8")
 
             if agent_name == "copilot":
                 self.write_copilot_prompt(project_root, cmd_name)
@@ -644,56 +625,13 @@ class CommandRegistrar:
                 )
                 self._ensure_inside(alias_file, commands_dir)
                 alias_file.parent.mkdir(parents=True, exist_ok=True)
-                self._write_registered_output(
-                    alias_file,
-                    alias_output,
-                    source_dir,
-                    agent_name,
-                    alias_output_name,
-                    agent_config["extension"],
-                    link_outputs,
-                )
+                alias_file.write_text(alias_output, encoding="utf-8")
                 if agent_name == "copilot":
                     self.write_copilot_prompt(project_root, alias)
                 registered.append(alias)
 
         return registered
 
-    @staticmethod
-    def _write_registered_output(
-        dest_file: Path,
-        content: str,
-        source_dir: Path,
-        agent_name: str,
-        output_name: str,
-        extension: str,
-        link_outputs: bool,
-    ) -> None:
-        """Write a rendered agent artifact, optionally as a dev-mode symlink."""
-        if not link_outputs:
-            dest_file.write_text(content, encoding="utf-8")
-            return
-
-        rel_output = Path(f"{output_name}{extension}")
-        cache_root = source_dir / ".specify-dev" / "agent-commands" / agent_name
-        cache_file = cache_root / rel_output
-        CommandRegistrar._ensure_inside(cache_file, cache_root)
-
-        try:
-            cache_file.parent.mkdir(parents=True, exist_ok=True)
-            cache_file.write_text(content, encoding="utf-8")
-            if dest_file.exists() or dest_file.is_symlink():
-                dest_file.unlink()
-            target = os.path.relpath(cache_file, dest_file.parent)
-            os.symlink(target, dest_file)
-        except (OSError, ValueError):
-            # Windows often requires Developer Mode or admin privileges for
-            # symlinks, and relpath can fail across drives. Keep dev installs
-            # functional by falling back to a copy.
-            if dest_file.is_symlink():
-                dest_file.unlink()
-            dest_file.write_text(content, encoding="utf-8")
-
     @staticmethod
     def write_copilot_prompt(project_root: Path, cmd_name: str) -> None:
         """Generate a companion .prompt.md file for a Copilot agent command.
@@ -716,28 +654,15 @@ class CommandRegistrar:
     ) -> Path:
         """Return the agent command directory, falling back to legacy_dir.
 
-        Supports project-relative paths (e.g. ``.claude/skills/``),
-        home-relative paths (e.g. ``~/.hermes/skills``), and absolute
-        paths — the ``agent_config["dir"]`` value is resolved verbatim
-        when absolute or starting with ``~/``, or joined with
-        ``project_root`` when relative.
-
-        When the canonical directory does not exist but a ``legacy_dir``
-        is configured and present on disk, returns the legacy path and
-        emits a deprecation warning advising the user to upgrade.
+        When the canonical directory (``agent_config["dir"]``) does not
+        exist but a ``legacy_dir`` is configured and present on disk,
+        returns the legacy path and emits a deprecation warning advising
+        the user to upgrade.
 
         Integrations that do not declare ``legacy_dir`` get the canonical
         path unconditionally — no fallback, no warning.
         """
-        dir_str = agent_config["dir"]
-        if dir_str.startswith("~"):
-            # Use Path.home() + remainder instead of expanduser() so tests
-            # that monkeypatch Path.home() can properly isolate the home dir.
-            # expanduser() uses OS env/user lookup and ignores monkeypatches.
-            agent_dir = Path.home() / dir_str[1:].lstrip("/")
-        else:
-            p = Path(dir_str)
-            agent_dir = p if p.is_absolute() else project_root / p
+        agent_dir = project_root / agent_config["dir"]
         if not agent_dir.exists():
             legacy = agent_config.get("legacy_dir")
             if legacy:
@@ -762,7 +687,6 @@ class CommandRegistrar:
         source_dir: Path,
         project_root: Path,
         context_note: str = None,
-        link_outputs: bool = False,
     ) -> Dict[str, List[str]]:
         """Register commands for all detected agents in the project.
 
@@ -772,8 +696,6 @@ class CommandRegistrar:
             source_dir: Directory containing command source files
             project_root: Path to project root
             context_note: Custom context comment for markdown output
-            link_outputs: If True, create dev-mode symlinks for rendered
-                command files when supported by the OS.
 
         Returns:
             Dictionary mapping agent names to list of registered commands
@@ -782,15 +704,6 @@ class CommandRegistrar:
 
         self._ensure_configs()
         for agent_name, agent_config in self.AGENT_CONFIGS.items():
-            # Check detect_dir first (project-local marker) if configured,
-            # falling back to the resolved dir for output.  This prevents
-            # global dirs (e.g. ~/.hermes/skills) from causing false
-            # detection in every project.
-            detect_dir_str = agent_config.get("detect_dir")
-            if detect_dir_str:
-                detect_path = project_root / detect_dir_str
-                if not detect_path.exists():
-                    continue
             agent_dir = self._resolve_agent_dir(
                 agent_name, agent_config, project_root,
             )
@@ -805,7 +718,6 @@ class CommandRegistrar:
                         project_root,
                         context_note=context_note,
                         _resolved_dir=agent_dir,
-                        link_outputs=link_outputs,
                     )
                     if registered:
                         results[agent_name] = registered
@@ -821,7 +733,6 @@ class CommandRegistrar:
         source_dir: Path,
         project_root: Path,
         context_note: Optional[str] = None,
-        link_outputs: bool = False,
     ) -> Dict[str, List[str]]:
         """Register commands for all non-skill agents in the project.
 
@@ -835,8 +746,6 @@ class CommandRegistrar:
             source_dir: Directory containing command source files
             project_root: Path to project root
             context_note: Custom context comment for markdown output
-            link_outputs: If True, create dev-mode symlinks for rendered
-                command files when supported by the OS.
 
         Returns:
             Dictionary mapping agent names to list of registered commands
@@ -846,11 +755,6 @@ class CommandRegistrar:
         for agent_name, agent_config in self.AGENT_CONFIGS.items():
             if agent_config.get("extension") == "/SKILL.md":
                 continue
-            detect_dir_str = agent_config.get("detect_dir")
-            if detect_dir_str:
-                detect_path = project_root / detect_dir_str
-                if not detect_path.exists():
-                    continue
             agent_dir = self._resolve_agent_dir(
                 agent_name, agent_config, project_root,
             )
@@ -864,7 +768,6 @@ class CommandRegistrar:
                         project_root,
                         context_note=context_note,
                         _resolved_dir=agent_dir,
-                        link_outputs=link_outputs,
                     )
                     if registered:
                         results[agent_name] = registered
@@ -913,7 +816,7 @@ class CommandRegistrar:
                     cmd_file = (
                         target_dir / f"{output_name}{agent_config['extension']}"
                     )
-                    if cmd_file.exists() or cmd_file.is_symlink():
+                    if cmd_file.exists():
                         cmd_file.unlink()
                         # For SKILL.md agents each command lives in its own
                         # subdirectory (e.g. .agents/skills/speckit-ext-cmd/

src/specify_cli/commands/init.py

@@ -153,7 +153,6 @@ def register(app: typer.Typer) -> None:
             _install_shared_infra_or_exit,
             _parse_integration_options,
             _print_cli_warning,
-            _update_agent_context_config_file,
             _write_integration_json,
             ensure_executable_scripts,
             save_init_options,
@@ -395,7 +394,6 @@ def register(app: typer.Typer) -> None:
             ("constitution", "Constitution setup"),
             ("git", "Install git extension"),
             ("workflow", "Install bundled workflow"),
-            ("agent-context", "Install agent-context extension"),
             ("final", "Finalize"),
         ]:
             tracker.add(key, label)
@@ -537,10 +535,13 @@ def register(app: typer.Typer) -> None:
                     sanitized_wf = str(wf_err).replace('\n', ' ').strip()
                     tracker.error("workflow", f"install failed: {sanitized_wf[:120]}")
 
+                ensure_executable_scripts(project_path, tracker=tracker)
+
                 init_opts = {
                     "ai": selected_ai,
                     "integration": resolved_integration.key,
                     "branch_numbering": branch_numbering or "sequential",
+                    "context_file": resolved_integration.context_file,
                     "here": here,
                     "script": selected_script,
                     "speckit_version": get_speckit_version(),
@@ -550,47 +551,6 @@ def register(app: typer.Typer) -> None:
                     init_opts["ai_skills"] = True
                 save_init_options(project_path, init_opts)
 
-                # --- agent-context extension (bundled, auto-installed) ---
-                # Installed after init-options.json is written so that skill
-                # registration can read ai_skills + integration key.
-                try:
-                    from ..extensions import ExtensionManager as _ExtMgr
-                    bundled_ac = _locate_bundled_extension("agent-context")
-                    if bundled_ac:
-                        ac_mgr = _ExtMgr(project_path)
-                        if ac_mgr.registry.is_installed("agent-context"):
-                            tracker.complete("agent-context", "already installed")
-                        else:
-                            ac_mgr.install_from_directory(
-                                bundled_ac, get_speckit_version()
-                            )
-                            tracker.complete("agent-context", "extension installed")
-                    else:
-                        from ..extensions import REINSTALL_COMMAND as _ac_reinstall
-                        tracker.error(
-                            "agent-context",
-                            f"bundled extension not found — installation may be "
-                            f"incomplete. Run: {_ac_reinstall}",
-                        )
-                except Exception as ac_err:
-                    sanitized_ac = str(ac_err).replace('\n', ' ').strip()
-                    tracker.error(
-                        "agent-context",
-                        f"extension install failed: {sanitized_ac[:120]}",
-                    )
-
-                # Write context_file to the agent-context extension config
-                # AFTER the extension install (which copies the template config
-                # with an empty context_file).
-                if resolved_integration.context_file:
-                    _update_agent_context_config_file(
-                        project_path,
-                        resolved_integration.context_file,
-                        preserve_markers=True,
-                    )
-
-                ensure_executable_scripts(project_path, tracker=tracker)
-
                 if preset:
                     try:
                         from ..presets import PresetManager, PresetCatalog, PresetError

src/specify_cli/extensions.py

@@ -823,7 +823,6 @@ class ExtensionManager:
         self,
         manifest: ExtensionManifest,
         extension_dir: Path,
-        link_outputs: bool = False,
     ) -> List[str]:
         """Generate SKILL.md files for extension commands as agent skills.
 
@@ -835,8 +834,6 @@ class ExtensionManager:
         Args:
             manifest: Extension manifest.
             extension_dir: Installed extension directory.
-            link_outputs: If True, create dev-mode symlinks for rendered
-                skill files when supported by the OS.
 
         Returns:
             List of skill names that were created (for registry storage).
@@ -889,18 +886,9 @@ class ExtensionManager:
             # Check if skill already exists before creating the directory
             skill_subdir = skills_dir / skill_name
             skill_file = skill_subdir / "SKILL.md"
-            cache_root = extension_dir / ".specify-dev" / "extension-skills"
-            cache_file = cache_root / skill_name / "SKILL.md"
-            CommandRegistrar._ensure_inside(cache_file, cache_root)
-            if skill_file.exists() or skill_file.is_symlink():
-                # Do not overwrite user-customized skills, but allow dev-mode
-                # symlinks that point back to this extension's generated cache
-                # to be refreshed on a subsequent dev install.
-                if not (
-                    link_outputs
-                    and self._is_expected_dev_symlink(skill_file, cache_file)
-                ):
-                    continue
+            if skill_file.exists():
+                # Do not overwrite user-customized skills
+                continue
 
             # Create skill directory; track whether we created it so we can clean
             # up safely if reading the source file subsequently fails.
@@ -952,35 +940,11 @@ class ExtensionManager:
                     skill_content
                 )
 
-            if link_outputs:
-                try:
-                    cache_file.parent.mkdir(parents=True, exist_ok=True)
-                    cache_file.write_text(skill_content, encoding="utf-8")
-                    if skill_file.exists() or skill_file.is_symlink():
-                        skill_file.unlink()
-                    target = os.path.relpath(cache_file, skill_file.parent)
-                    os.symlink(target, skill_file)
-                except (OSError, ValueError):
-                    if skill_file.is_symlink():
-                        skill_file.unlink()
-                    skill_file.write_text(skill_content, encoding="utf-8")
-            else:
-                skill_file.write_text(skill_content, encoding="utf-8")
+            skill_file.write_text(skill_content, encoding="utf-8")
             written.append(skill_name)
 
         return written
 
-    @staticmethod
-    def _is_expected_dev_symlink(skill_file: Path, cache_file: Path) -> bool:
-        """Return True when an existing skill file links to its dev cache."""
-        if not skill_file.is_symlink():
-            return False
-
-        try:
-            return skill_file.resolve(strict=False) == cache_file.resolve(strict=False)
-        except OSError:
-            return False
-
     def _unregister_extension_skills(
         self,
         skill_names: List[str],
@@ -1151,7 +1115,6 @@ class ExtensionManager:
         speckit_version: str,
         register_commands: bool = True,
         priority: int = 10,
-        link_commands: bool = False,
     ) -> ExtensionManifest:
         """Install extension from a local directory.
 
@@ -1160,8 +1123,6 @@ class ExtensionManager:
             speckit_version: Current spec-kit version
             register_commands: If True, register commands with AI agents
             priority: Resolution priority (lower = higher precedence, default 10)
-            link_commands: If True, register rendered agent artifacts as
-                symlinks to a dev cache when supported by the OS.
 
         Returns:
             Installed extension manifest
@@ -1205,14 +1166,12 @@ class ExtensionManager:
             registrar = CommandRegistrar()
             # Register for all detected agents
             registered_commands = registrar.register_commands_for_all_agents(
-                manifest, dest_dir, self.project_root, link_outputs=link_commands
+                manifest, dest_dir, self.project_root
             )
 
         # Auto-register extension commands as agent skills when --ai-skills
         # was used during project initialisation (feature parity).
-        registered_skills = self._register_extension_skills(
-            manifest, dest_dir, link_outputs=link_commands
-        )
+        registered_skills = self._register_extension_skills(manifest, dest_dir)
 
         # Register hooks and update installed list in extensions.yml
         hook_executor = HookExecutor(self.project_root)
@@ -1648,8 +1607,7 @@ class CommandRegistrar:
         agent_name: str,
         manifest: ExtensionManifest,
         extension_dir: Path,
-        project_root: Path,
-        link_outputs: bool = False,
+        project_root: Path
     ) -> List[str]:
         """Register extension commands for a specific agent."""
         if agent_name not in self.AGENT_CONFIGS:
@@ -1657,23 +1615,20 @@ class CommandRegistrar:
         context_note = f"\n<!-- Extension: {manifest.id} -->\n<!-- Config: .specify/extensions/{manifest.id}/ -->\n"
         return self._registrar.register_commands(
             agent_name, manifest.commands, manifest.id, extension_dir, project_root,
-            context_note=context_note,
-            link_outputs=link_outputs,
+            context_note=context_note
         )
 
     def register_commands_for_all_agents(
         self,
         manifest: ExtensionManifest,
         extension_dir: Path,
-        project_root: Path,
-        link_outputs: bool = False,
+        project_root: Path
     ) -> Dict[str, List[str]]:
         """Register extension commands for all detected agents."""
         context_note = f"\n<!-- Extension: {manifest.id} -->\n<!-- Config: .specify/extensions/{manifest.id}/ -->\n"
         return self._registrar.register_commands_for_all_agents(
             manifest.commands, manifest.id, extension_dir, project_root,
-            context_note=context_note,
-            link_outputs=link_outputs,
+            context_note=context_note
         )
 
     def unregister_commands(
@@ -1688,13 +1643,10 @@ class CommandRegistrar:
         self,
         manifest: ExtensionManifest,
         extension_dir: Path,
-        project_root: Path,
-        link_outputs: bool = False,
+        project_root: Path
     ) -> List[str]:
         """Register extension commands for Claude Code agent."""
-        return self.register_commands_for_agent(
-            "claude", manifest, extension_dir, project_root, link_outputs=link_outputs
-        )
+        return self.register_commands_for_agent("claude", manifest, extension_dir, project_root)
 
 
 class ExtensionCatalog(CatalogStackBase):

src/specify_cli/integrations/__init__.py

@@ -61,7 +61,6 @@ def _register_builtins() -> None:
     from .gemini import GeminiIntegration
     from .generic import GenericIntegration
     from .goose import GooseIntegration
-    from .hermes import HermesIntegration
     from .iflow import IflowIntegration
     from .junie import JunieIntegration
     from .kilocode import KilocodeIntegration
@@ -94,7 +93,6 @@ def _register_builtins() -> None:
     _register(GeminiIntegration())
     _register(GenericIntegration())
     _register(GooseIntegration())
-    _register(HermesIntegration())
     _register(IflowIntegration())
     _register(JunieIntegration())
     _register(KilocodeIntegration())

src/specify_cli/integrations/agy/__init__.py

@@ -5,7 +5,6 @@ Antigravity uses ``.agents/skills/speckit-<name>/SKILL.md`` layout (enforced sin
 
 from __future__ import annotations
 
-import re
 from pathlib import Path
 from typing import TYPE_CHECKING, Any
 
@@ -14,15 +13,6 @@ from ..base import SkillsIntegration
 if TYPE_CHECKING:
     from ..manifest import IntegrationManifest
 
-# Note injected into hook sections so agy maps dot-notation command
-# names (from extensions.yml) to the hyphenated skill names it uses.
-# Without this, agy emits ``/speckit.git.commit`` (which does not
-# resolve) instead of ``/speckit-git-commit``.
-_HOOK_COMMAND_NOTE = (
-    "- When constructing slash commands from hook command names, "
-    "replace dots (`.`) with hyphens (`-`). "
-    "For example, `speckit.git.commit` → `/speckit-git-commit`.\n"
-)
 
 
 class AgyIntegration(SkillsIntegration):
@@ -33,8 +23,8 @@ class AgyIntegration(SkillsIntegration):
         "name": "Antigravity",
         "folder": ".agents/",
         "commands_subdir": "skills",
-        "install_url": "https://antigravity.google/",
-        "requires_cli": True,
+        "install_url": None,
+        "requires_cli": False,
     }
     registrar_config = {
         "dir": ".agents/skills",
@@ -44,54 +34,6 @@ class AgyIntegration(SkillsIntegration):
     }
     context_file = "AGENTS.md"
 
-    @staticmethod
-    def _inject_hook_command_note(content: str) -> str:
-        """Insert a dot-to-hyphen note before each hook output instruction.
-
-        Targets the line ``- For each executable hook, output the following``
-        and inserts the note on the line before it, matching its indentation.
-        Skips if the note is already present.
-        """
-        if "replace dots" in content:
-            return content
-
-        def repl(m: re.Match[str]) -> str:
-            indent = m.group(1)
-            instruction = m.group(2)
-            # ``eol`` is empty when the regex matched via ``$`` because the
-            # instruction was the final line of a file with no trailing
-            # newline. Default to ``\n`` so the note never collapses onto
-            # the same line as the instruction.
-            eol = m.group(3) or "\n"
-            return (
-                indent
-                + _HOOK_COMMAND_NOTE.rstrip("\n")
-                + eol
-                + indent
-                + instruction
-                + eol
-            )
-
-        return re.sub(
-            r"(?m)^(\s*)(- For each executable hook, output the following[^\r\n]*)(\r\n|\n|$)",
-            repl,
-            content,
-        )
-
-    def post_process_skill_content(self, content: str) -> str:
-        """Inject the dot-to-hyphen hook command note."""
-        return self._inject_hook_command_note(content)
-
-    def build_exec_args(
-        self,
-        prompt: str,
-        *,
-        model: str | None = None,
-        output_json: bool = True,
-    ) -> list[str] | None:
-        # agy does not support --model or JSON output; both params are ignored
-        return [self._resolve_executable(), "--print", prompt]
-
     def setup(
         self,
         project_root: Path,
@@ -107,21 +49,4 @@ class AgyIntegration(SkillsIntegration):
             fg="yellow",
             err=True,
         )
-        created = super().setup(project_root, manifest, parsed_options=parsed_options, **opts)
-
-        skills_dir = self.skills_dest(project_root).resolve()
-        for path in created:
-            try:
-                path.resolve().relative_to(skills_dir)
-            except ValueError:
-                continue
-            if path.name != "SKILL.md":
-                continue
-
-            content = path.read_bytes().decode("utf-8")
-            updated = self.post_process_skill_content(content)
-            if updated != content:
-                path.write_bytes(updated.encode("utf-8"))
-                self.record_file_in_manifest(path, project_root, manifest)
-
-        return created
+        return super().setup(project_root, manifest, parsed_options=parsed_options, **opts)

src/specify_cli/integrations/base.py

@@ -13,10 +13,7 @@ Provides:
 
 from __future__ import annotations
 
-import json
-import os
 import re
-import shlex
 import shutil
 from abc import ABC
 from dataclasses import dataclass
@@ -28,12 +25,6 @@ import yaml
 if TYPE_CHECKING:
     from .manifest import IntegrationManifest
 
-_HOOK_COMMAND_NOTE = (
-    "- When constructing slash commands from hook command names, "
-    "replace dots (`.`) with hyphens (`-`). "
-    "For example, `speckit.git.commit` → `/speckit-git-commit`.\n"
-)
-
 
 # ---------------------------------------------------------------------------
 # IntegrationOption
@@ -147,65 +138,6 @@ class IntegrationBase(ABC):
         """
         return None
 
-    def _resolve_executable(self) -> str:
-        """Return the executable for this integration's CLI tool.
-
-        Checks ``SPECKIT_INTEGRATION_<KEY>_EXECUTABLE`` first, allowing
-        operators to override the binary path without modifying the
-        integration configuration — useful when the tool is installed in
-        a non-standard location or a specific version must be pinned.
-        Hyphens in the integration key are replaced with underscores and
-        the key is uppercased so that, for example, ``kiro-cli`` maps to
-        ``SPECKIT_INTEGRATION_KIRO_CLI_EXECUTABLE``.
-
-        Falls back to ``self.key`` when the env var is unset or
-        whitespace-only so existing behaviour is unchanged.
-
-        See issue #2596.
-        """
-        env_name = (
-            f"SPECKIT_INTEGRATION_{self.key.upper().replace('-', '_')}_EXECUTABLE"
-        )
-        override = os.environ.get(env_name, "").strip()
-        return override if override else self.key
-
-    def _apply_extra_args_env_var(self, args: list[str]) -> None:
-        """Append `SPECKIT_INTEGRATION_<KEY>_EXTRA_ARGS` env-var value to *args*.
-
-        Operators can inject extra CLI flags into the spawned agent
-        subprocess by setting an env var named for the integration key,
-        e.g. `SPECKIT_INTEGRATION_CLAUDE_EXTRA_ARGS="--dangerously-skip-permissions"`.
-        The `INTEGRATION` segment scopes the variable to this subsystem
-        so it does not collide with other Spec Kit env-var namespaces.
-        Hyphens in the integration key are replaced with underscores
-        and the key is uppercased
-        (e.g. `kiro-cli` → `SPECKIT_INTEGRATION_KIRO_CLI_EXTRA_ARGS`).
-
-        Useful in CI / non-interactive contexts where the spawned agent
-        needs flags that change its prompt-handling behaviour.
-        Default behaviour (env var unset or whitespace-only) is a no-op
-        — *args* is unchanged. Multi-token values are parsed via
-        `shlex.split`.
-
-        See issue #2595.
-        """
-        env_name = (
-            f"SPECKIT_INTEGRATION_{self.key.upper().replace('-', '_')}_EXTRA_ARGS"
-        )
-        extra = os.environ.get(env_name, "").strip()
-        if not extra:
-            return
-        try:
-            tokens = shlex.split(extra)
-        except ValueError as exc:
-            raise ValueError(
-                f"{env_name} is not parseable as a POSIX-quoted command line "
-                f"(value: {extra!r}). shlex reported: {exc}. "
-                f"Use single or double quotes to group multi-word values, e.g. "
-                f'{env_name}=\'--flag "value with spaces"\'.'
-            ) from exc
-        args.extend(tokens)
-
     def build_command_invocation(self, command_name: str, args: str = "") -> str:
         """Build the native slash-command invocation for a Spec Kit command.
 
@@ -550,91 +482,6 @@ class IntegrationBase(ABC):
             lines.append(f"at {plan_path}")
         return "\n".join(lines)
 
-    @staticmethod
-    def _agent_context_extension_enabled(project_root: Path) -> bool:
-        """Return whether the bundled ``agent-context`` extension is enabled.
-
-        The extension is the single source of truth for managing coding
-        agent context/instruction files (e.g. ``CLAUDE.md``,
-        ``.github/copilot-instructions.md``).
-
-        Returns ``True`` (enabled) when:
-        - the extension registry does not exist (legacy project, backwards
-          compatibility), or
-        - the registry has no ``agent-context`` entry (older project layout
-          predating the extension), or
-        - the entry is present and not explicitly disabled.
-
-        Returns ``False`` only when an entry exists with ``enabled: false``.
-        """
-        registry_path = (
-            project_root / ".specify" / "extensions" / ".registry"
-        )
-        if not registry_path.exists():
-            return True
-        try:
-            data = json.loads(registry_path.read_text(encoding="utf-8"))
-        except (OSError, ValueError, UnicodeError):
-            return True
-        if not isinstance(data, dict):
-            return True
-        extensions = data.get("extensions")
-        if not isinstance(extensions, dict):
-            return True
-        entry = extensions.get("agent-context")
-        if not isinstance(entry, dict):
-            return True
-        return entry.get("enabled", True) is not False
-
-    def _resolve_context_markers(self, project_root: Path) -> tuple[str, str]:
-        """Return the (start, end) context markers to use for *project_root*.
-
-        Reads ``context_markers.start`` / ``context_markers.end`` from the
-        agent-context extension config
-        (``.specify/extensions/agent-context/agent-context-config.yml``)
-        when present.  Falls back to the class-level constants
-        ``CONTEXT_MARKER_START`` / ``CONTEXT_MARKER_END`` when the file is
-        missing, the section is absent, or the values are not non-empty
-        strings.
-        """
-        from .._console import console  # local import to avoid cycles
-
-        start = self.CONTEXT_MARKER_START
-        end = self.CONTEXT_MARKER_END
-        config_path = (
-            project_root
-            / ".specify"
-            / "extensions"
-            / "agent-context"
-            / "agent-context-config.yml"
-        )
-        try:
-            raw = config_path.read_text(encoding="utf-8")
-            cfg = yaml.safe_load(raw)
-        except (OSError, UnicodeError, ValueError, yaml.YAMLError):
-            return start, end
-        markers = cfg.get("context_markers") if isinstance(cfg, dict) else None
-        if isinstance(markers, dict):
-            cm_start = markers.get("start")
-            cm_end = markers.get("end")
-            s_valid = isinstance(cm_start, str) and cm_start
-            e_valid = isinstance(cm_end, str) and cm_end
-            if not s_valid and cm_start is not None:
-                console.print(
-                    f"[yellow]agent-context: ignoring invalid context_markers.start "
-                    f"({cm_start!r}), using default[/yellow]"
-                )
-            if not e_valid and cm_end is not None:
-                console.print(
-                    f"[yellow]agent-context: ignoring invalid context_markers.end "
-                    f"({cm_end!r}), using default[/yellow]"
-                )
-            if s_valid:
-                start = cm_start  # type: ignore[assignment]
-            if e_valid:
-                end = cm_end  # type: ignore[assignment]
-        return start, end
-
     def upsert_context_section(
         self,
         project_root: Path,
@@ -643,54 +490,34 @@ class IntegrationBase(ABC):
         """Create or update the managed section in the agent context file.
 
         If the context file does not exist it is created with just the
-        managed section.  If it exists, the content between the configured
-        start/end markers (default ``<!-- SPECKIT START -->`` /
-        ``<!-- SPECKIT END -->``) is replaced, or appended when no markers
-        are found. Markers are read from the agent-context extension config
-        (``.specify/extensions/agent-context/agent-context-config.yml``)
-        when present, falling back to the class-level constants.
+        managed section.  If it exists, the content between
+        ``<!-- SPECKIT START -->`` and ``<!-- SPECKIT END -->`` markers
+        is replaced (or appended when no markers are found).
 
         Returns the path to the context file, or ``None`` when
-        ``context_file`` is not set or the ``agent-context`` extension is
-        disabled.
+        ``context_file`` is not set.
         """
         if not self.context_file:
             return None
 
-        if not self._agent_context_extension_enabled(project_root):
-            return None
-
-        from .._console import console  # local import to avoid cycles
-
-        console.print(
-            "[yellow]Deprecation:[/yellow] Inline agent-context updates during "
-            "integration setup will be disabled in v0.12.0. Context file "
-            "management has moved to the bundled [bold]agent-context[/bold] "
-            "extension. Run [cyan]specify extension disable agent-context[/cyan] "
-            "to opt out early.",
-            highlight=False,
-        )
-
-        marker_start, marker_end = self._resolve_context_markers(project_root)
-
         ctx_path = project_root / self.context_file
         section = (
-            f"{marker_start}\n"
+            f"{self.CONTEXT_MARKER_START}\n"
             f"{self._build_context_section(plan_path)}\n"
-            f"{marker_end}\n"
+            f"{self.CONTEXT_MARKER_END}\n"
         )
 
         if ctx_path.exists():
             content = ctx_path.read_text(encoding="utf-8-sig")
-            start_idx = content.find(marker_start)
+            start_idx = content.find(self.CONTEXT_MARKER_START)
             end_idx = content.find(
-                marker_end,
+                self.CONTEXT_MARKER_END,
                 start_idx if start_idx != -1 else 0,
             )
 
             if start_idx != -1 and end_idx != -1 and end_idx > start_idx:
                 # Replace existing section (include the end marker + newline)
-                end_of_marker = end_idx + len(marker_end)
+                end_of_marker = end_idx + len(self.CONTEXT_MARKER_END)
                 # Consume trailing line ending (CRLF or LF)
                 if end_of_marker < len(content) and content[end_of_marker] == "\r":
                     end_of_marker += 1
@@ -702,7 +529,7 @@ class IntegrationBase(ABC):
                 new_content = content[:start_idx] + section
             elif end_idx != -1:
                 # Corrupted: end marker without start — replace BOF through end marker
-                end_of_marker = end_idx + len(marker_end)
+                end_of_marker = end_idx + len(self.CONTEXT_MARKER_END)
                 if end_of_marker < len(content) and content[end_of_marker] == "\r":
                     end_of_marker += 1
                 if end_of_marker < len(content) and content[end_of_marker] == "\n":
@@ -736,27 +563,20 @@ class IntegrationBase(ABC):
         """Remove the managed section from the agent context file.
 
         Returns ``True`` if the section was found and removed.  If the
-        file becomes empty (or whitespace-only) after removal it is deleted.
-        Markers are read from the agent-context extension config
-        (``.specify/extensions/agent-context/agent-context-config.yml``)
-        when present, falling back to the class-level constants.
+        file becomes empty (or whitespace-only) after removal it is
+        deleted.
         """
         if not self.context_file:
             return False
 
-        if not self._agent_context_extension_enabled(project_root):
-            return False
-
         ctx_path = project_root / self.context_file
         if not ctx_path.exists():
             return False
 
-        marker_start, marker_end = self._resolve_context_markers(project_root)
-
         content = ctx_path.read_text(encoding="utf-8-sig")
-        start_idx = content.find(marker_start)
+        start_idx = content.find(self.CONTEXT_MARKER_START)
         end_idx = content.find(
-            marker_end,
+            self.CONTEXT_MARKER_END,
             start_idx if start_idx != -1 else 0,
         )
 
@@ -767,7 +587,7 @@ class IntegrationBase(ABC):
             return False
 
         removal_start = start_idx
-        removal_end = end_idx + len(marker_end)
+        removal_end = end_idx + len(self.CONTEXT_MARKER_END)
 
         # Consume trailing line ending (CRLF or LF)
         if removal_end < len(content) and content[removal_end] == "\r":
@@ -1030,8 +850,7 @@ class MarkdownIntegration(IntegrationBase):
     ) -> list[str] | None:
         if not self.config or not self.config.get("requires_cli"):
             return None
-        args = [self._resolve_executable(), "-p", prompt]
-        self._apply_extra_args_env_var(args)
+        args = [self.key, "-p", prompt]
         if model:
             args.extend(["--model", model])
         if output_json:
@@ -1118,8 +937,7 @@ class TomlIntegration(IntegrationBase):
     ) -> list[str] | None:
         if not self.config or not self.config.get("requires_cli"):
             return None
-        args = [self._resolve_executable(), "-p", prompt]
-        self._apply_extra_args_env_var(args)
+        args = [self.key, "-p", prompt]
         if model:
             args.extend(["-m", model])
         if output_json:
@@ -1537,8 +1355,7 @@ class SkillsIntegration(IntegrationBase):
     ) -> list[str] | None:
         if not self.config or not self.config.get("requires_cli"):
             return None
-        args = [self._resolve_executable(), "-p", prompt]
-        self._apply_extra_args_env_var(args)
+        args = [self.key, "-p", prompt]
         if model:
             args.extend(["--model", model])
         if output_json:
@@ -1574,53 +1391,15 @@ class SkillsIntegration(IntegrationBase):
             invocation = f"{invocation} {args}"
         return invocation
 
-    @staticmethod
-    def _inject_hook_command_note(content: str) -> str:
-        """Insert a dot-to-hyphen note before each hook output instruction.
-
-        Targets the line ``- For each executable hook, output the following``
-        and inserts the note on the line before it, matching its indentation.
-        Skips individual instructions that already have the note immediately
-        above them.
-        """
-        note = _HOOK_COMMAND_NOTE.rstrip("\n")
-
-        def repl(m: re.Match[str]) -> str:
-            indent = m.group(1)
-            instruction = m.group(2)
-            previous_lines = content[:m.start()].splitlines()
-            if previous_lines and previous_lines[-1] == indent + note:
-                return m.group(0)
-            # ``eol`` is empty when the regex matched via ``$`` because the
-            # instruction was the final line of a file with no trailing
-            # newline. Default to ``\n`` so the note never collapses onto
-            # the same line as the instruction.
-            eol = m.group(3) or "\n"
-            return (
-                indent
-                + note
-                + eol
-                + indent
-                + instruction
-                + eol
-            )
-
-        return re.sub(
-            r"(?m)^([ \t]*)(- For each executable hook, output the following[^\r\n]*)(\r\n|\n|$)",
-            repl,
-            content,
-        )
-
     def post_process_skill_content(self, content: str) -> str:
         """Post-process a SKILL.md file's content after generation.
 
         Called by external skill generators (presets, extensions) to let
         the integration inject agent-specific frontmatter or body
-        transformations.  The base implementation injects shared skills
-        guidance for converting dotted hook command names to hyphenated
-        slash commands.  Subclasses may override — see ``ClaudeIntegration``.
+        transformations.  The default implementation returns *content*
+        unchanged.  Subclasses may override — see ``ClaudeIntegration``.
         """
-        return self._inject_hook_command_note(content)
+        return content
 
     def setup(
         self,
@@ -1723,8 +1502,6 @@ class SkillsIntegration(IntegrationBase):
                 f"{processed_body}"
             )
 
-            skill_content = self.post_process_skill_content(skill_content)
-
             # Write speckit-<name>/SKILL.md
             skill_dir = skills_dir / skill_name
             skill_file = skill_dir / "SKILL.md"

src/specify_cli/integrations/claude/__init__.py

@@ -5,11 +5,21 @@ from __future__ import annotations
 from pathlib import Path
 from typing import Any
 
+import re
+
 import yaml
 
 from ..base import SkillsIntegration
 from ..manifest import IntegrationManifest
 
+# Note injected into hook sections so Claude maps dot-notation command
+# names (from extensions.yml) to the hyphenated skill names it uses.
+_HOOK_COMMAND_NOTE = (
+    "- When constructing slash commands from hook command names, "
+    "replace dots (`.`) with hyphens (`-`). "
+    "For example, `speckit.git.commit` → `/speckit-git-commit`.\n"
+)
+
 # Mapping of command template stem → argument-hint text shown inline
 # when a user invokes the slash command in Claude Code.
 ARGUMENT_HINTS: dict[str, str] = {
@@ -149,11 +159,41 @@ class ClaudeIntegration(SkillsIntegration):
             out.append(line)
         return "".join(out)
 
+    @staticmethod
+    def _inject_hook_command_note(content: str) -> str:
+        """Insert a dot-to-hyphen note before each hook output instruction.
+
+        Targets the line ``- For each executable hook, output the following``
+        and inserts the note on the line before it, matching its indentation.
+        Skips if the note is already present.
+        """
+        if "replace dots" in content:
+            return content
+
+        def repl(m: re.Match[str]) -> str:
+            indent = m.group(1)
+            instruction = m.group(2)
+            eol = m.group(3)
+            return (
+                indent
+                + _HOOK_COMMAND_NOTE.rstrip("\n")
+                + eol
+                + indent
+                + instruction
+                + eol
+            )
+
+        return re.sub(
+            r"(?m)^(\s*)(- For each executable hook, output the following[^\r\n]*)(\r\n|\n|$)",
+            repl,
+            content,
+        )
+
     def post_process_skill_content(self, content: str) -> str:
         """Inject Claude-specific frontmatter flags and hook notes."""
-        updated = super().post_process_skill_content(content)
-        updated = self._inject_frontmatter_flag(updated, "user-invocable")
+        updated = self._inject_frontmatter_flag(content, "user-invocable")
         updated = self._inject_frontmatter_flag(updated, "disable-model-invocation", "false")
+        updated = self._inject_hook_command_note(updated)
         return updated
 
     def setup(
@@ -163,9 +203,10 @@ class ClaudeIntegration(SkillsIntegration):
         parsed_options: dict[str, Any] | None = None,
         **opts: Any,
     ) -> list[Path]:
-        """Install Claude skills, then inject argument-hints."""
+        """Install Claude skills, then inject Claude-specific flags and argument-hints."""
         created = super().setup(project_root, manifest, parsed_options, **opts)
 
+        # Post-process generated skill files
         skills_dir = self.skills_dest(project_root).resolve()
 
         for path in created:
@@ -180,7 +221,7 @@ class ClaudeIntegration(SkillsIntegration):
             content_bytes = path.read_bytes()
             content = content_bytes.decode("utf-8")
 
-            updated = content
+            updated = self.post_process_skill_content(content)
 
             # Inject argument-hint if available for this skill
             skill_dir_name = path.parent.name  # e.g. "speckit-plan"

src/specify_cli/integrations/codex/__init__.py

@@ -6,7 +6,22 @@ Commands are deprecated; ``--skills`` defaults to ``True``.
 
 from __future__ import annotations
 
+import re
+from pathlib import Path
+from typing import Any
+
 from ..base import IntegrationOption, SkillsIntegration
+from ..manifest import IntegrationManifest
+
+# Note injected into hook sections so Codex maps dot-notation command
+# names (from extensions.yml) to the hyphenated skill names it uses.
+# Without this, Codex emits ``/speckit.git.commit`` (which does not
+# resolve) instead of ``/speckit-git-commit``.
+_HOOK_COMMAND_NOTE = (
+    "- When constructing slash commands from hook command names, "
+    "replace dots (`.`) with hyphens (`-`). "
+    "For example, `speckit.git.commit` → `/speckit-git-commit`.\n"
+)
 
 
 class CodexIntegration(SkillsIntegration):
@@ -37,10 +52,7 @@ class CodexIntegration(SkillsIntegration):
         output_json: bool = True,
     ) -> list[str] | None:
         # Codex uses ``codex exec "prompt"`` for non-interactive mode.
-        # Resolve argv[0] via the shared executable resolver so operators can
-        # override the binary with SPECKIT_INTEGRATION_CODEX_EXECUTABLE.
-        args: list[str] = [self._resolve_executable(), "exec", prompt]
-        self._apply_extra_args_env_var(args)
+        args: list[str] = ["codex", "exec", prompt]
         if model:
             args.extend(["--model", model])
         if output_json:
@@ -57,3 +69,68 @@ class CodexIntegration(SkillsIntegration):
                 help="Install as agent skills (default for Codex)",
             ),
         ]
+
+    @staticmethod
+    def _inject_hook_command_note(content: str) -> str:
+        """Insert a dot-to-hyphen note before each hook output instruction.
+
+        Targets the line ``- For each executable hook, output the following``
+        and inserts the note on the line before it, matching its indentation.
+        Skips if the note is already present.
+        """
+        if "replace dots" in content:
+            return content
+
+        def repl(m: re.Match[str]) -> str:
+            indent = m.group(1)
+            instruction = m.group(2)
+            # ``eol`` is empty when the regex matched via ``$`` because the
+            # instruction was the final line of a file with no trailing
+            # newline. Default to ``\n`` so the note never collapses onto
+            # the same line as the instruction.
+            eol = m.group(3) or "\n"
+            return (
+                indent
+                + _HOOK_COMMAND_NOTE.rstrip("\n")
+                + eol
+                + indent
+                + instruction
+                + eol
+            )
+
+        return re.sub(
+            r"(?m)^(\s*)(- For each executable hook, output the following[^\r\n]*)(\r\n|\n|$)",
+            repl,
+            content,
+        )
+
+    def post_process_skill_content(self, content: str) -> str:
+        """Inject the dot-to-hyphen hook command note."""
+        return self._inject_hook_command_note(content)
+
+    def setup(
+        self,
+        project_root: Path,
+        manifest: IntegrationManifest,
+        parsed_options: dict[str, Any] | None = None,
+        **opts: Any,
+    ) -> list[Path]:
+        """Install Codex skills, then inject the hook command note."""
+        created = super().setup(project_root, manifest, parsed_options, **opts)
+
+        skills_dir = self.skills_dest(project_root).resolve()
+        for path in created:
+            try:
+                path.resolve().relative_to(skills_dir)
+            except ValueError:
+                continue
+            if path.name != "SKILL.md":
+                continue
+
+            content = path.read_bytes().decode("utf-8")
+            updated = self.post_process_skill_content(content)
+            if updated != content:
+                path.write_bytes(updated.encode("utf-8"))
+                self.record_file_in_manifest(path, project_root, manifest)
+
+        return created

src/specify_cli/integrations/copilot/__init__.py

@@ -134,18 +134,6 @@ class CopilotIntegration(IntegrationBase):
             ),
         ]
 
-    def _resolve_executable(self) -> str:
-        """Return the Copilot CLI executable, respecting the env-var override.
-
-        Checks ``SPECKIT_INTEGRATION_COPILOT_EXECUTABLE`` first.  Falls
-        back to the platform-specific default from ``_copilot_executable()``
-        (``copilot.cmd`` on Windows, ``copilot`` elsewhere) so that
-        existing behaviour is preserved when the env var is unset.
-        """
-        env_name = "SPECKIT_INTEGRATION_COPILOT_EXECUTABLE"
-        override = os.environ.get(env_name, "").strip()
-        return override if override else _copilot_executable()
-
     def build_exec_args(
         self,
         prompt: str,
@@ -160,8 +148,7 @@ class CopilotIntegration(IntegrationBase):
         # Controlled by SPECKIT_COPILOT_ALLOW_ALL_TOOLS env var
         # (default: enabled).  The deprecated SPECKIT_ALLOW_ALL_TOOLS
         # is also honoured as a fallback.
-        args = [self._resolve_executable(), "-p", prompt]
-        self._apply_extra_args_env_var(args)
+        args = [_copilot_executable(), "-p", prompt]
         if _allow_all():
             args.append("--yolo")
         if model:
@@ -229,12 +216,7 @@ class CopilotIntegration(IntegrationBase):
             agent_name = f"speckit.{stem}"
             prompt = args or ""
 
-        cli_args = [self._resolve_executable(), "-p", prompt]
-        # Honour SPECKIT_INTEGRATION_COPILOT_EXTRA_ARGS for real workflow
-        # runs.  `dispatch_command` builds cli_args inline rather than
-        # going through `build_exec_args`, so the hook must be invoked
-        # here too — otherwise the env var is silently ignored.
-        self._apply_extra_args_env_var(cli_args)
+        cli_args = [_copilot_executable(), "-p", prompt]
         if not skills_mode:
             cli_args.extend(["--agent", agent_name])
         if _allow_all():
@@ -283,13 +265,12 @@ class CopilotIntegration(IntegrationBase):
         return f"speckit.{template_name}.agent.md"
 
     def post_process_skill_content(self, content: str) -> str:
-        """Inject shared hook guidance and Copilot ``mode:`` frontmatter.
+        """Inject Copilot-specific ``mode:`` field into SKILL.md frontmatter.
 
         Inserts ``mode: speckit.<stem>`` before the closing ``---`` so
         Copilot can associate the skill with its agent mode.
         """
-        updated = _CopilotSkillsHelper().post_process_skill_content(content)
-        lines = updated.splitlines(keepends=True)
+        lines = content.splitlines(keepends=True)
 
         # Extract skill name from frontmatter to derive the mode value
         dash_count = 0
@@ -303,7 +284,7 @@ class CopilotIntegration(IntegrationBase):
                 continue
             if dash_count == 1:
                 if stripped.startswith("mode:"):
-                    return updated  # already present
+                    return content  # already present
                 if stripped.startswith("name:"):
                     # Parse: name: "speckit-plan" → speckit.plan
                     val = stripped.split(":", 1)[1].strip().strip('"').strip("'")
@@ -314,7 +295,7 @@ class CopilotIntegration(IntegrationBase):
                         skill_name = val
 
         if not skill_name:
-            return updated
+            return content
 
         # Inject mode: before the closing --- of frontmatter
         out: list[str] = []

src/specify_cli/integrations/devin/__init__.py

@@ -48,8 +48,7 @@ class DevinIntegration(SkillsIntegration):
         stdout instead of structured JSON. ``requires_cli=True`` is
         kept on the integration for tool detection.
         """
-        args = [self._resolve_executable(), "-p", prompt]
-        self._apply_extra_args_env_var(args)
+        args = [self.key, "-p", prompt]
         if model:
             args.extend(["--model", model])
         return args

src/specify_cli/integrations/hermes/__init__.py

@@ -1,280 +0,0 @@
-"""Hermes Agent integration — skills-based agent.
-
-Hermes Agent (https://github.com/NousResearch/hermes-agent) is an open-source
-AI agent framework by Nous Research.  It stores skills in
-``~/.hermes/skills/`` (user-global) rather than a project-local directory.
-
-Usage::
-
-    specify init my-project --integration hermes
-    specify init --here --ai hermes
-"""
-
-from __future__ import annotations
-
-from pathlib import Path
-from shutil import rmtree
-from typing import Any
-
-import yaml
-
-from ..base import IntegrationOption, SkillsIntegration
-from ..manifest import IntegrationManifest
-
-
-class HermesIntegration(SkillsIntegration):
-    """Integration for Hermes Agent skills.
-
-    Hermes loads skills from ``~/.hermes/skills/`` (user home directory)
-    rather than a project-local path.  Skills are installed directly to
-    the global directory — no project-local copies are created since
-    Hermes discovers them globally.  A project-local marker directory
-    (``.hermes/skills/`` empty) is created so extension commands (e.g.
-    git) can detect Hermes as an active integration.  Uninstall removes
-    both the marker and all global ``speckit-*`` skills, matching the
-    standard integration teardown behaviour.
-    """
-
-    key = "hermes"
-    config = {
-        "name": "Hermes Agent",
-        "folder": ".hermes/",
-        "commands_subdir": "skills",
-        "install_url": "https://github.com/NousResearch/hermes-agent",
-        "requires_cli": True,
-    }
-    registrar_config = {
-        "dir": "~/.hermes/skills",
-        "detect_dir": ".hermes/skills",
-        "format": "markdown",
-        "args": "$ARGUMENTS",
-        "extension": "/SKILL.md",
-    }
-    context_file = "AGENTS.md"
-
-    # -- Helpers -----------------------------------------------------------
-
-    @staticmethod
-    def _hermes_home_skills_dir() -> Path:
-        """Return ``~/.hermes/skills/`` — the global skills directory."""
-        return Path.home() / ".hermes" / "skills"
-
-    # -- Options -----------------------------------------------------------
-
-    @classmethod
-    def options(cls) -> list[IntegrationOption]:
-        return [
-            IntegrationOption(
-                "--skills",
-                is_flag=True,
-                default=True,
-                help="Install as agent skills (default for Hermes Agent)",
-            ),
-        ]
-
-    # -- Setup -------------------------------------------------------------
-
-    def setup(
-        self,
-        project_root: Path,
-        manifest: IntegrationManifest,
-        parsed_options: dict[str, Any] | None = None,
-        **opts: Any,
-    ) -> list[Path]:
-        """Install command templates as global Hermes skills.
-
-        Writes each skill directly to
-        ``~/.hermes/skills/speckit-<name>/SKILL.md`` where Hermes
-        discovers them at runtime.  No project-local SKILL.md copies are
-        created — the global directory is the single source of truth.
-        A project-local marker (``.hermes/skills/`` empty) is created
-        so extension commands (e.g. git) can detect Hermes as an active
-        integration.
-        """
-        templates = self.list_command_templates()
-        if not templates:
-            return []
-
-        # Safety check: verify manifest project_root matches (standard pattern)
-        project_root_resolved = project_root.resolve()
-        if manifest.project_root != project_root_resolved:
-            raise ValueError(
-                f"manifest.project_root ({manifest.project_root}) does not match "
-                f"project_root ({project_root_resolved})"
-            )
-
-        script_type = opts.get("script_type", "sh")
-        arg_placeholder = (
-            self.registrar_config.get("args", "$ARGUMENTS")
-            if self.registrar_config
-            else "$ARGUMENTS"
-        )
-
-        global_skills_dir = self._hermes_home_skills_dir()
-        global_skills_dir.mkdir(parents=True, exist_ok=True)
-
-        created: list[Path] = []
-
-        for src_file in templates:
-            raw = src_file.read_text(encoding="utf-8")
-
-            # Derive the skill name from the template stem
-            command_name = src_file.stem  # e.g. "plan"
-            skill_name = f"speckit-{command_name.replace('.', '-')}"
-
-            # Parse frontmatter for description
-            frontmatter: dict[str, Any] = {}
-            if raw.startswith("---"):
-                parts = raw.split("---", 2)
-                if len(parts) >= 3:
-                    try:
-                        fm = yaml.safe_load(parts[1])
-                        if isinstance(fm, dict):
-                            frontmatter = fm
-                    except yaml.YAMLError:
-                        pass
-
-            # Process body through the standard template pipeline
-            processed_body = self.process_template(
-                raw,
-                self.key,
-                script_type,
-                arg_placeholder,
-                context_file=self.context_file or "",
-                invoke_separator=self.invoke_separator,
-            )
-            # Strip the processed frontmatter — we rebuild it for skills.
-            if processed_body.startswith("---"):
-                parts = processed_body.split("---", 2)
-                if len(parts) >= 3:
-                    processed_body = parts[2]
-
-            # Select description
-            description = frontmatter.get("description", "")
-            if not description:
-                description = f"Spec Kit: {command_name} workflow"
-
-            # Build SKILL.md with manually formatted frontmatter
-            def _quote(v: str) -> str:
-                escaped = v.replace("\\", "\\\\").replace('"', '\\"')
-                return f'"{escaped}"'
-
-            skill_content = (
-                f"---\n"
-                f"name: {_quote(skill_name)}\n"
-                f"description: {_quote(description)}\n"
-                f"compatibility: "
-                f"{_quote('Requires spec-kit project structure with .specify/ directory')}\n"
-                f"metadata:\n"
-                f"  author: {_quote('github-spec-kit')}\n"
-                f"  source: {_quote('templates/commands/' + src_file.name)}\n"
-                f"---\n"
-                f"{processed_body}"
-            )
-
-            skill_content = self.post_process_skill_content(skill_content)
-
-            # Write directly to global ~/.hermes/skills/speckit-<name>/SKILL.md
-            skill_dir = global_skills_dir / skill_name
-            skill_dir.mkdir(parents=True, exist_ok=True)
-            skill_file = skill_dir / "SKILL.md"
-            normalized = skill_content.replace("\r\n", "\n")
-            skill_file.write_bytes(normalized.encode("utf-8"))
-            created.append(skill_file)
-
-        # Upsert managed context section into the agent context file
-        self.upsert_context_section(project_root)
-
-        # Create project-local marker directory so extension commands
-        # (e.g. git) can detect Hermes as an active integration.
-        # Hermes itself ignores this directory — skills live globally.
-        (project_root / ".hermes" / "skills").mkdir(parents=True, exist_ok=True)
-
-        return created
-
-    # -- Uninstall ---------------------------------------------------------
-
-    def teardown(
-        self,
-        project_root: Path,
-        manifest: IntegrationManifest,
-        *,
-        force: bool = False,
-    ) -> tuple[list[Path], list[Path]]:
-        """Uninstall integration files including global Hermes skills.
-
-        Removes the managed context section from AGENTS.md, removes the
-        project-local marker directory (if empty), delegates to
-        ``manifest.uninstall()`` for project-local tracked files, and
-        removes all ``speckit-*`` skills under ``~/.hermes/skills/``.
-
-        Global skills are always removed on teardown — this matches the
-        standard integration behaviour where all files created by the
-        integration are removed on ``specify integration uninstall``.
-        """
-        # Remove managed context section from AGENTS.md
-        self.remove_context_section(project_root)
-
-        # Delegate to manifest for project-local tracked files (scripts,
-        # templates, context entries tracked in the manifest).
-        removed, skipped = manifest.uninstall(project_root, force=force)
-
-        # Remove project-local marker directory if empty
-        local_skills_dir = project_root / ".hermes" / "skills"
-        if local_skills_dir.is_dir() and not any(local_skills_dir.iterdir()):
-            local_skills_dir.rmdir()
-            hermes_dir = project_root / ".hermes"
-            if hermes_dir.is_dir() and not any(hermes_dir.iterdir()):
-                hermes_dir.rmdir()
-
-        # Remove all global Hermes skills for speckit — these are always
-        # removed on uninstall regardless of the force flag, matching the
-        # standard behaviour where all integration files are cleaned up.
-        global_skills_dir = self._hermes_home_skills_dir()
-        if global_skills_dir.is_dir():
-            for skill_dir in sorted(global_skills_dir.iterdir()):
-                if skill_dir.is_dir() and skill_dir.name.startswith("speckit-"):
-                    try:
-                        rmtree(skill_dir)
-                        removed.append(skill_dir)
-                    except OSError:
-                        skipped.append(skill_dir)
-
-        return removed, skipped
-
-    # -- CLI dispatch ------------------------------------------------------
-
-    def build_exec_args(
-        self,
-        prompt: str,
-        *,
-        model: str | None = None,
-        output_json: bool = True,
-    ) -> list[str] | None:
-        """Build Hermes CLI invocation for programmatic dispatch.
-
-        Uses ``hermes chat -Q -q`` for one-shot queries in quiet mode,
-        mapping slash-command invocations to the appropriate skill-based
-        dispatch.
-        """
-        args = [self._resolve_executable(), "chat", "-Q"]
-
-        if model:
-            args.extend(["-m", model])
-        if output_json:
-            args.append("--json")
-
-        # If prompt starts with a slash command, pass it directly
-        # so Hermes can dispatch to the appropriate skill.
-        if prompt.startswith("/"):
-            command, _, remainder = prompt[1:].partition(" ")
-            if command:
-                args.extend(["-s", command])
-                if remainder:
-                    args.extend(["-q", remainder])
-            else:
-                args.extend(["-q", prompt])
-        else:
-            args.extend(["-q", prompt])
-
-        return args

src/specify_cli/integrations/opencode/__init__.py

@@ -28,12 +28,7 @@ class OpencodeIntegration(MarkdownIntegration):
         model: str | None = None,
         output_json: bool = True,
     ) -> list[str] | None:
-        args = [self._resolve_executable(), "run"]
-        # Apply operator-injected extra args before the prompt-derived
-        # --command and the canonical --format/-m flags so Spec Kit's
-        # later appends remain authoritative under repeated-flag CLI
-        # semantics.
-        self._apply_extra_args_env_var(args)
+        args = [self.key, "run"]
 
         message = prompt
         if prompt.startswith("/"):

src/specify_cli/integrations/vibe/__init__.py

@@ -81,13 +81,13 @@ class VibeIntegration(SkillsIntegration):
             out.append(line)
         return "".join(out)
 
+
     def post_process_skill_content(self, content: str) -> str:
         """
-        Inject shared hook guidance and Vibe-specific frontmatter flags:
+        Inject Vibe-specific frontmatter flags:
         - user-invocable: allows the skill to be invoked by the user (not just other agents)
         """
-        updated = super().post_process_skill_content(content)
-        updated = self._inject_frontmatter_flag(updated, "user-invocable")
+        updated = self._inject_frontmatter_flag(content, "user-invocable")
         return updated
 
     def setup(
@@ -107,4 +107,27 @@ class VibeIntegration(SkillsIntegration):
             err=True,
         )
 
-        return super().setup(project_root, manifest, parsed_options=parsed_options, **opts)
+        created = super().setup(project_root, manifest, parsed_options=parsed_options, **opts)
+
+        # Post-process generated skill files
+        skills_dir = self.skills_dest(project_root).resolve()
+
+        for path in created:
+            # Only touch SKILL.md files under the skills directory
+            try:
+                path.resolve().relative_to(skills_dir)
+            except ValueError:
+                continue
+            if path.name != "SKILL.md":
+                continue
+
+            content_bytes = path.read_bytes()
+            content = content_bytes.decode("utf-8")
+
+            updated = self.post_process_skill_content(content)
+
+            if updated != content:
+                path.write_bytes(updated.encode("utf-8"))
+                self.record_file_in_manifest(path, project_root, manifest)
+
+        return created

src/specify_cli/shared_infra.py

@@ -369,16 +369,7 @@ def install_shared_infra(
 
                         if not _ensure_or_bucket_dir(dst_path.parent):
                             continue
-                        content = src_path.read_text(encoding="utf-8")
-                        content = IntegrationBase.resolve_command_refs(content, invoke_separator)
-                        planned_copies.append(
-                            (
-                                dst_path,
-                                rel,
-                                content.encode("utf-8"),
-                                src_path.stat().st_mode & 0o777,
-                            )
-                        )
+                        planned_copies.append((dst_path, rel, src_path.read_bytes(), src_path.stat().st_mode & 0o777))
 
     templates_src = shared_templates_source(core_pack=core_pack, repo_root=repo_root)
     if templates_src.is_dir():

src/specify_cli/workflows/engine.py

@@ -11,7 +11,6 @@ The engine is the orchestrator that:
 from __future__ import annotations
 
 import json
-import os
 import re
 import uuid
 from datetime import datetime, timezone
@@ -426,7 +425,7 @@ class WorkflowEngine:
         inputs:
             User-provided input values.
         run_id:
-            Optional run ID (uses SPECKIT_WORKFLOW_RUN_ID when set, otherwise auto-generated).
+            Optional run ID (auto-generated if not provided).
 
         Returns
         -------
@@ -434,14 +433,8 @@ class WorkflowEngine:
         """
         from . import STEP_REGISTRY
 
-        effective_run_id = run_id
-        if effective_run_id is None:
-            env_run_id = os.environ.get("SPECKIT_WORKFLOW_RUN_ID", "").strip()
-            if env_run_id:
-                effective_run_id = env_run_id
-
         state = RunState(
-            run_id=effective_run_id,
+            run_id=run_id,
             workflow_id=definition.id,
             project_root=self.project_root,
         )

templates/commands/checklist.md

@@ -74,9 +74,7 @@ You **MUST** consider the user input before proceeding (if not empty).
    - All file paths must be absolute.
    - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
 
-2. **IF EXISTS**: Load `/memory/constitution.md` for project principles and governance constraints.
-
-3. **Clarify intent (dynamic)**: Derive up to THREE initial contextual clarifying questions (no pre-baked catalog). They MUST:
+2. **Clarify intent (dynamic)**: Derive up to THREE initial contextual clarifying questions (no pre-baked catalog). They MUST:
    - Be generated from the user's phrasing + extracted signals from spec/plan/tasks
    - Only ask about information that materially changes checklist content
    - Be skipped individually if already unambiguous in `$ARGUMENTS`
@@ -108,13 +106,13 @@ You **MUST** consider the user input before proceeding (if not empty).
 
    Output the questions (label Q1/Q2/Q3). After answers: if ≥2 scenario classes (Alternate / Exception / Recovery / Non-Functional domain) remain unclear, you MAY ask up to TWO more targeted follow‑ups (Q4/Q5) with a one-line justification each (e.g., "Unresolved recovery path risk"). Do not exceed five total questions. Skip escalation if user explicitly declines more.
 
-4. **Understand user request**: Combine `$ARGUMENTS` + clarifying answers:
+3. **Understand user request**: Combine `$ARGUMENTS` + clarifying answers:
    - Derive checklist theme (e.g., security, review, deploy, ux)
    - Consolidate explicit must-have items mentioned by user
    - Map focus selections to category scaffolding
    - Infer any missing context from spec/plan/tasks (do NOT hallucinate)
 
-5. **Load feature context**: Read from FEATURE_DIR:
+4. **Load feature context**: Read from FEATURE_DIR:
    - spec.md: Feature requirements and scope
    - plan.md (if exists): Technical details, dependencies
    - tasks.md (if exists): Implementation tasks
@@ -125,7 +123,7 @@ You **MUST** consider the user input before proceeding (if not empty).
    - Use progressive disclosure: add follow-on retrieval only if gaps detected
    - If source docs are large, generate interim summary items instead of embedding raw text
 
-6. **Generate checklist** - Create "Unit Tests for Requirements":
+5. **Generate checklist** - Create "Unit Tests for Requirements":
    - Create `FEATURE_DIR/checklists/` directory if it doesn't exist
    - Generate unique checklist filename:
      - Use short, descriptive name based on domain (e.g., `ux.md`, `api.md`, `security.md`)
@@ -243,9 +241,9 @@ You **MUST** consider the user input before proceeding (if not empty).
    - ✅ "Are [edge cases/scenarios] addressed in requirements?"
    - ✅ "Does the spec define [missing aspect]?"
 
-7. **Structure Reference**: Generate the checklist following the canonical template in `templates/checklist-template.md` for title, meta section, category headings, and ID formatting. If template is unavailable, use: H1 title, purpose/created meta lines, `##` category sections containing `- [ ] CHK### <requirement item>` lines with globally incrementing IDs starting at CHK001.
+6. **Structure Reference**: Generate the checklist following the canonical template in `templates/checklist-template.md` for title, meta section, category headings, and ID formatting. If template is unavailable, use: H1 title, purpose/created meta lines, `##` category sections containing `- [ ] CHK### <requirement item>` lines with globally incrementing IDs starting at CHK001.
 
-8. **Report**: Output full path to checklist file, item count, and summarize whether the run created a new file or appended to an existing one. Summarize:
+7. **Report**: Output full path to checklist file, item count, and summarize whether the run created a new file or appended to an existing one. Summarize:
    - Focus areas selected
    - Depth level
    - Actor/timing

templates/commands/clarify.md

@@ -66,9 +66,7 @@ Execution steps:
    - If JSON parsing fails, abort and instruct user to re-run `__SPECKIT_COMMAND_SPECIFY__` or verify feature branch environment.
    - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
 
-2. **IF EXISTS**: Load `/memory/constitution.md` for project principles and governance constraints.
-
-3. Load the current spec file. Perform a structured ambiguity & coverage scan using this taxonomy. For each category, mark status: Clear / Partial / Missing. Produce an internal coverage map used for prioritization (do not output raw map unless no questions will be asked).
+2. Load the current spec file. Perform a structured ambiguity & coverage scan using this taxonomy. For each category, mark status: Clear / Partial / Missing. Produce an internal coverage map used for prioritization (do not output raw map unless no questions will be asked).
 
    Functional Scope & Behavior:
    - Core user goals & success criteria
@@ -124,7 +122,7 @@ Execution steps:
    - Clarification would not materially change implementation or validation strategy
    - Information is better deferred to planning phase (note internally)
 
-4. Generate (internally) a prioritized queue of candidate clarification questions (maximum 5). Do NOT output them all at once. Apply these constraints:
+3. Generate (internally) a prioritized queue of candidate clarification questions (maximum 5). Do NOT output them all at once. Apply these constraints:
     - Maximum of 5 total questions across the whole session.
     - Each question must be answerable with EITHER:
        - A short multiple‑choice selection (2–5 distinct, mutually exclusive options), OR
@@ -135,7 +133,7 @@ Execution steps:
     - Favor clarifications that reduce downstream rework risk or prevent misaligned acceptance tests.
     - If more than 5 categories remain unresolved, select the top 5 by (Impact * Uncertainty) heuristic.
 
-5. Sequential questioning loop (interactive):
+4. Sequential questioning loop (interactive):
     - Present EXACTLY ONE question at a time.
     - For multiple‑choice questions:
        - **Analyze all options** and determine the **most suitable option** based on:
@@ -171,7 +169,7 @@ Execution steps:
     - Never reveal future queued questions in advance.
     - If no valid questions exist at start, immediately report no critical ambiguities.
 
-6. Integration after EACH accepted answer (incremental update approach):
+5. Integration after EACH accepted answer (incremental update approach):
     - Maintain in-memory representation of the spec (loaded once at start) plus the raw file contents.
     - For the first integrated answer in this session:
        - Ensure a `## Clarifications` section exists (create it just after the highest-level contextual/overview section per the spec template if missing).
@@ -189,7 +187,7 @@ Execution steps:
     - Preserve formatting: do not reorder unrelated sections; keep heading hierarchy intact.
     - Keep each inserted clarification minimal and testable (avoid narrative drift).
 
-7. Validation (performed after EACH write plus final pass):
+6. Validation (performed after EACH write plus final pass):
    - Clarifications session contains exactly one bullet per accepted answer (no duplicates).
    - Total asked (accepted) questions ≤ 5.
    - Updated sections contain no lingering vague placeholders the new answer was meant to resolve.
@@ -197,9 +195,9 @@ Execution steps:
    - Markdown structure valid; only allowed new headings: `## Clarifications`, `### Session YYYY-MM-DD`.
    - Terminology consistency: same canonical term used across all updated sections.
 
-8. Write the updated spec back to `FEATURE_SPEC`.
+7. Write the updated spec back to `FEATURE_SPEC`.
 
-9. **Re-validate Spec Quality Checklist** (if it exists):
+8. **Re-validate Spec Quality Checklist** (if it exists):
    - Check if `FEATURE_DIR/checklists/requirements.md` exists.
    - If it does NOT exist, skip this step silently.
    - If it exists:

templates/commands/specify.md

@@ -109,9 +109,7 @@ Given that feature description, do this:
 
 4. Load `templates/spec-template.md` to understand required sections.
 
-5. **IF EXISTS**: Load `/memory/constitution.md` for project principles and governance constraints.
-
-6. Follow this execution flow:
+5. Follow this execution flow:
     1. Parse user description from arguments
        If empty: ERROR "No feature description provided"
     2. Extract key concepts from description

templates/commands/tasks.md

@@ -63,7 +63,6 @@ You **MUST** consider the user input before proceeding (if not empty).
 2. **Load design documents**: Read from FEATURE_DIR:
    - **Required**: plan.md (tech stack, libraries, structure), spec.md (user stories with priorities)
    - **Optional**: data-model.md (entities), contracts/ (interface contracts), research.md (decisions), quickstart.md (test scenarios)
-   - **IF EXISTS**: Load `/memory/constitution.md` for project principles and governance constraints
    - Note: Not all projects have all documents. Generate tasks based on what's available.
 
 3. **Execute task generation workflow**:

templates/commands/taskstoissues.md

@@ -51,7 +51,6 @@ You **MUST** consider the user input before proceeding (if not empty).
 ## Outline
 
 1. Run `{SCRIPT}` from repo root and parse FEATURE_DIR and AVAILABLE_DOCS list. All paths must be absolute. For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
-1. **IF EXISTS**: Load `/memory/constitution.md` for project principles and governance constraints.
 1. From the executed script, extract the path to **tasks**.
 1. Get the Git remote by running:
 

tests/extensions/test_extension_agent_context.py

@@ -1,455 +0,0 @@
-"""Tests for the bundled ``agent-context`` extension and related plumbing."""
-
-from __future__ import annotations
-
-import json
-from pathlib import Path
-
-import yaml
-
-from specify_cli import (
-    _load_agent_context_config,
-    _save_agent_context_config,
-    load_init_options,
-    save_init_options,
-)
-from specify_cli.integrations.base import IntegrationBase
-from specify_cli.integrations.claude import ClaudeIntegration
-
-
-PROJECT_ROOT = Path(__file__).resolve().parent.parent.parent
-EXT_DIR = PROJECT_ROOT / "extensions" / "agent-context"
-
-
-def _write_ext_config(project_root: Path, **overrides: object) -> None:
-    """Write a minimal agent-context extension config."""
-    cfg: dict = {
-        "context_file": overrides.get("context_file", ""),
-        "context_markers": overrides.get(
-            "context_markers",
-            {
-                "start": IntegrationBase.CONTEXT_MARKER_START,
-                "end": IntegrationBase.CONTEXT_MARKER_END,
-            },
-        ),
-    }
-    _save_agent_context_config(project_root, cfg)
-
-
-# ── Bundled extension layout ─────────────────────────────────────────────────
-
-
-class TestExtensionLayout:
-    """The bundled agent-context extension ships a complete package."""
-
-    def test_extension_yml_exists(self):
-        assert (EXT_DIR / "extension.yml").is_file()
-
-    def test_extension_yml_has_required_fields(self):
-        manifest = yaml.safe_load((EXT_DIR / "extension.yml").read_text())
-        assert manifest["extension"]["id"] == "agent-context"
-        assert manifest["extension"]["name"] == "Coding Agent Context"
-        assert manifest["extension"]["author"] == "spec-kit-core"
-        # Provides at least the manual update command
-        commands = {c["name"] for c in manifest["provides"]["commands"]}
-        assert "speckit.agent-context.update" in commands
-
-    def test_readme_exists(self):
-        readme = EXT_DIR / "README.md"
-        assert readme.is_file()
-        text = readme.read_text(encoding="utf-8")
-        assert "Coding Agent Context Extension" in text
-
-    def test_config_template_exists(self):
-        cfg = EXT_DIR / "agent-context-config.yml"
-        assert cfg.is_file()
-        parsed = yaml.safe_load(cfg.read_text(encoding="utf-8"))
-        assert "context_file" in parsed
-        assert "context_markers" in parsed
-
-    def test_command_file_exists(self):
-        cmd = EXT_DIR / "commands" / "speckit.agent-context.update.md"
-        assert cmd.is_file()
-        assert "agent-context-config.yml" in cmd.read_text(encoding="utf-8")
-
-    def test_bundled_scripts_exist(self):
-        assert (EXT_DIR / "scripts" / "bash" / "update-agent-context.sh").is_file()
-        assert (EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1").is_file()
-
-    def test_bash_script_reads_extension_config(self):
-        text = (EXT_DIR / "scripts" / "bash" / "update-agent-context.sh").read_text(
-            encoding="utf-8"
-        )
-        # The script must consult the extension config, not init-options.json
-        assert "agent-context-config.yml" in text
-        assert "context_file" in text
-        assert "context_markers" in text
-
-
-# ── Catalog registration ─────────────────────────────────────────────────────
-
-
-class TestCatalogEntry:
-    def test_catalog_lists_agent_context_as_bundled(self):
-        catalog = json.loads(
-            (PROJECT_ROOT / "extensions" / "catalog.json").read_text(encoding="utf-8")
-        )
-        entry = catalog["extensions"]["agent-context"]
-        assert entry["bundled"] is True
-        assert entry["id"] == "agent-context"
-        assert entry["author"] == "spec-kit-core"
-
-
-# ── Marker resolution from extension config ──────────────────────────────────
-
-
-class _CtxIntegration(ClaudeIntegration):
-    """Use Claude as a concrete integration with a context_file."""
-
-
-class TestContextMarkerResolution:
-    def test_defaults_when_ext_config_missing(self, tmp_path):
-        i = _CtxIntegration()
-        start, end = i._resolve_context_markers(tmp_path)
-        assert start == IntegrationBase.CONTEXT_MARKER_START
-        assert end == IntegrationBase.CONTEXT_MARKER_END
-
-    def test_defaults_when_markers_field_missing(self, tmp_path):
-        """Config file exists with context_file but no context_markers key."""
-        cfg_path = (
-            tmp_path / ".specify" / "extensions" / "agent-context"
-            / "agent-context-config.yml"
-        )
-        cfg_path.parent.mkdir(parents=True, exist_ok=True)
-        cfg_path.write_text("context_file: CLAUDE.md\n", encoding="utf-8")
-        i = _CtxIntegration()
-        start, end = i._resolve_context_markers(tmp_path)
-        assert start == IntegrationBase.CONTEXT_MARKER_START
-        assert end == IntegrationBase.CONTEXT_MARKER_END
-
-    def test_custom_markers_respected(self, tmp_path):
-        _write_ext_config(
-            tmp_path,
-            context_markers={"start": "<!-- BEGIN -->", "end": "<!-- END -->"},
-        )
-        i = _CtxIntegration()
-        start, end = i._resolve_context_markers(tmp_path)
-        assert start == "<!-- BEGIN -->"
-        assert end == "<!-- END -->"
-
-    def test_partial_override_falls_back_for_missing_side(self, tmp_path):
-        _write_ext_config(tmp_path, context_markers={"start": "<!-- ONLY START -->"})
-        i = _CtxIntegration()
-        start, end = i._resolve_context_markers(tmp_path)
-        assert start == "<!-- ONLY START -->"
-        assert end == IntegrationBase.CONTEXT_MARKER_END
-
-    def test_invalid_markers_fall_back(self, tmp_path):
-        _write_ext_config(tmp_path, context_markers={"start": 42, "end": ""})
-        i = _CtxIntegration()
-        start, end = i._resolve_context_markers(tmp_path)
-        assert start == IntegrationBase.CONTEXT_MARKER_START
-        assert end == IntegrationBase.CONTEXT_MARKER_END
-
-
-# ── upsert_context_section / remove_context_section honor markers ───────────
-
-
-class TestUpsertWithCustomMarkers:
-    def _setup(self, tmp_path: Path, markers: dict | None = None) -> _CtxIntegration:
-        _write_ext_config(
-            tmp_path,
-            context_file="CLAUDE.md",
-            **({"context_markers": markers} if markers is not None else {}),
-        )
-        return _CtxIntegration()
-
-    def test_upsert_uses_default_markers(self, tmp_path):
-        i = self._setup(tmp_path)
-        result = i.upsert_context_section(tmp_path)
-        assert result is not None
-        text = (tmp_path / "CLAUDE.md").read_text(encoding="utf-8")
-        assert IntegrationBase.CONTEXT_MARKER_START in text
-        assert IntegrationBase.CONTEXT_MARKER_END in text
-
-    def test_upsert_uses_custom_markers(self, tmp_path):
-        i = self._setup(
-            tmp_path, {"start": "<!-- BEGIN -->", "end": "<!-- END -->"}
-        )
-        i.upsert_context_section(tmp_path)
-        text = (tmp_path / "CLAUDE.md").read_text(encoding="utf-8")
-        assert "<!-- BEGIN -->" in text
-        assert "<!-- END -->" in text
-        # Defaults must not appear
-        assert IntegrationBase.CONTEXT_MARKER_START not in text
-        assert IntegrationBase.CONTEXT_MARKER_END not in text
-
-    def test_upsert_replaces_existing_custom_section(self, tmp_path):
-        i = self._setup(
-            tmp_path, {"start": "<!-- BEGIN -->", "end": "<!-- END -->"}
-        )
-        ctx = tmp_path / "CLAUDE.md"
-        ctx.write_text(
-            "# header\n\n<!-- BEGIN -->\nold body\n<!-- END -->\n\nfooter\n",
-            encoding="utf-8",
-        )
-        i.upsert_context_section(tmp_path, plan_path="specs/001-foo/plan.md")
-        text = ctx.read_text(encoding="utf-8")
-        assert "old body" not in text
-        assert "specs/001-foo/plan.md" in text
-        assert text.startswith("# header\n")
-        assert "footer" in text
-
-    def test_remove_uses_custom_markers(self, tmp_path):
-        i = self._setup(
-            tmp_path, {"start": "<!-- BEGIN -->", "end": "<!-- END -->"}
-        )
-        ctx = tmp_path / "CLAUDE.md"
-        ctx.write_text(
-            "preamble\n\n<!-- BEGIN -->\nbody\n<!-- END -->\nepilogue\n",
-            encoding="utf-8",
-        )
-        removed = i.remove_context_section(tmp_path)
-        assert removed is True
-        remaining = ctx.read_text(encoding="utf-8")
-        assert "<!-- BEGIN -->" not in remaining
-        assert "<!-- END -->" not in remaining
-        assert "body" not in remaining
-        assert "preamble" in remaining
-        assert "epilogue" in remaining
-
-    def test_remove_with_default_markers_unchanged_when_custom_in_file(self, tmp_path):
-        # Extension config absent → default markers used. File contains only
-        # custom markers — nothing should be removed.
-        i = _CtxIntegration()
-        ctx = tmp_path / "CLAUDE.md"
-        original = "x\n<!-- BEGIN -->\nbody\n<!-- END -->\n"
-        ctx.write_text(original, encoding="utf-8")
-        assert i.remove_context_section(tmp_path) is False
-        assert ctx.read_text(encoding="utf-8") == original
-
-
-# ── Extension disabled gates setup/teardown ──────────────────────────────────
-
-
-def _write_registry(project_root: Path, *, enabled: bool) -> None:
-    registry = project_root / ".specify" / "extensions" / ".registry"
-    registry.parent.mkdir(parents=True, exist_ok=True)
-    registry.write_text(
-        json.dumps(
-            {
-                "schema_version": "1.0",
-                "extensions": {
-                    "agent-context": {
-                        "version": "1.0.0",
-                        "enabled": enabled,
-                    }
-                },
-            }
-        ),
-        encoding="utf-8",
-    )
-
-
-class TestExtensionEnabledGate:
-    def test_enabled_helper_default_when_no_registry(self, tmp_path):
-        assert IntegrationBase._agent_context_extension_enabled(tmp_path) is True
-
-    def test_enabled_helper_when_entry_present(self, tmp_path):
-        _write_registry(tmp_path, enabled=True)
-        assert IntegrationBase._agent_context_extension_enabled(tmp_path) is True
-
-    def test_disabled_helper_when_entry_disabled(self, tmp_path):
-        _write_registry(tmp_path, enabled=False)
-        assert IntegrationBase._agent_context_extension_enabled(tmp_path) is False
-
-    def test_upsert_skipped_when_disabled(self, tmp_path):
-        _write_registry(tmp_path, enabled=False)
-        i = _CtxIntegration()
-        result = i.upsert_context_section(tmp_path)
-        assert result is None
-        assert not (tmp_path / "CLAUDE.md").exists()
-
-    def test_remove_skipped_when_disabled(self, tmp_path):
-        _write_registry(tmp_path, enabled=False)
-        i = _CtxIntegration()
-        ctx = tmp_path / "CLAUDE.md"
-        original = (
-            f"head\n{IntegrationBase.CONTEXT_MARKER_START}\nbody\n"
-            f"{IntegrationBase.CONTEXT_MARKER_END}\ntail\n"
-        )
-        ctx.write_text(original, encoding="utf-8")
-        assert i.remove_context_section(tmp_path) is False
-        # File must be unchanged when extension is disabled
-        assert ctx.read_text(encoding="utf-8") == original
-
-
-# ── Extension config writers ─────────────────────────────────────────────────
-
-
-class TestExtensionConfigWriters:
-    def test_clear_init_options_clears_ext_config_context_file(self, tmp_path):
-        from specify_cli import _clear_init_options_for_integration
-
-        save_init_options(
-            tmp_path,
-            {"integration": "claude", "ai": "claude"},
-        )
-        _write_ext_config(tmp_path, context_file="CLAUDE.md")
-        _clear_init_options_for_integration(tmp_path, "claude")
-        cfg = _load_agent_context_config(tmp_path)
-        assert cfg.get("context_file") == ""
-
-    def test_clear_init_options_creates_ext_config_when_missing(self, tmp_path):
-        from specify_cli import _clear_init_options_for_integration
-
-        save_init_options(
-            tmp_path,
-            {"integration": "claude", "ai": "claude"},
-        )
-        _clear_init_options_for_integration(tmp_path, "claude")
-        cfg = _load_agent_context_config(tmp_path)
-        assert cfg.get("context_file") == ""
-
-    def test_clear_init_options_removes_legacy_context_keys_even_when_not_active(
-        self, tmp_path
-    ):
-        from specify_cli import _clear_init_options_for_integration
-
-        save_init_options(
-            tmp_path,
-            {
-                "integration": "copilot",
-                "ai": "copilot",
-                "context_file": "CLAUDE.md",
-                "context_markers": {"start": "<!-- X -->", "end": "<!-- Y -->"},
-            },
-        )
-        _clear_init_options_for_integration(tmp_path, "claude")
-        opts = load_init_options(tmp_path)
-        assert opts["integration"] == "copilot"
-        assert opts["ai"] == "copilot"
-        assert "context_file" not in opts
-        assert "context_markers" not in opts
-
-    def test_update_init_options_writes_context_file_to_ext_config(self, tmp_path):
-        from specify_cli import _update_init_options_for_integration
-
-        # Pre-create the extension config so _update_init_options_for_integration
-        # updates it (rather than skipping it when ext config doesn't exist yet).
-        _write_ext_config(tmp_path, context_file="")
-        i = _CtxIntegration()
-        _update_init_options_for_integration(tmp_path, i, script_type="sh")
-        # init-options.json must NOT have context_file or context_markers
-        opts = load_init_options(tmp_path)
-        assert "context_file" not in opts
-        assert "context_markers" not in opts
-        # Extension config must have them
-        cfg = _load_agent_context_config(tmp_path)
-        assert cfg["context_file"] == i.context_file
-        assert "context_markers" in cfg
-
-    def test_update_init_options_preserves_custom_markers(self, tmp_path):
-        from specify_cli import _update_init_options_for_integration
-
-        _write_ext_config(
-            tmp_path,
-            context_file="",
-            context_markers={"start": "<!-- B -->", "end": "<!-- E -->"},
-        )
-        i = _CtxIntegration()
-        _update_init_options_for_integration(tmp_path, i)
-        cfg = _load_agent_context_config(tmp_path)
-        assert cfg["context_markers"] == {"start": "<!-- B -->", "end": "<!-- E -->"}
-
-    def test_reinit_preserves_custom_markers(self, tmp_path):
-        """specify init (reinit) must not overwrite user-customised markers."""
-        from specify_cli import _update_agent_context_config_file
-
-        # Simulate existing project with custom markers
-        _write_ext_config(
-            tmp_path,
-            context_file="CLAUDE.md",
-            context_markers={"start": "<!-- CUSTOM -->", "end": "<!-- /CUSTOM -->"},
-        )
-        # Re-running init updates context_file but must preserve markers
-        _update_agent_context_config_file(
-            tmp_path, "CLAUDE.md", preserve_markers=True
-        )
-        cfg = _load_agent_context_config(tmp_path)
-        assert cfg["context_markers"] == {
-            "start": "<!-- CUSTOM -->",
-            "end": "<!-- /CUSTOM -->",
-        }
-
-
-# ── Deprecation warning on upsert ────────────────────────────────────────────
-
-
-class TestDeprecationWarning:
-    def test_upsert_emits_deprecation_warning(self, tmp_path, capsys):
-        """upsert_context_section must emit a deprecation notice on stdout."""
-        from tests.conftest import strip_ansi
-
-        i = _CtxIntegration()
-        _write_ext_config(tmp_path, context_file="CLAUDE.md")
-        i.upsert_context_section(tmp_path)
-        captured = capsys.readouterr()
-        plain = strip_ansi(captured.out)
-        assert "Deprecation" in plain
-        assert "v0.12.0" in plain
-        assert "agent-context" in plain
-
-    def test_upsert_no_warning_when_disabled(self, tmp_path, capsys):
-        """No deprecation warning when agent-context extension is disabled."""
-        _write_registry(tmp_path, enabled=False)
-        i = _CtxIntegration()
-        i.upsert_context_section(tmp_path)
-        captured = capsys.readouterr()
-        assert "Deprecation" not in captured.out
-
-
-# ── Corrupt / invalid extension config ───────────────────────────────────────
-
-
-class TestCorruptExtensionConfig:
-    def test_marker_resolution_with_corrupt_yaml(self, tmp_path):
-        """Corrupt YAML in agent-context-config.yml falls back to defaults."""
-        cfg_path = (
-            tmp_path / ".specify" / "extensions" / "agent-context"
-            / "agent-context-config.yml"
-        )
-        cfg_path.parent.mkdir(parents=True, exist_ok=True)
-        cfg_path.write_text(": invalid: yaml: {{{\n", encoding="utf-8")
-        i = _CtxIntegration()
-        start, end = i._resolve_context_markers(tmp_path)
-        assert start == IntegrationBase.CONTEXT_MARKER_START
-        assert end == IntegrationBase.CONTEXT_MARKER_END
-
-    def test_upsert_with_corrupt_config_uses_defaults(self, tmp_path):
-        """upsert_context_section still works when config YAML is corrupt."""
-        cfg_path = (
-            tmp_path / ".specify" / "extensions" / "agent-context"
-            / "agent-context-config.yml"
-        )
-        cfg_path.parent.mkdir(parents=True, exist_ok=True)
-        cfg_path.write_text("not valid yaml: {{{\n", encoding="utf-8")
-        i = _CtxIntegration()
-        result = i.upsert_context_section(tmp_path)
-        assert result is not None
-        text = (tmp_path / "CLAUDE.md").read_text(encoding="utf-8")
-        assert IntegrationBase.CONTEXT_MARKER_START in text
-        assert IntegrationBase.CONTEXT_MARKER_END in text
-
-    def test_marker_resolution_with_non_dict_yaml(self, tmp_path):
-        """Config file containing a scalar (not a dict) falls back to defaults."""
-        cfg_path = (
-            tmp_path / ".specify" / "extensions" / "agent-context"
-            / "agent-context-config.yml"
-        )
-        cfg_path.parent.mkdir(parents=True, exist_ok=True)
-        cfg_path.write_text("just a string\n", encoding="utf-8")
-        i = _CtxIntegration()
-        start, end = i._resolve_context_markers(tmp_path)
-        assert start == IntegrationBase.CONTEXT_MARKER_START
-        assert end == IntegrationBase.CONTEXT_MARKER_END

tests/integrations/test_cli.py

@@ -87,14 +87,7 @@ class TestInitIntegrationFlag:
 
         opts = json.loads((project / ".specify" / "init-options.json").read_text(encoding="utf-8"))
         assert opts["integration"] == "copilot"
-        # context_file lives in the agent-context extension config, not init-options.json
-        assert "context_file" not in opts
-
-        import yaml as _yaml
-        ext_cfg_path = project / ".specify" / "extensions" / "agent-context" / "agent-context-config.yml"
-        assert ext_cfg_path.exists(), "agent-context extension config must be created on init"
-        ext_cfg = _yaml.safe_load(ext_cfg_path.read_text(encoding="utf-8"))
-        assert ext_cfg["context_file"] == ".github/copilot-instructions.md"
+        assert opts["context_file"] == ".github/copilot-instructions.md"
 
         assert (project / ".specify" / "integrations" / "copilot.manifest.json").exists()
 
@@ -930,23 +923,7 @@ class TestGitExtensionAutoInstall:
 
 
 class TestSharedInfraCommandRefs:
-    """Verify _install_shared_infra resolves __SPECKIT_COMMAND_*__ in shared infra."""
-
-    @staticmethod
-    def _combined_script_content(project, script_type):
-        script_dir = "bash" if script_type == "sh" else "powershell"
-        suffix = "sh" if script_type == "sh" else "ps1"
-        names = [
-            f"check-prerequisites.{suffix}",
-            f"common.{suffix}",
-            f"setup-tasks.{suffix}",
-        ]
-        return "\n".join(
-            (project / ".specify" / "scripts" / script_dir / name).read_text(
-                encoding="utf-8"
-            )
-            for name in names
-        )
+    """Verify _install_shared_infra resolves __SPECKIT_COMMAND_*__ in page templates."""
 
     def test_dot_separator_in_page_templates(self, tmp_path):
         """Markdown agents get /speckit.<name> in page templates."""
@@ -991,46 +968,6 @@ class TestSharedInfraCommandRefs:
         assert "__SPECKIT_COMMAND_" not in content
         assert "/speckit-tasks" in content
 
-    @pytest.mark.parametrize("script_type", ["sh", "ps"])
-    def test_dot_separator_in_shared_scripts(self, tmp_path, script_type):
-        """Markdown agents get /speckit.<name> in shared script hints."""
-        from specify_cli import _install_shared_infra
-
-        project = tmp_path / f"dot-script-{script_type}"
-        project.mkdir()
-        (project / ".specify").mkdir()
-
-        _install_shared_infra(project, script_type, invoke_separator=".")
-
-        content = self._combined_script_content(project, script_type)
-        assert "__SPECKIT_COMMAND_" not in content
-        assert "/speckit.specify" in content
-        assert "/speckit.plan" in content
-        assert "/speckit.tasks" in content
-        assert "/speckit-specify" not in content
-        assert "/speckit-plan" not in content
-        assert "/speckit-tasks" not in content
-
-    @pytest.mark.parametrize("script_type", ["sh", "ps"])
-    def test_hyphen_separator_in_shared_scripts(self, tmp_path, script_type):
-        """Skills agents get /speckit-<name> in shared script hints."""
-        from specify_cli import _install_shared_infra
-
-        project = tmp_path / f"hyphen-script-{script_type}"
-        project.mkdir()
-        (project / ".specify").mkdir()
-
-        _install_shared_infra(project, script_type, invoke_separator="-")
-
-        content = self._combined_script_content(project, script_type)
-        assert "__SPECKIT_COMMAND_" not in content
-        assert "/speckit-specify" in content
-        assert "/speckit-plan" in content
-        assert "/speckit-tasks" in content
-        assert "/speckit.specify" not in content
-        assert "/speckit.plan" not in content
-        assert "/speckit.tasks" not in content
-
     def test_full_init_claude_resolves_page_templates(self, tmp_path):
         """Full CLI init with Claude (skills agent) produces hyphen refs in page templates."""
         from typer.testing import CliRunner
@@ -1058,10 +995,6 @@ class TestSharedInfraCommandRefs:
         assert "/speckit-plan" in content, "Claude (skills) should use /speckit-plan"
         assert "__SPECKIT_COMMAND_" not in content
 
-        script_content = self._combined_script_content(project, "sh")
-        assert "/speckit-specify" in script_content
-        assert "/speckit.specify" not in script_content
-
     def test_full_init_copilot_resolves_page_templates(self, tmp_path):
         """Full CLI init with Copilot (markdown agent) produces dot refs in page templates."""
         from typer.testing import CliRunner
@@ -1089,10 +1022,6 @@ class TestSharedInfraCommandRefs:
         assert "/speckit.plan" in content, "Copilot (markdown) should use /speckit.plan"
         assert "__SPECKIT_COMMAND_" not in content
 
-        script_content = self._combined_script_content(project, "sh")
-        assert "/speckit.specify" in script_content
-        assert "/speckit-specify" not in script_content
-
     def test_full_init_copilot_skills_resolves_page_templates(self, tmp_path):
         """Full CLI init with Copilot --skills produces hyphen refs in page templates."""
         from typer.testing import CliRunner
@@ -1122,10 +1051,6 @@ class TestSharedInfraCommandRefs:
         assert "/speckit.plan" not in content, "dot-notation leaked into Copilot skills page template"
         assert "__SPECKIT_COMMAND_" not in content
 
-        script_content = self._combined_script_content(project, "sh")
-        assert "/speckit-specify" in script_content
-        assert "/speckit.specify" not in script_content
-
 
 class TestIntegrationCatalogDiscoveryCLI:
     """End-to-end CLI tests for `integration search`, `info`, and `catalog …`.

tests/integrations/test_extra_args.py

@@ -1,638 +0,0 @@
-"""Tests for the per-integration `SPECKIT_INTEGRATION_<KEY>_EXTRA_ARGS` and
-`SPECKIT_INTEGRATION_<KEY>_EXECUTABLE` env-var hooks.
-
-The hooks are implemented in `IntegrationBase._apply_extra_args_env_var` and
-`IntegrationBase._resolve_executable` and wired into every concrete
-`build_exec_args` — `MarkdownIntegration`, `TomlIntegration`,
-`SkillsIntegration`, plus override integrations.
-These tests cover both the shared mechanisms (via `SkillsIntegration` stubs
-near the top of the file) and override integrations end-to-end (further down).
-See issues #2595 and #2596."""
-
-import os
-
-import pytest
-
-from specify_cli.integrations.base import (
-    MarkdownIntegration,
-    SkillsIntegration,
-    TomlIntegration,
-)
-
-
-class _ClaudeStub(SkillsIntegration):
-    """Minimal Claude-like SkillsIntegration for testing."""
-
-    key = "claude"
-    config = {
-        "name": "Claude (test stub)",
-        "folder": ".claude/",
-        "commands_subdir": "skills",
-        "install_url": None,
-        "requires_cli": True,
-    }
-    registrar_config = {
-        "dir": ".claude/skills",
-        "format": "markdown",
-        "args": "$ARGUMENTS",
-        "extension": "/SKILL.md",
-    }
-    context_file = "CLAUDE.md"
-
-
-class _KiroCliStub(SkillsIntegration):
-    """SkillsIntegration with a hyphenated key to exercise key
-    normalization (`kiro-cli` → `KIRO_CLI`)."""
-
-    key = "kiro-cli"
-    config = {
-        "name": "Kiro CLI (test stub)",
-        "folder": ".kiro/",
-        "commands_subdir": "commands",
-        "install_url": None,
-        "requires_cli": True,
-    }
-    registrar_config = {
-        "dir": ".kiro/commands",
-        "format": "markdown",
-        "args": "$ARGUMENTS",
-        "extension": ".md",
-    }
-    context_file = "KIRO.md"
-
-
-class _NoCliStub(SkillsIntegration):
-    """SkillsIntegration with requires_cli=False — build_exec_args
-    must return None and the env-var hook must not fire."""
-
-    key = "no-cli"
-    config = {
-        "name": "No-CLI agent (test stub)",
-        "folder": ".no-cli/",
-        "commands_subdir": "commands",
-        "install_url": None,
-        "requires_cli": False,
-    }
-    registrar_config = {
-        "dir": ".no-cli/commands",
-        "format": "markdown",
-        "args": "$ARGUMENTS",
-        "extension": ".md",
-    }
-    context_file = "NOCLI.md"
-
-
-class _MarkdownAgentStub(MarkdownIntegration):
-    """Bare MarkdownIntegration subclass — does NOT override
-    `build_exec_args`. Locks the base implementation in
-    `MarkdownIntegration.build_exec_args` for the common case
-    (most concrete integrations: Amp, Auggie, Generic, …)."""
-
-    key = "md-agent"
-    config = {
-        "name": "Markdown agent (test stub)",
-        "folder": ".md-agent/",
-        "commands_subdir": "commands",
-        "install_url": None,
-        "requires_cli": True,
-    }
-    registrar_config = {
-        "dir": ".md-agent/commands",
-        "format": "markdown",
-        "args": "$ARGUMENTS",
-        "extension": ".md",
-    }
-    context_file = "MDAGENT.md"
-
-
-class _TomlAgentStub(TomlIntegration):
-    """Bare TomlIntegration subclass — does NOT override
-    `build_exec_args`. Locks the base implementation in
-    `TomlIntegration.build_exec_args` (Gemini, Tabnine)."""
-
-    key = "toml-agent"
-    config = {
-        "name": "TOML agent (test stub)",
-        "folder": ".toml-agent/",
-        "commands_subdir": "commands",
-        "install_url": None,
-        "requires_cli": True,
-    }
-    registrar_config = {
-        "dir": ".toml-agent/commands",
-        "format": "toml",
-        "args": "$ARGUMENTS",
-        "extension": ".toml",
-    }
-    context_file = "TOMLAGENT.md"
-
-
-@pytest.fixture(autouse=True)
-def _clean_extra_args_env(monkeypatch):
-    """Strip any leaked SPECKIT_INTEGRATION_*_EXTRA_ARGS and
-    SPECKIT_INTEGRATION_*_EXECUTABLE vars from the test env so a
-    developer's shell setting doesn't pollute results."""
-    for key in list(os.environ):
-        if key.startswith("SPECKIT_INTEGRATION_") and (
-            key.endswith("_EXTRA_ARGS") or key.endswith("_EXECUTABLE")
-        ):
-            monkeypatch.delenv(key, raising=False)
-
-
-def test_env_var_unset_byte_identical_argv():
-    """Default behaviour: env var unset → no extra args inserted.
-
-    Locks the backward-compatibility guarantee that existing
-    operators see no change.
-    """
-    args = _ClaudeStub().build_exec_args("hello prompt")
-    assert args == ["claude", "-p", "hello prompt", "--output-format", "json"]
-
-
-def test_env_var_set_flag_inserted_before_model_and_output_format(
-    monkeypatch,
-):
-    monkeypatch.setenv(
-        "SPECKIT_INTEGRATION_CLAUDE_EXTRA_ARGS", "--dangerously-skip-permissions"
-    )
-    args = _ClaudeStub().build_exec_args("hello prompt", model="sonnet")
-    assert args == [
-        "claude",
-        "-p",
-        "hello prompt",
-        "--dangerously-skip-permissions",
-        "--model",
-        "sonnet",
-        "--output-format",
-        "json",
-    ]
-
-
-def test_env_var_multi_token_parsed_via_shlex(monkeypatch):
-    monkeypatch.setenv(
-        "SPECKIT_INTEGRATION_CLAUDE_EXTRA_ARGS",
-        "--dangerously-skip-permissions --max-turns 3",
-    )
-    args = _ClaudeStub().build_exec_args("p")
-    assert args == [
-        "claude",
-        "-p",
-        "p",
-        "--dangerously-skip-permissions",
-        "--max-turns",
-        "3",
-        "--output-format",
-        "json",
-    ]
-
-
-def test_malformed_quoting_raises_actionable_value_error(monkeypatch):
-    """An unmatched quote in the env-var value must surface a clear
-    error naming the offending env var and showing the invalid value,
-    rather than crashing workflow dispatch with a bare shlex traceback."""
-    monkeypatch.setenv(
-        "SPECKIT_INTEGRATION_CLAUDE_EXTRA_ARGS",
-        '--flag "unterminated',
-    )
-    with pytest.raises(ValueError) as excinfo:
-        _ClaudeStub().build_exec_args("p")
-    msg = str(excinfo.value)
-    assert "SPECKIT_INTEGRATION_CLAUDE_EXTRA_ARGS" in msg
-    assert "--flag \"unterminated" in msg
-
-
-def test_env_var_empty_or_whitespace_is_noop(monkeypatch):
-    """An env var set to '' or '   ' is treated as unset."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_CLAUDE_EXTRA_ARGS", "   ")
-    args = _ClaudeStub().build_exec_args("p")
-    assert args == ["claude", "-p", "p", "--output-format", "json"]
-
-
-def test_other_integration_env_var_ignored(monkeypatch):
-    """`SPECKIT_INTEGRATION_GEMINI_EXTRA_ARGS` set must NOT leak into
-    Claude's argv (per-integration scoping)."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_GEMINI_EXTRA_ARGS", "--gemini-only-flag")
-    args = _ClaudeStub().build_exec_args("p")
-    assert args == ["claude", "-p", "p", "--output-format", "json"]
-
-
-def test_key_normalization_hyphen_to_underscore_uppercase(monkeypatch):
-    """`kiro-cli` key looks up `SPECKIT_INTEGRATION_KIRO_CLI_EXTRA_ARGS`
-    (hyphens replaced with underscores, then uppercased)."""
-    monkeypatch.setenv(
-        "SPECKIT_INTEGRATION_KIRO_CLI_EXTRA_ARGS", "--some-kiro-flag"
-    )
-    args = _KiroCliStub().build_exec_args("p")
-    assert args == [
-        "kiro-cli",
-        "-p",
-        "p",
-        "--some-kiro-flag",
-        "--output-format",
-        "json",
-    ]
-
-
-def test_requires_cli_false_returns_none(monkeypatch):
-    """`requires_cli: False` short-circuits to None — the env-var
-    hook is never reached and no argv is built."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_NO_CLI_EXTRA_ARGS", "--should-not-appear")
-    assert _NoCliStub().build_exec_args("p") is None
-
-
-# ---------------------------------------------------------------------------
-# Base-class coverage
-#
-# Most integrations inherit `build_exec_args` from `MarkdownIntegration`
-# or `TomlIntegration` without overriding it. The tests above use
-# `SkillsIntegration` stubs (which share the same hook mechanism) — these
-# tests exercise the two other base implementations directly so all three
-# concrete bases are covered.
-# ---------------------------------------------------------------------------
-
-
-def test_markdown_integration_base_honours_extra_args(monkeypatch):
-    """A bare `MarkdownIntegration` subclass — which does not override
-    `build_exec_args` — must honour the env var via the base
-    implementation. Covers the most common integration pattern."""
-    monkeypatch.setenv(
-        "SPECKIT_INTEGRATION_MD_AGENT_EXTRA_ARGS", "--debug --max-tokens 100"
-    )
-    args = _MarkdownAgentStub().build_exec_args("p")
-    assert args == [
-        "md-agent",
-        "-p",
-        "p",
-        "--debug",
-        "--max-tokens",
-        "100",
-        "--output-format",
-        "json",
-    ]
-
-
-def test_toml_integration_base_honours_extra_args(monkeypatch):
-    """A bare `TomlIntegration` subclass — which does not override
-    `build_exec_args` — must honour the env var via the base
-    implementation. Covers Gemini/Tabnine-style integrations."""
-    monkeypatch.setenv(
-        "SPECKIT_INTEGRATION_TOML_AGENT_EXTRA_ARGS", "--yolo"
-    )
-    args = _TomlAgentStub().build_exec_args("p", model="gemini-pro")
-    # TomlIntegration uses `-m` for model (vs Markdown's `--model`).
-    assert args == [
-        "toml-agent",
-        "-p",
-        "p",
-        "--yolo",
-        "-m",
-        "gemini-pro",
-        "--output-format",
-        "json",
-    ]
-
-
-# ---------------------------------------------------------------------------
-# Override-integration coverage
-#
-# CodexIntegration, DevinIntegration, OpencodeIntegration and
-# CopilotIntegration each override `build_exec_args` rather than using the
-# base implementations. The env-var hook must be wired into every override
-# so the documented behaviour ("works for every requires_cli integration")
-# is honoured. These tests lock that contract per integration.
-# ---------------------------------------------------------------------------
-
-
-def test_codex_integration_honours_extra_args(monkeypatch):
-    from specify_cli.integrations.codex import CodexIntegration
-
-    monkeypatch.setenv("SPECKIT_INTEGRATION_CODEX_EXTRA_ARGS", "--sandbox read-only")
-    args = CodexIntegration().build_exec_args("p", model="gpt-5")
-    assert args == [
-        "codex",
-        "exec",
-        "p",
-        "--sandbox",
-        "read-only",
-        "--model",
-        "gpt-5",
-        "--json",
-    ]
-
-
-def test_devin_integration_honours_extra_args(monkeypatch):
-    from specify_cli.integrations.devin import DevinIntegration
-
-    monkeypatch.setenv("SPECKIT_INTEGRATION_DEVIN_EXTRA_ARGS", "--no-confirm")
-    args = DevinIntegration().build_exec_args("p")
-    assert args == ["devin", "-p", "p", "--no-confirm"]
-
-
-def test_opencode_integration_honours_extra_args(monkeypatch):
-    from specify_cli.integrations.opencode import OpencodeIntegration
-
-    monkeypatch.setenv("SPECKIT_INTEGRATION_OPENCODE_EXTRA_ARGS", "--quiet")
-    args = OpencodeIntegration().build_exec_args("p")
-    assert args == [
-        "opencode",
-        "run",
-        "--quiet",
-        "--format",
-        "json",
-        "p",
-    ]
-
-
-def test_opencode_extra_args_cannot_clobber_prompt_derived_command(
-    monkeypatch,
-):
-    """Operator-injected extra args must appear BEFORE the prompt-derived
-    ``--command <X>`` so that Spec Kit's command selection wins under
-    repeated-flag CLI semantics (last value typically takes precedence).
-
-    Locks against the regression where an operator setting
-    ``SPECKIT_INTEGRATION_OPENCODE_EXTRA_ARGS="--command malicious"`` could redirect
-    a slash-prefixed prompt to a different command.
-    """
-    from specify_cli.integrations.opencode import OpencodeIntegration
-
-    monkeypatch.setenv(
-        "SPECKIT_INTEGRATION_OPENCODE_EXTRA_ARGS", "--command operator-override"
-    )
-    args = OpencodeIntegration().build_exec_args("/speckit body text")
-    # Prompt-derived "--command speckit" appears AFTER the
-    # operator-injected one, so a CLI that resolves repeated flags
-    # last-wins will honour Spec Kit's choice.
-    assert args == [
-        "opencode",
-        "run",
-        "--command",
-        "operator-override",
-        "--command",
-        "speckit",
-        "--format",
-        "json",
-        "body text",
-    ]
-
-
-def test_copilot_integration_honours_extra_args(monkeypatch):
-    from specify_cli.integrations.copilot import (
-        CopilotIntegration,
-        _copilot_executable,
-    )
-
-    # Disable --yolo so the argv shape stays deterministic.
-    monkeypatch.setenv("SPECKIT_COPILOT_ALLOW_ALL_TOOLS", "0")
-    monkeypatch.setenv(
-        "SPECKIT_INTEGRATION_COPILOT_EXTRA_ARGS", "--allow-tool 'shell(echo)'"
-    )
-    args = CopilotIntegration().build_exec_args("p")
-    # `_copilot_executable()` returns "copilot.cmd" on Windows and
-    # "copilot" elsewhere; the test must mirror that to stay portable.
-    assert args == [
-        _copilot_executable(),
-        "-p",
-        "p",
-        "--allow-tool",
-        "shell(echo)",
-        "--output-format",
-        "json",
-    ]
-
-
-# ---------------------------------------------------------------------------
-# `dispatch_command` end-to-end coverage
-#
-# Workflow execution calls `impl.dispatch_command(...)`, not
-# `build_exec_args` directly. `IntegrationBase.dispatch_command` delegates
-# to `build_exec_args` (so the override fixes above flow through), but
-# `CopilotIntegration` overrides `dispatch_command` and constructs
-# `cli_args` inline — the hook must be invoked there too or the env var
-# is silently ignored at workflow runtime. These tests monkeypatch
-# `subprocess.run` and assert the env-var args reach the executed argv.
-# ---------------------------------------------------------------------------
-
-
-class _RunCapture:
-    """Test double that captures argv passed to subprocess.run."""
-
-    def __init__(self):
-        self.captured_args: list[str] | None = None
-
-    def __call__(self, args, **kwargs):
-        self.captured_args = list(args)
-
-        class _Result:
-            returncode = 0
-            stdout = ""
-            stderr = ""
-
-        return _Result()
-
-
-def test_copilot_dispatch_command_includes_extra_args(monkeypatch):
-    """Locks the bypass fix: `CopilotIntegration.dispatch_command`
-    must honour `SPECKIT_INTEGRATION_COPILOT_EXTRA_ARGS`, not just `build_exec_args`.
-    """
-    import subprocess
-
-    from specify_cli.integrations.copilot import CopilotIntegration
-
-    capture = _RunCapture()
-    monkeypatch.setattr(subprocess, "run", capture)
-    monkeypatch.setenv("SPECKIT_COPILOT_ALLOW_ALL_TOOLS", "0")
-    monkeypatch.setenv(
-        "SPECKIT_INTEGRATION_COPILOT_EXTRA_ARGS", "--allow-tool 'shell(echo)'"
-    )
-
-    CopilotIntegration().dispatch_command(
-        "speckit.plan", args="body", stream=False
-    )
-
-    assert capture.captured_args is not None
-    # Hook inserted between `-p prompt` and the canonical Copilot flags.
-    p_idx = capture.captured_args.index("-p")
-    agent_idx = capture.captured_args.index("--agent")
-    extra_idx = capture.captured_args.index("--allow-tool")
-    assert p_idx < extra_idx < agent_idx
-    assert "shell(echo)" in capture.captured_args
-
-
-def test_codex_dispatch_command_includes_extra_args(monkeypatch):
-    """Lock the inherited `IntegrationBase.dispatch_command` path:
-    Codex (and by transitivity Devin, Opencode) flow through
-    `build_exec_args`, so the env var must reach argv at workflow
-    runtime.
-    """
-    import subprocess
-
-    from specify_cli.integrations.codex import CodexIntegration
-
-    capture = _RunCapture()
-    monkeypatch.setattr(subprocess, "run", capture)
-    monkeypatch.setenv("SPECKIT_INTEGRATION_CODEX_EXTRA_ARGS", "--sandbox read-only")
-
-    CodexIntegration().dispatch_command(
-        "speckit.plan", args="body", stream=False
-    )
-
-    assert capture.captured_args is not None
-    assert "--sandbox" in capture.captured_args
-    assert "read-only" in capture.captured_args
-
-
-# ---------------------------------------------------------------------------
-# SPECKIT_INTEGRATION_<KEY>_EXECUTABLE tests
-#
-# The `_resolve_executable()` method on `IntegrationBase` checks
-# `SPECKIT_INTEGRATION_<KEY>_EXECUTABLE` and, when set, substitutes that
-# value for `self.key` as the first token in argv.  The tests below lock
-# the behaviour across shared and override integration paths:
-#   - the shared SkillsIntegration/MarkdownIntegration/TomlIntegration bases,
-#   - representative override integrations,
-#   - the hyphen→underscore key normalisation, and
-#   - whitespace/unset no-op guarantee.
-# ---------------------------------------------------------------------------
-
-
-def test_executable_env_var_unset_uses_key():
-    """Default: no override → executable is the integration key."""
-    args = _ClaudeStub().build_exec_args("p")
-    assert args[0] == "claude"
-
-
-def test_executable_env_var_replaces_first_argv_token(monkeypatch):
-    """Setting the env var substitutes the executable name in argv."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_CLAUDE_EXECUTABLE", "/opt/claude/bin/claude")
-    args = _ClaudeStub().build_exec_args("hello")
-    assert args[0] == "/opt/claude/bin/claude"
-    assert args[1:] == ["-p", "hello", "--output-format", "json"]
-
-
-def test_executable_env_var_whitespace_only_falls_back_to_key(monkeypatch):
-    """Whitespace-only value is treated as unset → falls back to self.key."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_CLAUDE_EXECUTABLE", "   ")
-    args = _ClaudeStub().build_exec_args("p")
-    assert args[0] == "claude"
-
-
-def test_executable_env_var_key_normalization_hyphen_to_underscore(monkeypatch):
-    """`kiro-cli` key maps to `SPECKIT_INTEGRATION_KIRO_CLI_EXECUTABLE`."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_KIRO_CLI_EXECUTABLE", "/usr/local/bin/kiro-cli")
-    args = _KiroCliStub().build_exec_args("p")
-    assert args[0] == "/usr/local/bin/kiro-cli"
-
-
-def test_executable_env_var_other_integration_ignored(monkeypatch):
-    """`SPECKIT_INTEGRATION_GEMINI_EXECUTABLE` must NOT affect Claude."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_GEMINI_EXECUTABLE", "/custom/gemini")
-    args = _ClaudeStub().build_exec_args("p")
-    assert args[0] == "claude"
-
-
-def test_executable_env_var_markdown_integration(monkeypatch):
-    """MarkdownIntegration base honours the executable env var."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_MD_AGENT_EXECUTABLE", "/custom/md-agent")
-    args = _MarkdownAgentStub().build_exec_args("p")
-    assert args[0] == "/custom/md-agent"
-
-
-def test_executable_env_var_toml_integration(monkeypatch):
-    """TomlIntegration base honours the executable env var."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_TOML_AGENT_EXECUTABLE", "/custom/toml-agent")
-    args = _TomlAgentStub().build_exec_args("p")
-    assert args[0] == "/custom/toml-agent"
-
-
-def test_executable_env_var_requires_cli_false_returns_none(monkeypatch):
-    """`requires_cli: False` still returns None even when executable is set."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_NO_CLI_EXECUTABLE", "/custom/no-cli")
-    assert _NoCliStub().build_exec_args("p") is None
-
-
-def test_executable_env_var_codex_integration(monkeypatch):
-    """CodexIntegration honours the executable env var."""
-    from specify_cli.integrations.codex import CodexIntegration
-
-    monkeypatch.setenv("SPECKIT_INTEGRATION_CODEX_EXECUTABLE", "/opt/codex")
-    args = CodexIntegration().build_exec_args("p")
-    assert args[0] == "/opt/codex"
-    assert args[1] == "exec"
-
-
-def test_executable_env_var_devin_integration(monkeypatch):
-    """DevinIntegration honours the executable env var."""
-    from specify_cli.integrations.devin import DevinIntegration
-
-    monkeypatch.setenv("SPECKIT_INTEGRATION_DEVIN_EXECUTABLE", "/opt/devin")
-    args = DevinIntegration().build_exec_args("p")
-    assert args[0] == "/opt/devin"
-
-
-def test_executable_env_var_opencode_integration(monkeypatch):
-    """OpencodeIntegration honours the executable env var."""
-    from specify_cli.integrations.opencode import OpencodeIntegration
-
-    monkeypatch.setenv("SPECKIT_INTEGRATION_OPENCODE_EXECUTABLE", "/opt/opencode")
-    args = OpencodeIntegration().build_exec_args("p")
-    assert args[0] == "/opt/opencode"
-    assert args[1] == "run"
-
-
-def test_executable_env_var_copilot_integration(monkeypatch):
-    """CopilotIntegration honours the executable env var, overriding the
-    platform-specific default from `_copilot_executable()`."""
-    from specify_cli.integrations.copilot import CopilotIntegration
-
-    monkeypatch.setenv("SPECKIT_INTEGRATION_COPILOT_EXECUTABLE", "/opt/copilot")
-    monkeypatch.setenv("SPECKIT_COPILOT_ALLOW_ALL_TOOLS", "0")
-    args = CopilotIntegration().build_exec_args("p")
-    assert args[0] == "/opt/copilot"
-
-
-def test_executable_env_var_copilot_unset_uses_platform_default(monkeypatch):
-    """When `SPECKIT_INTEGRATION_COPILOT_EXECUTABLE` is unset, Copilot
-    falls back to the platform-specific default from `_copilot_executable()`."""
-    from specify_cli.integrations.copilot import CopilotIntegration, _copilot_executable
-
-    monkeypatch.setenv("SPECKIT_COPILOT_ALLOW_ALL_TOOLS", "0")
-    args = CopilotIntegration().build_exec_args("p")
-    assert args[0] == _copilot_executable()
-
-
-def test_executable_env_var_copilot_dispatch_command(monkeypatch):
-    """CopilotIntegration.dispatch_command honours the executable env var."""
-    import subprocess
-
-    from specify_cli.integrations.copilot import CopilotIntegration
-
-    capture = _RunCapture()
-    monkeypatch.setattr(subprocess, "run", capture)
-    monkeypatch.setenv("SPECKIT_INTEGRATION_COPILOT_EXECUTABLE", "/opt/copilot")
-    monkeypatch.setenv("SPECKIT_COPILOT_ALLOW_ALL_TOOLS", "0")
-
-    CopilotIntegration().dispatch_command("speckit.plan", args="body", stream=False)
-
-    assert capture.captured_args is not None
-    assert capture.captured_args[0] == "/opt/copilot"
-
-
-def test_executable_and_extra_args_both_honoured(monkeypatch):
-    """Both the executable override and extra args env vars can be set
-    simultaneously — they are independent hooks."""
-    monkeypatch.setenv("SPECKIT_INTEGRATION_CLAUDE_EXECUTABLE", "/opt/claude")
-    monkeypatch.setenv(
-        "SPECKIT_INTEGRATION_CLAUDE_EXTRA_ARGS", "--dangerously-skip-permissions"
-    )
-    args = _ClaudeStub().build_exec_args("hello", model="sonnet")
-    assert args == [
-        "/opt/claude",
-        "-p",
-        "hello",
-        "--dangerously-skip-permissions",
-        "--model",
-        "sonnet",
-        "--output-format",
-        "json",
-    ]

tests/integrations/test_integration_agy.py

@@ -1,7 +1,5 @@
 """Tests for AgyIntegration (Antigravity)."""
 
-from specify_cli.integrations import get_integration
-
 from .test_integration_base_skills import SkillsIntegrationTests
 
 
@@ -14,21 +12,10 @@ class TestAgyIntegration(SkillsIntegrationTests):
 
     def test_options_include_skills_flag(self):
         """Override inherited test: AgyIntegration should not expose a --skills flag because .agents/ is its only layout."""
+        from specify_cli.integrations import get_integration
         i = get_integration(self.KEY)
         skills_opts = [o for o in i.options() if o.name == "--skills"]
         assert len(skills_opts) == 0
-
-    def test_requires_cli_is_true(self):
-        """agy is a CLI tool; requires_cli must be True."""
-        i = get_integration(self.KEY)
-        assert i.config["requires_cli"] is True
-
-    def test_install_url_is_set(self):
-        """install_url must point to the official installation page."""
-        i = get_integration(self.KEY)
-        assert i.config["install_url"] == "https://antigravity.google/"
-
-
 class TestAgyAutoPromote:
     """--ai agy auto-promotes to integration path."""
 
@@ -39,7 +26,7 @@ class TestAgyAutoPromote:
 
         runner = CliRunner()
         target = tmp_path / "test-proj"
-        result = runner.invoke(app, ["init", str(target), "--ai", "agy", "--no-git", "--script", "sh", "--ignore-agent-tools"])
+        result = runner.invoke(app, ["init", str(target), "--ai", "agy", "--no-git", "--script", "sh"])
 
         assert result.exit_code == 0, f"init --ai agy failed: {result.output}"
         assert (target / ".agents" / "skills" / "speckit-plan" / "SKILL.md").exists()
@@ -49,87 +36,10 @@ class TestAgyAutoPromote:
         from typer.testing import CliRunner
         from specify_cli import app
 
-        # Click >= 8.2 separates stdout and stderr natively
+        # Click >= 8.2 separates stdout and stderr natively, mix_stderr is removed
         runner = CliRunner()
         target = tmp_path / "test-proj2"
-        result = runner.invoke(app, ["init", str(target), "--ai", "agy", "--no-git", "--script", "sh", "--ignore-agent-tools"])
+        result = runner.invoke(app, ["init", str(target), "--ai", "agy", "--no-git", "--script", "sh"])
 
         assert result.exit_code == 0
         assert "Warning: The .agents/ layout requires Antigravity v1.20.5 or newer" in result.stderr
-
-
-class TestAgyBuildExecArgs:
-    """agy non-interactive execution argument building."""
-
-    def test_build_exec_args_returns_print_command(self):
-        """build_exec_args should return ['agy', '--print', prompt]."""
-        from specify_cli.integrations import get_integration
-        i = get_integration("agy")
-        result = i.build_exec_args("describe my feature")
-        assert result == ["agy", "--print", "describe my feature"]
-
-    def test_build_exec_args_ignores_model(self):
-        """agy does not support --model; model param must be ignored."""
-        from specify_cli.integrations import get_integration
-        i = get_integration("agy")
-        result = i.build_exec_args("my prompt", model="gemini-pro")
-        assert result == ["agy", "--print", "my prompt"]
-
-    def test_build_exec_args_ignores_output_json(self):
-        """agy does not support JSON output; output_json param must be ignored."""
-        from specify_cli.integrations import get_integration
-        i = get_integration("agy")
-        result = i.build_exec_args("my prompt", output_json=False)
-        assert result == ["agy", "--print", "my prompt"]
-
-
-class TestAgyHookCommandNote:
-    """Verify dot-to-hyphen normalization note is injected into hook sections."""
-
-    def test_hook_note_injected_in_skills_with_hooks(self, tmp_path):
-        """Skills with hook sections should contain the normalization note."""
-        from specify_cli.integrations import get_integration
-        from specify_cli.integrations.manifest import IntegrationManifest
-
-        i = get_integration("agy")
-        m = IntegrationManifest("agy", tmp_path)
-        i.setup(tmp_path, m, script_type="sh")
-        specify_skill = tmp_path / ".agents/skills/speckit-specify/SKILL.md"
-        assert specify_skill.exists()
-        content = specify_skill.read_text(encoding="utf-8")
-        assert "replace dots" in content, (
-            "speckit-specify should have dot-to-hyphen hook note"
-        )
-
-    def test_hook_note_not_in_skills_without_hooks(self):
-        """Skills without hook sections should not get the note."""
-        from specify_cli.integrations.agy import AgyIntegration
-
-        content = "---\nname: test\ndescription: test\n---\n\nNo hooks here.\n"
-        result = AgyIntegration._inject_hook_command_note(content)
-        assert "replace dots" not in result
-
-    def test_hook_note_idempotent(self):
-        """Injecting the note twice must not duplicate it."""
-        from specify_cli.integrations.agy import AgyIntegration
-
-        content = (
-            "---\nname: test\n---\n\n"
-            "- For each executable hook, output the following based on its flag:\n"
-        )
-        once = AgyIntegration._inject_hook_command_note(content)
-        twice = AgyIntegration._inject_hook_command_note(once)
-        assert once == twice, "Hook note injection should be idempotent"
-
-    def test_hook_note_preserves_indentation(self):
-        """The injected note must match the indentation of the target line."""
-        from specify_cli.integrations.agy import AgyIntegration
-
-        content = (
-            "---\nname: test\n---\n\n"
-            "   - For each executable hook, output the following\n"
-        )
-        result = AgyIntegration._inject_hook_command_note(content)
-        lines = result.splitlines()
-        note_line = [l for l in lines if "replace dots" in l][0]
-        assert note_line.startswith("   "), "Note should preserve indentation"

tests/integrations/test_integration_base_markdown.py

@@ -226,8 +226,8 @@ class MarkdownIntegrationTests:
         assert len(commands) > 0, f"No command files in {cmd_dir}"
 
     def test_init_options_includes_context_file(self, tmp_path):
-        """agent-context extension config must include context_file for the active integration."""
-        import yaml
+        """init-options.json must include context_file for the active integration."""
+        import json
         from typer.testing import CliRunner
         from specify_cli import app
 
@@ -243,17 +243,15 @@ class MarkdownIntegrationTests:
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0
-        ext_cfg_path = project / ".specify" / "extensions" / "agent-context" / "agent-context-config.yml"
-        ext_cfg = yaml.safe_load(ext_cfg_path.read_text(encoding="utf-8")) if ext_cfg_path.exists() else {}
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
         i = get_integration(self.KEY)
-        assert ext_cfg.get("context_file") == i.context_file, (
-            f"Expected context_file={i.context_file!r}, got {ext_cfg.get('context_file')!r}"
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
         )
 
     # -- Complete file inventory ------------------------------------------
 
     COMMAND_STEMS = [
-        "agent-context.update",
         "analyze", "checklist", "clarify", "constitution",
         "implement", "plan", "specify", "tasks", "taskstoissues",
     ]
@@ -293,16 +291,6 @@ class MarkdownIntegrationTests:
         files.append(".specify/workflows/speckit/workflow.yml")
         files.append(".specify/workflows/workflow-registry.json")
 
-        # Bundled agent-context extension
-        files.append(".specify/extensions.yml")
-        files.append(".specify/extensions/.registry")
-        files.append(".specify/extensions/agent-context/README.md")
-        files.append(".specify/extensions/agent-context/agent-context-config.yml")
-        files.append(".specify/extensions/agent-context/commands/speckit.agent-context.update.md")
-        files.append(".specify/extensions/agent-context/extension.yml")
-        files.append(".specify/extensions/agent-context/scripts/bash/update-agent-context.sh")
-        files.append(".specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1")
-
         # Agent context file (if set)
         if i.context_file:
             files.append(i.context_file)

tests/integrations/test_integration_base_skills.py

@@ -176,39 +176,6 @@ class SkillsIntegrationTests:
                 f"skills agents must use /speckit-<name>"
             )
 
-    def test_hook_sections_explain_dotted_command_conversion(self, tmp_path):
-        """Generated skills with hook sections must explain dotted command conversion."""
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        i.setup(tmp_path, m)
-        specify_skill = i.skills_dest(tmp_path) / "speckit-specify" / "SKILL.md"
-        assert specify_skill.exists()
-        content = specify_skill.read_text(encoding="utf-8")
-        assert "replace dots" in content, (
-            "speckit-specify should explain dotted hook command conversion"
-        )
-        assert content.count("replace dots") == content.count(
-            "- For each executable hook, output the following"
-        )
-
-    def test_hook_note_injected_for_each_instruction_independently(self):
-        """Existing hook notes should not suppress later missing notes."""
-        content = (
-            "---\n"
-            "name: test\n"
-            "---\n\n"
-            "- When constructing slash commands from hook command names, "
-            "replace dots (`.`) with hyphens (`-`). "
-            "For example, `speckit.git.commit` → `/speckit-git-commit`.\n"
-            "- For each executable hook, output the following first block:\n"
-            "\n"
-            "- For each executable hook, output the following second block:\n"
-        )
-
-        result = SkillsIntegration._inject_hook_command_note(content)
-
-        assert result.count("replace dots (`.`) with hyphens") == 2
-
     def test_skill_body_has_content(self, tmp_path):
         """Each SKILL.md body should contain template content after the frontmatter."""
         i = get_integration(self.KEY)
@@ -357,8 +324,8 @@ class SkillsIntegrationTests:
         assert skills_dir.is_dir(), f"Skills directory {skills_dir} not created"
 
     def test_init_options_includes_context_file(self, tmp_path):
-        """agent-context extension config must include context_file for the active integration."""
-        import yaml
+        """init-options.json must include context_file for the active integration."""
+        import json
         from typer.testing import CliRunner
         from specify_cli import app
 
@@ -374,11 +341,10 @@ class SkillsIntegrationTests:
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0
-        ext_cfg_path = project / ".specify" / "extensions" / "agent-context" / "agent-context-config.yml"
-        ext_cfg = yaml.safe_load(ext_cfg_path.read_text(encoding="utf-8")) if ext_cfg_path.exists() else {}
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
         i = get_integration(self.KEY)
-        assert ext_cfg.get("context_file") == i.context_file, (
-            f"Expected context_file={i.context_file!r}, got {ext_cfg.get('context_file')!r}"
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
         )
 
     # -- IntegrationOption ------------------------------------------------
@@ -403,11 +369,9 @@ class SkillsIntegrationTests:
         skills_prefix = i.config["folder"].rstrip("/") + "/" + i.config.get("commands_subdir", "skills")
 
         files = []
-        # Skill files (core commands)
+        # Skill files
         for cmd in self._SKILL_COMMANDS:
             files.append(f"{skills_prefix}/speckit-{cmd}/SKILL.md")
-        # Extension-installed skill (agent-context)
-        files.append(f"{skills_prefix}/speckit-agent-context-update/SKILL.md")
         # Integration metadata
         files += [
             ".specify/init-options.json",
@@ -446,15 +410,6 @@ class SkillsIntegrationTests:
             ".specify/workflows/speckit/workflow.yml",
             ".specify/workflows/workflow-registry.json",
         ]
-        # Bundled agent-context extension
-        files.append(".specify/extensions.yml")
-        files.append(".specify/extensions/.registry")
-        files.append(".specify/extensions/agent-context/README.md")
-        files.append(".specify/extensions/agent-context/agent-context-config.yml")
-        files.append(".specify/extensions/agent-context/commands/speckit.agent-context.update.md")
-        files.append(".specify/extensions/agent-context/extension.yml")
-        files.append(".specify/extensions/agent-context/scripts/bash/update-agent-context.sh")
-        files.append(".specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1")
         # Agent context file (if set)
         if i.context_file:
             files.append(i.context_file)

tests/integrations/test_integration_base_toml.py

@@ -457,8 +457,8 @@ class TomlIntegrationTests:
         assert len(commands) > 0, f"No command files in {cmd_dir}"
 
     def test_init_options_includes_context_file(self, tmp_path):
-        """agent-context extension config must include context_file for the active integration."""
-        import yaml
+        """init-options.json must include context_file for the active integration."""
+        import json
         from typer.testing import CliRunner
         from specify_cli import app
 
@@ -474,17 +474,15 @@ class TomlIntegrationTests:
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0
-        ext_cfg_path = project / ".specify" / "extensions" / "agent-context" / "agent-context-config.yml"
-        ext_cfg = yaml.safe_load(ext_cfg_path.read_text(encoding="utf-8")) if ext_cfg_path.exists() else {}
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
         i = get_integration(self.KEY)
-        assert ext_cfg.get("context_file") == i.context_file, (
-            f"Expected context_file={i.context_file!r}, got {ext_cfg.get('context_file')!r}"
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
         )
 
     # -- Complete file inventory ------------------------------------------
 
     COMMAND_STEMS = [
-        "agent-context.update",
         "analyze",
         "checklist",
         "clarify",
@@ -545,16 +543,6 @@ class TomlIntegrationTests:
         files.append(".specify/workflows/speckit/workflow.yml")
         files.append(".specify/workflows/workflow-registry.json")
 
-        # Bundled agent-context extension
-        files.append(".specify/extensions.yml")
-        files.append(".specify/extensions/.registry")
-        files.append(".specify/extensions/agent-context/README.md")
-        files.append(".specify/extensions/agent-context/agent-context-config.yml")
-        files.append(".specify/extensions/agent-context/commands/speckit.agent-context.update.md")
-        files.append(".specify/extensions/agent-context/extension.yml")
-        files.append(".specify/extensions/agent-context/scripts/bash/update-agent-context.sh")
-        files.append(".specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1")
-
         # Agent context file (if set)
         if i.context_file:
             files.append(i.context_file)

tests/integrations/test_integration_base_yaml.py

@@ -336,8 +336,8 @@ class YamlIntegrationTests:
         assert len(commands) > 0, f"No command files in {cmd_dir}"
 
     def test_init_options_includes_context_file(self, tmp_path):
-        """agent-context extension config must include context_file for the active integration."""
-        import yaml
+        """init-options.json must include context_file for the active integration."""
+        import json
         from typer.testing import CliRunner
         from specify_cli import app
 
@@ -353,17 +353,15 @@ class YamlIntegrationTests:
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0
-        ext_cfg_path = project / ".specify" / "extensions" / "agent-context" / "agent-context-config.yml"
-        ext_cfg = yaml.safe_load(ext_cfg_path.read_text(encoding="utf-8")) if ext_cfg_path.exists() else {}
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
         i = get_integration(self.KEY)
-        assert ext_cfg.get("context_file") == i.context_file, (
-            f"Expected context_file={i.context_file!r}, got {ext_cfg.get('context_file')!r}"
+        assert opts.get("context_file") == i.context_file, (
+            f"Expected context_file={i.context_file!r}, got {opts.get('context_file')!r}"
         )
 
     # -- Complete file inventory ------------------------------------------
 
     COMMAND_STEMS = [
-        "agent-context.update",
         "analyze",
         "checklist",
         "clarify",
@@ -424,16 +422,6 @@ class YamlIntegrationTests:
         files.append(".specify/workflows/speckit/workflow.yml")
         files.append(".specify/workflows/workflow-registry.json")
 
-        # Bundled agent-context extension
-        files.append(".specify/extensions.yml")
-        files.append(".specify/extensions/.registry")
-        files.append(".specify/extensions/agent-context/README.md")
-        files.append(".specify/extensions/agent-context/agent-context-config.yml")
-        files.append(".specify/extensions/agent-context/commands/speckit.agent-context.update.md")
-        files.append(".specify/extensions/agent-context/extension.yml")
-        files.append(".specify/extensions/agent-context/scripts/bash/update-agent-context.sh")
-        files.append(".specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1")
-
         # Agent context file (if set)
         if i.context_file:
             files.append(i.context_file)

tests/integrations/test_integration_claude.py

@@ -8,7 +8,7 @@ from unittest.mock import patch
 import yaml
 
 from specify_cli.integrations import INTEGRATION_REGISTRY, get_integration
-from specify_cli.integrations.base import IntegrationBase, SkillsIntegration
+from specify_cli.integrations.base import IntegrationBase
 from specify_cli.integrations.claude import ARGUMENT_HINTS
 from specify_cli.integrations.manifest import IntegrationManifest
 
@@ -487,8 +487,8 @@ class TestClaudeDisableModelInvocation:
         assert "disable-model-invocation" not in fm
         assert "user-invocable" not in fm
 
-    def test_skills_default_post_process_preserves_content_without_hooks(self, tmp_path):
-        """SkillsIntegration agents without an override preserve non-hook content."""
+    def test_skills_default_post_process_is_identity(self, tmp_path):
+        """SkillsIntegration agents without an override leave content unchanged."""
         # ``agy`` is a plain SkillsIntegration with no post-process override,
         # so it stands in for the base-class default behavior.
         agy = get_integration("agy")
@@ -505,7 +505,7 @@ class TestClaudeHookCommandNote:
         """Skills that have hook sections should get the normalization note."""
         i = get_integration("claude")
         m = IntegrationManifest("claude", tmp_path)
-        i.setup(tmp_path, m, script_type="sh")
+        created = i.setup(tmp_path, m, script_type="sh")
         specify_skill = tmp_path / ".claude/skills/speckit-specify/SKILL.md"
         assert specify_skill.exists()
         content = specify_skill.read_text(encoding="utf-8")
@@ -516,54 +516,35 @@ class TestClaudeHookCommandNote:
 
     def test_hook_note_not_in_skills_without_hooks(self, tmp_path):
         """Skills without hook sections should not get the note."""
+        from specify_cli.integrations.claude import ClaudeIntegration
+
         content = "---\nname: test\ndescription: test\n---\n\nNo hooks here.\n"
-        result = SkillsIntegration._inject_hook_command_note(content)
+        result = ClaudeIntegration._inject_hook_command_note(content)
         assert "replace dots" not in result
 
     def test_hook_note_idempotent(self, tmp_path):
         """Injecting the note twice should not duplicate it."""
+        from specify_cli.integrations.claude import ClaudeIntegration
+
         content = (
             "---\nname: test\n---\n\n"
             "- For each executable hook, output the following based on its flag:\n"
         )
-        once = SkillsIntegration._inject_hook_command_note(content)
-        twice = SkillsIntegration._inject_hook_command_note(once)
+        once = ClaudeIntegration._inject_hook_command_note(content)
+        twice = ClaudeIntegration._inject_hook_command_note(once)
         assert once == twice, "Hook note injection should be idempotent"
 
-    def test_hook_note_fills_missing_repeated_instructions(self, tmp_path):
-        """Already-noted hook sections should not suppress later sections."""
-        from specify_cli.integrations.base import _HOOK_COMMAND_NOTE
-
-        content = (
-            "---\nname: test\n---\n\n"
-            f"{_HOOK_COMMAND_NOTE}"
-            "- For each executable hook, output the following based on its flag:\n"
-            "\n"
-            "  - For each executable hook, output the following based on its flag:\n"
-        )
-        result = SkillsIntegration._inject_hook_command_note(content)
-        assert result.count("replace dots (`.`) with hyphens") == 2
-
-    def test_hook_note_not_suppressed_by_unrelated_phrase(self, tmp_path):
-        """Unrelated text should not trip the hook-note idempotence guard."""
-        content = (
-            "---\nname: test\n---\n\n"
-            "This paragraph says replace dots in a different context.\n"
-            "- For each executable hook, output the following based on its flag:\n"
-        )
-        result = SkillsIntegration._inject_hook_command_note(content)
-        assert "This paragraph says replace dots in a different context." in result
-        assert result.count("replace dots (`.`) with hyphens") == 1
-
     def test_hook_note_preserves_indentation(self, tmp_path):
         """The injected note should match the indentation of the target line."""
+        from specify_cli.integrations.claude import ClaudeIntegration
+
         content = (
             "---\nname: test\n---\n\n"
             "   - For each executable hook, output the following\n"
         )
-        result = SkillsIntegration._inject_hook_command_note(content)
+        result = ClaudeIntegration._inject_hook_command_note(content)
         lines = result.splitlines()
-        note_line = [line for line in lines if "replace dots" in line][0]
+        note_line = [l for l in lines if "replace dots" in l][0]
         assert note_line.startswith("   "), "Note should preserve indentation"
 
     def test_post_process_injects_all_claude_flags(self):

tests/integrations/test_integration_codex.py

@@ -71,34 +71,6 @@ class TestCodexHookCommandNote:
         twice = CodexIntegration._inject_hook_command_note(once)
         assert once == twice, "Hook note injection should be idempotent"
 
-    def test_hook_note_fills_missing_repeated_instructions(self):
-        """Already-noted hook sections should not suppress later sections."""
-        from specify_cli.integrations.base import _HOOK_COMMAND_NOTE
-        from specify_cli.integrations.codex import CodexIntegration
-
-        content = (
-            "---\nname: test\n---\n\n"
-            f"{_HOOK_COMMAND_NOTE}"
-            "- For each executable hook, output the following based on its flag:\n"
-            "\n"
-            "  - For each executable hook, output the following based on its flag:\n"
-        )
-        result = CodexIntegration._inject_hook_command_note(content)
-        assert result.count("replace dots (`.`) with hyphens") == 2
-
-    def test_hook_note_not_suppressed_by_unrelated_phrase(self):
-        """Unrelated text should not trip the hook-note idempotence guard."""
-        from specify_cli.integrations.codex import CodexIntegration
-
-        content = (
-            "---\nname: test\n---\n\n"
-            "This paragraph says replace dots in a different context.\n"
-            "- For each executable hook, output the following based on its flag:\n"
-        )
-        result = CodexIntegration._inject_hook_command_note(content)
-        assert "This paragraph says replace dots in a different context." in result
-        assert result.count("replace dots (`.`) with hyphens") == 1
-
     def test_hook_note_preserves_indentation(self):
         """The injected note should match the indentation of the target line."""
         from specify_cli.integrations.codex import CodexIntegration
@@ -109,7 +81,7 @@ class TestCodexHookCommandNote:
         )
         result = CodexIntegration._inject_hook_command_note(content)
         lines = result.splitlines()
-        note_line = [line for line in lines if "replace dots" in line][0]
+        note_line = [l for l in lines if "replace dots" in l][0]
         assert note_line.startswith("   "), "Note should preserve indentation"
 
     def test_hook_note_when_instruction_is_final_line_without_newline(self):
@@ -130,11 +102,11 @@ class TestCodexHookCommandNote:
         result = CodexIntegration._inject_hook_command_note(content)
         lines = result.splitlines()
         note_line_idx = next(
-            i for i, line in enumerate(lines) if "replace dots" in line
+            i for i, l in enumerate(lines) if "replace dots" in l
         )
         instruction_line_idx = next(
-            i for i, line in enumerate(lines)
-            if line.lstrip().startswith("- For each executable hook")
+            i for i, l in enumerate(lines)
+            if l.lstrip().startswith("- For each executable hook")
         )
         assert note_line_idx < instruction_line_idx, (
             "Note must appear before the instruction"

tests/integrations/test_integration_copilot.py

@@ -178,7 +178,6 @@ class TestCopilotIntegration:
         assert result.exit_code == 0
         actual = sorted(p.relative_to(project).as_posix() for p in project.rglob("*") if p.is_file())
         expected = sorted([
-            ".github/agents/speckit.agent-context.update.agent.md",
             ".github/agents/speckit.analyze.agent.md",
             ".github/agents/speckit.checklist.agent.md",
             ".github/agents/speckit.clarify.agent.md",
@@ -188,7 +187,6 @@ class TestCopilotIntegration:
             ".github/agents/speckit.specify.agent.md",
             ".github/agents/speckit.tasks.agent.md",
             ".github/agents/speckit.taskstoissues.agent.md",
-            ".github/prompts/speckit.agent-context.update.prompt.md",
             ".github/prompts/speckit.analyze.prompt.md",
             ".github/prompts/speckit.checklist.prompt.md",
             ".github/prompts/speckit.clarify.prompt.md",
@@ -200,14 +198,6 @@ class TestCopilotIntegration:
             ".github/prompts/speckit.taskstoissues.prompt.md",
             ".vscode/settings.json",
             ".github/copilot-instructions.md",
-            ".specify/extensions.yml",
-            ".specify/extensions/.registry",
-            ".specify/extensions/agent-context/README.md",
-            ".specify/extensions/agent-context/agent-context-config.yml",
-            ".specify/extensions/agent-context/commands/speckit.agent-context.update.md",
-            ".specify/extensions/agent-context/extension.yml",
-            ".specify/extensions/agent-context/scripts/bash/update-agent-context.sh",
-            ".specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1",
             ".specify/integration.json",
             ".specify/init-options.json",
             ".specify/integrations/copilot.manifest.json",
@@ -248,7 +238,6 @@ class TestCopilotIntegration:
         assert result.exit_code == 0
         actual = sorted(p.relative_to(project).as_posix() for p in project.rglob("*") if p.is_file())
         expected = sorted([
-            ".github/agents/speckit.agent-context.update.agent.md",
             ".github/agents/speckit.analyze.agent.md",
             ".github/agents/speckit.checklist.agent.md",
             ".github/agents/speckit.clarify.agent.md",
@@ -258,7 +247,6 @@ class TestCopilotIntegration:
             ".github/agents/speckit.specify.agent.md",
             ".github/agents/speckit.tasks.agent.md",
             ".github/agents/speckit.taskstoissues.agent.md",
-            ".github/prompts/speckit.agent-context.update.prompt.md",
             ".github/prompts/speckit.analyze.prompt.md",
             ".github/prompts/speckit.checklist.prompt.md",
             ".github/prompts/speckit.clarify.prompt.md",
@@ -270,14 +258,6 @@ class TestCopilotIntegration:
             ".github/prompts/speckit.taskstoissues.prompt.md",
             ".vscode/settings.json",
             ".github/copilot-instructions.md",
-            ".specify/extensions.yml",
-            ".specify/extensions/.registry",
-            ".specify/extensions/agent-context/README.md",
-            ".specify/extensions/agent-context/agent-context-config.yml",
-            ".specify/extensions/agent-context/commands/speckit.agent-context.update.md",
-            ".specify/extensions/agent-context/extension.yml",
-            ".specify/extensions/agent-context/scripts/bash/update-agent-context.sh",
-            ".specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1",
             ".specify/integration.json",
             ".specify/init-options.json",
             ".specify/integrations/copilot.manifest.json",
@@ -424,20 +404,6 @@ class TestCopilotSkillsMode:
         updated = copilot.post_process_skill_content(content)
         assert "mode: speckit.plan" in updated
 
-    def test_post_process_skill_content_injects_hook_note(self):
-        """post_process_skill_content() should inject shared hook guidance."""
-        copilot = self._make_copilot()
-        content = (
-            "---\n"
-            'name: "speckit-specify"\n'
-            'description: "Specify workflow"\n'
-            "---\n"
-            "\n- For each executable hook, output the following\n"
-        )
-        updated = copilot.post_process_skill_content(content)
-        assert "replace dots" in updated
-        assert "mode: speckit.specify" in updated
-
     def test_post_process_idempotent(self):
         """post_process_skill_content() must be idempotent."""
         copilot = self._make_copilot()
@@ -468,14 +434,6 @@ class TestCopilotSkillsMode:
             stem = skill_dir_name.removeprefix("speckit-")
             assert fm["mode"] == f"speckit.{stem}"
 
-    def test_skills_hook_sections_explain_dotted_command_conversion(self, tmp_path):
-        """Generated skills with hook sections should include shared hook guidance."""
-        copilot = self._make_copilot()
-        self._setup_skills(copilot, tmp_path)
-        specify_skill = tmp_path / ".github" / "skills" / "speckit-specify" / "SKILL.md"
-        content = specify_skill.read_text(encoding="utf-8")
-        assert "replace dots" in content
-
     # -- Template processing ----------------------------------------------
 
     def test_skills_templates_are_processed(self, tmp_path):
@@ -644,20 +602,10 @@ class TestCopilotSkillsMode:
         assert result.exit_code == 0, f"init failed: {result.output}"
         actual = sorted(p.relative_to(project).as_posix() for p in project.rglob("*") if p.is_file())
         expected = sorted([
-            # Skill files (core + extension-installed agent-context command)
+            # Skill files
             *[f".github/skills/speckit-{cmd}/SKILL.md" for cmd in self._SKILL_COMMANDS],
-            ".github/skills/speckit-agent-context-update/SKILL.md",
             # Context file
             ".github/copilot-instructions.md",
-            # Bundled agent-context extension
-            ".specify/extensions.yml",
-            ".specify/extensions/.registry",
-            ".specify/extensions/agent-context/README.md",
-            ".specify/extensions/agent-context/agent-context-config.yml",
-            ".specify/extensions/agent-context/commands/speckit.agent-context.update.md",
-            ".specify/extensions/agent-context/extension.yml",
-            ".specify/extensions/agent-context/scripts/bash/update-agent-context.sh",
-            ".specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1",
             # Integration metadata
             ".specify/init-options.json",
             ".specify/integration.json",
@@ -776,4 +724,4 @@ class TestCopilotSkillsMode:
         # Must NOT show the dotted /speckit.plan form
         assert "/speckit.plan" not in result.output, (
             f"Should not show /speckit.plan in skills mode:\n{result.output}"
-        )
+        )

tests/integrations/test_integration_generic.py

@@ -195,39 +195,6 @@ class TestGenericIntegration:
         content = implement_file.read_text(encoding="utf-8")
         assert ".specify/memory/constitution.md" in content
 
-    @pytest.mark.parametrize(
-        "command_stem",
-        [
-            "analyze",
-            "checklist",
-            "clarify",
-            "implement",
-            "plan",
-            "specify",
-            "tasks",
-            "taskstoissues",
-        ],
-    )
-    def test_command_loads_constitution_context(self, tmp_path, command_stem):
-        """Every command except constitution must reference constitution.md."""
-        i = get_integration("generic")
-        m = IntegrationManifest("generic", tmp_path)
-        i.setup(tmp_path, m, parsed_options={"commands_dir": ".custom/cmds"})
-        cmd_file = tmp_path / ".custom" / "cmds" / f"speckit.{command_stem}.md"
-        assert cmd_file.exists(), f"Command file missing: {cmd_file.name}"
-        content = cmd_file.read_text(encoding="utf-8")
-        assert "constitution.md" in content, (
-            f"speckit.{command_stem}.md must reference constitution.md"
-        )
-
-    def test_constitution_command_exists(self, tmp_path):
-        """The constitution command itself must exist but is not required to load itself."""
-        i = get_integration("generic")
-        m = IntegrationManifest("generic", tmp_path)
-        i.setup(tmp_path, m, parsed_options={"commands_dir": ".custom/cmds"})
-        cmd_file = tmp_path / ".custom" / "cmds" / "speckit.constitution.md"
-        assert cmd_file.exists()
-
     # -- CLI --------------------------------------------------------------
 
     def test_cli_generic_without_commands_dir_fails(self, tmp_path):
@@ -244,8 +211,8 @@ class TestGenericIntegration:
         assert result.exit_code != 0
 
     def test_init_options_includes_context_file(self, tmp_path):
-        """agent-context extension config must include context_file for the generic integration."""
-        import yaml
+        """init-options.json must include context_file for the generic integration."""
+        import json
         from typer.testing import CliRunner
         from specify_cli import app
 
@@ -262,9 +229,8 @@ class TestGenericIntegration:
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0
-        ext_cfg_path = project / ".specify" / "extensions" / "agent-context" / "agent-context-config.yml"
-        ext_cfg = yaml.safe_load(ext_cfg_path.read_text(encoding="utf-8")) if ext_cfg_path.exists() else {}
-        assert ext_cfg.get("context_file") == "AGENTS.md"
+        opts = json.loads((project / ".specify" / "init-options.json").read_text())
+        assert opts.get("context_file") == "AGENTS.md"
 
     def test_complete_file_inventory_sh(self, tmp_path):
         """Every file produced by specify init --integration generic --ai-commands-dir ... --script sh."""
@@ -299,14 +265,6 @@ class TestGenericIntegration:
             ".myagent/commands/speckit.specify.md",
             ".myagent/commands/speckit.tasks.md",
             ".myagent/commands/speckit.taskstoissues.md",
-            ".specify/extensions.yml",
-            ".specify/extensions/.registry",
-            ".specify/extensions/agent-context/README.md",
-            ".specify/extensions/agent-context/agent-context-config.yml",
-            ".specify/extensions/agent-context/commands/speckit.agent-context.update.md",
-            ".specify/extensions/agent-context/extension.yml",
-            ".specify/extensions/agent-context/scripts/bash/update-agent-context.sh",
-            ".specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1",
             ".specify/init-options.json",
             ".specify/integration.json",
             ".specify/integrations/generic.manifest.json",
@@ -363,14 +321,6 @@ class TestGenericIntegration:
             ".myagent/commands/speckit.specify.md",
             ".myagent/commands/speckit.tasks.md",
             ".myagent/commands/speckit.taskstoissues.md",
-            ".specify/extensions.yml",
-            ".specify/extensions/.registry",
-            ".specify/extensions/agent-context/README.md",
-            ".specify/extensions/agent-context/agent-context-config.yml",
-            ".specify/extensions/agent-context/commands/speckit.agent-context.update.md",
-            ".specify/extensions/agent-context/extension.yml",
-            ".specify/extensions/agent-context/scripts/bash/update-agent-context.sh",
-            ".specify/extensions/agent-context/scripts/powershell/update-agent-context.ps1",
             ".specify/init-options.json",
             ".specify/integration.json",
             ".specify/integrations/generic.manifest.json",

tests/integrations/test_integration_hermes.py

@@ -1,362 +0,0 @@
-"""Tests for HermesIntegration.
-
-Hermes is special among SkillsIntegration subclasses: it writes skills
-to ``~/.hermes/skills/`` (global) rather than the project-local
-``.hermes/skills/`` directory.  A project-local marker (empty directory)
-is created so extension commands (e.g. git) can detect Hermes.
-
-All tests that touch ``~/.hermes/`` use ``monkeypatch`` to isolate
-``Path.home()`` to a temp directory so the test suite is hermetic and
-non-destructive to a developer's real Hermes installation.
-"""
-
-from pathlib import Path
-
-from specify_cli.integrations import get_integration
-from specify_cli.integrations.manifest import IntegrationManifest
-
-from .test_integration_base_skills import SkillsIntegrationTests
-
-
-def _fake_home(tmp_path: Path) -> Path:
-    """Create and return an isolated home directory under *tmp_path*."""
-    home = tmp_path / "home"
-    home.mkdir(exist_ok=True)
-    return home
-
-
-class TestHermesIntegration(SkillsIntegrationTests):
-    KEY = "hermes"
-    FOLDER = ".hermes/"
-    COMMANDS_SUBDIR = "skills"
-    REGISTRAR_DIR = "~/.hermes/skills"
-    CONTEXT_FILE = "AGENTS.md"
-
-    # -- Hermes-specific setup: skills go to ~/.hermes/skills/ -------------
-
-    def test_setup_writes_to_global_skills_dir(self, tmp_path, monkeypatch):
-        """Skills are written to ~/.hermes/skills/, not project-local."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
-        skill_files = [f for f in created if "scripts" not in f.parts]
-
-        assert len(skill_files) > 0, "No skill files were created"
-        for f in skill_files:
-            # Every skill file should be under ~/.hermes/skills/speckit-*/
-            expected_prefix = str(home / ".hermes" / "skills")
-            assert str(f).startswith(expected_prefix), (
-                f"{f} is not under ~/.hermes/skills/"
-            )
-
-    def test_local_marker_dir_created(self, tmp_path, monkeypatch):
-        """Project-local .hermes/skills/ should exist but be empty."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        i.setup(tmp_path, m)
-        marker = tmp_path / ".hermes" / "skills"
-        assert marker.is_dir(), "Marker directory was not created"
-        # Should be empty (no SKILL.md files)
-        children = list(marker.iterdir())
-        assert children == [], f"Marker directory should be empty, got: {children}"
-
-    # -- Override shared tests that assume project-local skills ------------
-
-    def test_setup_writes_to_correct_directory(self, tmp_path, monkeypatch):
-        """Override: Hermes writes to global, not project-local."""
-        self.test_setup_writes_to_global_skills_dir(tmp_path, monkeypatch)
-
-    def test_plan_references_correct_context_file(self, tmp_path, monkeypatch):
-        """Plan skill goes to global dir, but we check it still references AGENTS.md."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        i = get_integration(self.KEY)
-        if not i.context_file:
-            return
-        m = IntegrationManifest(self.KEY, tmp_path)
-        i.setup(tmp_path, m)
-        # Find the plan skill in global ~/.hermes/skills/
-        plan_file = home / ".hermes" / "skills" / "speckit-plan" / "SKILL.md"
-        assert plan_file.exists(), f"Plan skill {plan_file} not created globally"
-        content = plan_file.read_text(encoding="utf-8")
-        assert i.context_file in content, (
-            f"Plan skill should reference {i.context_file!r} but it was not found"
-        )
-        assert "__CONTEXT_FILE__" not in content, (
-            "Plan skill has unprocessed __CONTEXT_FILE__ placeholder"
-        )
-
-    def test_all_files_tracked_in_manifest(self, tmp_path, monkeypatch):
-        """Override: Hermes does not track skills in the project manifest
-        since they live globally.  Only project-local files (scripts,
-        templates, context) are tracked."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
-        for f in created:
-            # Global files (in ~/.hermes/) are not tracked in manifest
-            if str(f).startswith(str(home)):
-                continue
-            rel = f.resolve().relative_to(tmp_path.resolve()).as_posix()
-            assert rel in m.files, f"{rel} not tracked in manifest"
-
-    def test_install_uninstall_roundtrip(self, tmp_path, monkeypatch):
-        """Override: Hermes uninstall removes global skills + local marker."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.install(tmp_path, m)
-        assert len(created) > 0
-        m.save()
-        # All SKILL.md files should exist globally
-        for f in created:
-            if "SKILL.md" in str(f):
-                assert f.exists(), f"{f} does not exist"
-        # Global skills are removed on teardown without needing force
-        removed, skipped = i.teardown(tmp_path, m, force=False)
-        for f in created:
-            if "SKILL.md" in str(f):
-                assert not f.exists(), f"{f} should have been removed"
-        # Local marker should be gone
-        assert not (tmp_path / ".hermes" / "skills").exists()
-
-    def test_modified_file_survives_uninstall(self, tmp_path, monkeypatch):
-        """Override: Hermes global skills are ALWAYS removed on uninstall
-        (they live outside the project root and aren't hash-tracked in the
-        manifest), so a modified global skill is still removed — matching
-        the standard behaviour where all integration files are cleaned up."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.install(tmp_path, m)
-        m.save()
-        # Pick a global skill file
-        skill_files = [f for f in created if "SKILL.md" in str(f)]
-        assert len(skill_files) > 0
-        modified_file = skill_files[0]
-        modified_file.write_text("user modified this", encoding="utf-8")
-        removed, skipped = i.uninstall(tmp_path, m)
-        assert not modified_file.exists(), (
-            "Modified global skill should be removed on teardown (standard behaviour)"
-        )
-
-    def test_modified_global_skill_removed_on_teardown(self, tmp_path, monkeypatch):
-        """Override: Hermes global skills are removed on uninstall regardless
-        of the force flag, matching standard integration behaviour."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.install(tmp_path, m)
-        m.save()
-        # Pick a global skill file
-        skill_files = [f for f in created if "SKILL.md" in str(f)]
-        assert len(skill_files) > 0
-        modified_file = skill_files[0]
-        modified_file.write_text("user modified this", encoding="utf-8")
-        # Global skills are removed on teardown regardless of force flag
-        removed, skipped = i.teardown(tmp_path, m, force=False)
-        assert not modified_file.exists(), (
-            "Modified global skill should be removed on teardown (standard behaviour)"
-        )
-
-    def test_pre_existing_skills_not_removed(self, tmp_path, monkeypatch):
-        """Pre-existing non-speckit global skills should survive Hermes uninstall."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        i = get_integration(self.KEY)
-        # Create a foreign skill in the global dir first
-        global_skills_dir = i._hermes_home_skills_dir()
-        foreign_dir = global_skills_dir / "other-tool"
-        foreign_dir.mkdir(parents=True, exist_ok=True)
-        (foreign_dir / "SKILL.md").write_text("# Foreign skill\n")
-
-        m = IntegrationManifest(self.KEY, tmp_path)
-        i.setup(tmp_path, m)
-
-        # Run teardown to verify foreign skill survives uninstall
-        i.teardown(tmp_path, m)
-
-        assert (foreign_dir / "SKILL.md").exists(), (
-            "Foreign skill was removed by teardown"
-        )
-
-    def test_hook_sections_explain_dotted_command_conversion(self, tmp_path, monkeypatch):
-        """Override: Hermes skills live in global ~/.hermes/skills/."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        i.setup(tmp_path, m)
-        specify_skill = home / ".hermes" / "skills" / "speckit-specify" / "SKILL.md"
-        assert specify_skill.exists()
-        content = specify_skill.read_text(encoding="utf-8")
-        assert "replace dots" in content, (
-            "speckit-specify should explain dotted hook command conversion"
-        )
-        assert content.count("replace dots") == content.count(
-            "- For each executable hook, output the following"
-        )
-
-    def test_complete_file_inventory_sh(self, tmp_path, monkeypatch):
-        """Override: Hermes init produces no local SKILL.md files,
-        only the empty .hermes/skills/ marker."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        project = tmp_path / f"inventory-sh-{self.KEY}"
-        project.mkdir()
-        old_cwd = Path.cwd()
-        import os
-        try:
-            os.chdir(project)
-            result = CliRunner().invoke(app, [
-                "init", "--here", "--integration", self.KEY,
-                "--script", "sh", "--no-git", "--ignore-agent-tools",
-            ], catch_exceptions=False)
-        finally:
-            os.chdir(old_cwd)
-        assert result.exit_code == 0, f"init failed: {result.output}"
-        actual = sorted(
-            p.relative_to(project).as_posix()
-            for p in project.rglob("*") if p.is_file()
-        )
-        # Ensure no core .hermes/skills/speckit-*/SKILL.md in project dir
-        # (extension-installed skills like agent-context-update may appear)
-        hermes_skill_files = [
-            f for f in actual
-            if f.startswith(".hermes/skills/speckit-")
-            and "agent-context" not in f
-        ]
-        assert hermes_skill_files == [], (
-            f"Expected no local core SKILL.md files, found: {hermes_skill_files}"
-        )
-        # Ensure the marker exists (empty dir won't appear in file listing)
-        assert (project / ".hermes" / "skills").is_dir()
-
-    def test_complete_file_inventory_ps(self, tmp_path, monkeypatch):
-        """Override: Same as sh variant but for PowerShell script type."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        project = tmp_path / f"inventory-ps-{self.KEY}"
-        project.mkdir()
-        old_cwd = Path.cwd()
-        import os
-        try:
-            os.chdir(project)
-            result = CliRunner().invoke(app, [
-                "init", "--here", "--integration", self.KEY,
-                "--script", "ps", "--no-git", "--ignore-agent-tools",
-            ], catch_exceptions=False)
-        finally:
-            os.chdir(old_cwd)
-        assert result.exit_code == 0, f"init failed: {result.output}"
-        actual = sorted(
-            p.relative_to(project).as_posix()
-            for p in project.rglob("*") if p.is_file()
-        )
-        # Ensure no core .hermes/skills/speckit-*/SKILL.md in project dir
-        # (extension-installed skills like agent-context-update may appear)
-        hermes_skill_files = [
-            f for f in actual
-            if f.startswith(".hermes/skills/speckit-")
-            and "agent-context" not in f
-        ]
-        assert hermes_skill_files == [], (
-            f"Expected no local core SKILL.md files, found: {hermes_skill_files}"
-        )
-        assert (project / ".hermes" / "skills").is_dir()
-
-    def test_install_uninstall_cleanup(self, tmp_path, monkeypatch):
-        """Verify global skills are cleaned and local marker is removed."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        i = get_integration(self.KEY)
-        m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
-
-        # Verify global skills exist
-        global_skills = [
-            f for f in created
-            if "SKILL.md" in str(f)
-            and str(f).startswith(str(home / ".hermes"))
-        ]
-        assert len(global_skills) > 0
-        for f in global_skills:
-            assert f.exists()
-
-        # Verify local marker exists
-        assert (tmp_path / ".hermes" / "skills").is_dir()
-
-        # Teardown — global skills removed without needing force=True
-        removed, skipped = i.teardown(tmp_path, m, force=False)
-
-        # Global skills removed
-        for f in global_skills:
-            assert not f.exists(), f"{f} should have been removed"
-
-        # Local marker removed
-        assert not (tmp_path / ".hermes" / "skills").exists(), (
-            "Local marker should be removed on teardown"
-        )
-
-
-class TestHermesAutoPromote:
-    """--ai hermes auto-promotes to integration path."""
-
-    def test_ai_hermes_without_ai_skills_auto_promotes(self, tmp_path, monkeypatch):
-        """--ai hermes should work the same as --integration hermes,
-        creating global skills and a local marker."""
-        home = _fake_home(tmp_path)
-        monkeypatch.setattr(Path, "home", lambda: home)
-
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        runner = CliRunner()
-        target = tmp_path / "test-proj"
-        result = runner.invoke(app, [
-            "init", str(target),
-            "--ai", "hermes",
-            "--no-git",
-            "--ignore-agent-tools",
-            "--script", "sh",
-        ])
-
-        assert result.exit_code == 0, f"init --ai hermes failed: {result.output}"
-        # Skills should be in global ~/.hermes/skills/
-        assert (home / ".hermes" / "skills" / "speckit-plan" / "SKILL.md").exists()
-        # Local marker should exist
-        assert (target / ".hermes" / "skills").is_dir()
-        # No core SKILL.md files in project-local dir
-        # (extension-installed skills like agent-context-update may appear)
-        local_skills = [
-            d for d in (target / ".hermes" / "skills").iterdir()
-            if "agent-context" not in d.name
-        ]
-        assert local_skills == [], f"Local skills dir should be empty, got: {local_skills}"

tests/integrations/test_integration_subcommand.py

@@ -255,7 +255,7 @@ class TestIntegrationInstall:
         assert updated["speckit_version"] == "0.8.11"
         assert updated["integration"] == "claude"
         assert updated["ai"] == "claude"
-        assert "context_file" not in updated
+        assert updated["context_file"] == "CLAUDE.md"
 
     def test_install_additional_preserves_shared_manifest(self, tmp_path):
         project = _init_project(tmp_path, "claude")
@@ -386,10 +386,6 @@ class TestIntegrationInstall:
         # Shared infrastructure should be present
         assert (project / ".specify" / "scripts").is_dir()
         assert (project / ".specify" / "templates").is_dir()
-        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
-        script_content = script.read_text(encoding="utf-8")
-        assert "/speckit-specify" in script_content
-        assert "/speckit.specify" not in script_content
 
 
 # ── uninstall ────────────────────────────────────────────────────────
@@ -518,9 +514,7 @@ class TestIntegrationUninstall:
     def test_uninstall_default_refreshes_templates_for_fallback(self, tmp_path):
         project = _init_project(tmp_path, "gemini")
         template = project / ".specify" / "templates" / "plan-template.md"
-        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
         assert "/speckit.plan" in template.read_text(encoding="utf-8")
-        assert "/speckit.plan" in script.read_text(encoding="utf-8")
 
         old_cwd = os.getcwd()
         try:
@@ -539,7 +533,6 @@ class TestIntegrationUninstall:
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
         assert data["integration"] == "claude"
         assert "/speckit-plan" in template.read_text(encoding="utf-8")
-        assert "/speckit-plan" in script.read_text(encoding="utf-8")
 
     def test_uninstall_preserves_shared_infra(self, tmp_path):
         """Shared scripts and templates are not removed by integration uninstall."""
@@ -600,9 +593,7 @@ class TestIntegrationUse:
     def test_use_refreshes_shared_templates_between_command_styles(self, tmp_path):
         project = _init_project(tmp_path, "claude")
         template = project / ".specify" / "templates" / "plan-template.md"
-        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
         assert "/speckit-plan" in template.read_text(encoding="utf-8")
-        assert "/speckit-plan" in script.read_text(encoding="utf-8")
 
         old_cwd = os.getcwd()
         try:
@@ -616,14 +607,10 @@ class TestIntegrationUse:
             use_gemini = runner.invoke(app, ["integration", "use", "gemini"], catch_exceptions=False)
             assert use_gemini.exit_code == 0, use_gemini.output
             assert "/speckit.plan" in template.read_text(encoding="utf-8")
-            assert "/speckit.plan" in script.read_text(encoding="utf-8")
-            assert "/speckit-plan" not in script.read_text(encoding="utf-8")
 
             use_claude = runner.invoke(app, ["integration", "use", "claude"], catch_exceptions=False)
             assert use_claude.exit_code == 0, use_claude.output
             assert "/speckit-plan" in template.read_text(encoding="utf-8")
-            assert "/speckit-plan" in script.read_text(encoding="utf-8")
-            assert "/speckit.plan" not in script.read_text(encoding="utf-8")
         finally:
             os.chdir(old_cwd)
 
@@ -643,8 +630,6 @@ class TestIntegrationUse:
 
             use_gemini = runner.invoke(app, ["integration", "use", "gemini"], catch_exceptions=False)
             assert use_gemini.exit_code == 0, use_gemini.output
-            normalized = " ".join(use_gemini.output.split())
-            assert "specify integration use gemini --force" in normalized
             assert template.read_text(encoding="utf-8") == "custom template with /speckit-plan\n"
 
             force_use = runner.invoke(app, [
@@ -659,7 +644,8 @@ class TestIntegrationUse:
         assert "/speckit.plan" in updated
         assert "custom template" not in updated
 
-    def test_use_does_not_persist_default_when_shared_infra_refresh_fails(self, tmp_path, monkeypatch):
+    @pytest.mark.skipif(not hasattr(os, "symlink"), reason="symlinks are unavailable")
+    def test_use_does_not_persist_default_when_template_refresh_fails(self, tmp_path):
         project = _init_project(tmp_path, "claude")
         int_json = project / ".specify" / "integration.json"
         init_options = project / ".specify" / "init-options.json"
@@ -675,12 +661,12 @@ class TestIntegrationUse:
 
             before_state = json.loads(int_json.read_text(encoding="utf-8"))
             before_options = json.loads(init_options.read_text(encoding="utf-8"))
-            import specify_cli
 
-            def fail_refresh(*args, **kwargs):
-                raise ValueError("refuse refresh")
-
-            monkeypatch.setattr(specify_cli, "_install_shared_infra", fail_refresh)
+            outside = tmp_path / "outside-template.md"
+            outside.write_text("# outside\n", encoding="utf-8")
+            template = project / ".specify" / "templates" / "plan-template.md"
+            template.unlink()
+            os.symlink(outside, template)
 
             result = runner.invoke(app, [
                 "integration", "use", "codex",
@@ -690,9 +676,10 @@ class TestIntegrationUse:
             os.chdir(old_cwd)
 
         assert result.exit_code != 0
-        assert "Failed to refresh shared infrastructure" in result.output
+        assert "Failed to refresh shared templates" in result.output
         assert json.loads(int_json.read_text(encoding="utf-8")) == before_state
         assert json.loads(init_options.read_text(encoding="utf-8")) == before_options
+        assert outside.read_text(encoding="utf-8") == "# outside\n"
 
 
 # ── switch ───────────────────────────────────────────────────────────
@@ -750,9 +737,7 @@ class TestIntegrationSwitch:
     def test_switch_same_force_refreshes_shared_templates(self, tmp_path):
         project = _init_project(tmp_path, "claude")
         template = project / ".specify" / "templates" / "plan-template.md"
-        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
         template.write_text("# custom shared template\n", encoding="utf-8")
-        script.write_text("# custom shared script\n", encoding="utf-8")
 
         old_cwd = os.getcwd()
         try:
@@ -764,10 +749,8 @@ class TestIntegrationSwitch:
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0, result.output
-        assert "shared infrastructure refreshed" in result.output
-        assert "managed shared infrastructure refreshed" not in result.output
+        assert "managed shared templates refreshed" in result.output
         assert "/speckit-plan" in template.read_text(encoding="utf-8")
-        assert "/speckit-plan" in script.read_text(encoding="utf-8")
 
     def test_switch_installed_target_rejects_integration_options(self, tmp_path):
         project = _init_project(tmp_path, "claude")
@@ -796,8 +779,6 @@ class TestIntegrationSwitch:
         project = _init_project(tmp_path, "claude")
         # Verify claude files exist (claude uses skills)
         assert (project / ".claude" / "skills" / "speckit-plan" / "SKILL.md").exists()
-        shared_script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
-        assert "/speckit-specify" in shared_script.read_text(encoding="utf-8")
 
         old_cwd = os.getcwd()
         try:
@@ -816,8 +797,6 @@ class TestIntegrationSwitch:
 
         # New copilot files created
         assert (project / ".github" / "agents" / "speckit.plan.agent.md").exists()
-        assert "/speckit.specify" in shared_script.read_text(encoding="utf-8")
-        assert "/speckit-specify" not in shared_script.read_text(encoding="utf-8")
 
         # integration.json updated
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
@@ -959,13 +938,12 @@ class TestIntegrationSwitch:
         assert "claude" not in git_meta["registered_commands"]
         assert "opencode" not in git_meta["registered_commands"]
 
-    def test_switch_refreshes_managed_shared_script_refs(self, tmp_path):
-        """Switching refreshes managed shared scripts to the target command style."""
+    def test_switch_preserves_shared_infra(self, tmp_path):
+        """Switching preserves shared scripts, templates, and memory."""
         project = _init_project(tmp_path, "claude")
         shared_script = project / ".specify" / "scripts" / "bash" / "common.sh"
         assert shared_script.exists()
         shared_content = shared_script.read_text(encoding="utf-8")
-        assert "/speckit-plan" in shared_content
 
         old_cwd = os.getcwd()
         try:
@@ -978,10 +956,9 @@ class TestIntegrationSwitch:
             os.chdir(old_cwd)
         assert result.exit_code == 0
 
+        # Shared infra untouched
         assert shared_script.exists()
-        updated = shared_script.read_text(encoding="utf-8")
-        assert "/speckit.plan" in updated
-        assert "/speckit-plan" not in updated
+        assert shared_script.read_text(encoding="utf-8") == shared_content
 
     def test_switch_refreshes_stale_managed_shared_infra(self, tmp_path):
         """Regression for #2293: stale managed shared scripts get refreshed on switch."""
@@ -989,7 +966,7 @@ class TestIntegrationSwitch:
 
         project = _init_project(tmp_path, "claude")
         shared_script = project / ".specify" / "scripts" / "bash" / "common.sh"
-        assert "/speckit-plan" in shared_script.read_text(encoding="utf-8")
+        bundled_bytes = shared_script.read_bytes()
 
         # Simulate a stale vendored script: write truncated content as bytes
         # (write_text would translate \n→\r\n on Windows and break the hash)
@@ -1016,11 +993,8 @@ class TestIntegrationSwitch:
             os.chdir(old_cwd)
         assert result.exit_code == 0
 
-        # Stale managed file should be replaced by the target integration's rendered version.
-        updated = shared_script.read_text(encoding="utf-8")
-        assert "# stale vendored copy" not in updated
-        assert "/speckit.plan" in updated
-        assert "/speckit-plan" not in updated
+        # Stale managed file should be replaced by the bundled version
+        assert shared_script.read_bytes() == bundled_bytes
 
     def test_switch_preserves_user_customized_shared_infra(self, tmp_path):
         """User customizations (hash divergence from manifest) survive switch without --refresh-shared-infra."""
@@ -1050,11 +1024,10 @@ class TestIntegrationSwitch:
         """--refresh-shared-infra explicitly overwrites user customizations on switch."""
         project = _init_project(tmp_path, "claude")
         shared_script = project / ".specify" / "scripts" / "bash" / "common.sh"
-        assert "/speckit-plan" in shared_script.read_text(encoding="utf-8")
-        rendered_bytes = shared_script.read_bytes()
+        bundled_bytes = shared_script.read_bytes()
 
         # User customization (hash diverges from manifest)
-        custom_bytes = rendered_bytes + b"\n# user customization\n"
+        custom_bytes = bundled_bytes + b"\n# user customization\n"
         shared_script.write_bytes(custom_bytes)
 
         old_cwd = os.getcwd()
@@ -1068,11 +1041,8 @@ class TestIntegrationSwitch:
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0
-        # Customization is overwritten with the target integration's rendered version.
-        updated = shared_script.read_text(encoding="utf-8")
-        assert "# user customization" not in updated
-        assert "/speckit.plan" in updated
-        assert "/speckit-plan" not in updated
+        # Customization is overwritten with the bundled version
+        assert shared_script.read_bytes() == bundled_bytes
 
     def test_switch_skips_symlinked_parent_directory(self, tmp_path):
         """Regression: if .specify/scripts/bash is a symlink, switch must not write through it.
@@ -1250,9 +1220,9 @@ class TestIntegrationUpgrade:
         assert updated["speckit_version"] == "0.8.11"
         assert updated["integration"] == "gemini"
         assert updated["ai"] == "gemini"
-        assert "context_file" not in updated
+        assert updated["context_file"] == "GEMINI.md"
 
-    def test_upgrade_does_not_persist_state_when_shared_infra_refresh_fails(self, tmp_path, monkeypatch):
+    def test_upgrade_does_not_persist_state_when_template_refresh_fails(self, tmp_path, monkeypatch):
         project = _init_project(tmp_path, "claude")
         int_json = project / ".specify" / "integration.json"
         init_options = project / ".specify" / "init-options.json"
@@ -1264,16 +1234,10 @@ class TestIntegrationUpgrade:
 
         import specify_cli
 
-        real_install_shared_infra = specify_cli._install_shared_infra
-        calls = {"count": 0}
-
         def fail_refresh(*args, **kwargs):
-            calls["count"] += 1
-            if calls["count"] == 2:
-                raise ValueError("refuse refresh")
-            return real_install_shared_infra(*args, **kwargs)
+            raise ValueError("refuse refresh")
 
-        monkeypatch.setattr(specify_cli, "_install_shared_infra", fail_refresh)
+        monkeypatch.setattr(specify_cli, "_refresh_shared_templates", fail_refresh)
 
         result = _run_in_project(project, [
             "integration", "upgrade", "claude",
@@ -1281,40 +1245,15 @@ class TestIntegrationUpgrade:
         ])
 
         assert result.exit_code != 0
-        assert "Failed to refresh shared infrastructure" in result.output
+        assert "Failed to refresh shared templates" in result.output
         assert json.loads(int_json.read_text(encoding="utf-8")) == before_state
         assert json.loads(init_options.read_text(encoding="utf-8")) == before_options
         assert manifest_path.read_text(encoding="utf-8") == before_manifest
 
-    def test_upgrade_default_refreshes_shared_script_refs_for_option_separator_change(self, tmp_path):
-        project = _init_project(tmp_path, "copilot")
-        template = project / ".specify" / "templates" / "plan-template.md"
-        managed_script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
-        customized_script = project / ".specify" / "scripts" / "bash" / "setup-tasks.sh"
-
-        assert "/speckit.plan" in template.read_text(encoding="utf-8")
-        assert "/speckit.specify" in managed_script.read_text(encoding="utf-8")
-        customized_before = customized_script.read_text(encoding="utf-8") + "\n# user customization\n"
-        customized_script.write_text(customized_before, encoding="utf-8")
-
-        result = _run_in_project(project, [
-            "integration", "upgrade", "copilot",
-            "--integration-options", "--skills",
-        ])
-
-        assert result.exit_code == 0, result.output
-        assert "/speckit-plan" in template.read_text(encoding="utf-8")
-        managed_content = managed_script.read_text(encoding="utf-8")
-        assert "/speckit-specify" in managed_content
-        assert "/speckit.specify" not in managed_content
-        assert customized_script.read_text(encoding="utf-8") == customized_before
-
     def test_upgrade_non_default_keeps_default_template_invocations(self, tmp_path):
         project = _init_project(tmp_path, "gemini")
         template = project / ".specify" / "templates" / "plan-template.md"
-        script = project / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
         assert "/speckit.plan" in template.read_text(encoding="utf-8")
-        assert "/speckit.plan" in script.read_text(encoding="utf-8")
 
         old_cwd = os.getcwd()
         try:
@@ -1337,8 +1276,6 @@ class TestIntegrationUpgrade:
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
         assert data["integration"] == "gemini"
         assert "/speckit.plan" in template.read_text(encoding="utf-8")
-        assert "/speckit.plan" in script.read_text(encoding="utf-8")
-        assert "/speckit-plan" not in script.read_text(encoding="utf-8")
 
     def test_upgrade_migrates_opencode_legacy_dir(self, tmp_path):
         """Upgrade moves OpenCode commands from .opencode/command/ to .opencode/commands/."""
@@ -1376,16 +1313,11 @@ class TestIntegrationUpgrade:
         new_commands = sorted(canonical.glob("speckit.*.md"))
         assert len(new_commands) > 0, "Commands should exist in .opencode/commands/"
 
-        # Stale files removed from legacy dir (extension-installed commands
-        # like agent-context.update may still appear — only check the original
-        # core command stems that should have been migrated).
-        core_remaining = [
-            f for f in legacy.glob("speckit.*.md")
-            if "agent-context" not in f.name
-        ]
-        assert len(core_remaining) == 0, (
-            f"Legacy .opencode/command/ should have no core speckit files after upgrade, "
-            f"found: {[f.name for f in core_remaining]}"
+        # Stale files removed from legacy dir
+        remaining = list(legacy.glob("speckit.*.md"))
+        assert len(remaining) == 0, (
+            f"Legacy .opencode/command/ should have no speckit files after upgrade, "
+            f"found: {[f.name for f in remaining]}"
         )
 
 

tests/test_extension_skills.py

@@ -11,7 +11,6 @@ Tests cover:
 """
 
 import json
-import os
 import pytest
 import tempfile
 import shutil
@@ -117,18 +116,6 @@ def _create_extension_dir(temp_dir: Path, ext_id: str = "test-ext") -> Path:
     return ext_dir
 
 
-def _can_create_symlink(temp_dir: Path) -> bool:
-    """Return True when the current platform/user can create file symlinks."""
-    target = temp_dir / "symlink-target.txt"
-    link = temp_dir / "symlink-link.txt"
-    target.write_text("ok", encoding="utf-8")
-    try:
-        os.symlink(target, link)
-    except OSError:
-        return False
-    return link.is_symlink()
-
-
 # ===== Fixtures =====
 
 @pytest.fixture
@@ -337,149 +324,6 @@ class TestExtensionSkillRegistration:
         # The pre-existing one should NOT be in registered_skills (it was skipped)
         assert "speckit-test-ext-hello" not in metadata["registered_skills"]
 
-    def test_dev_skill_symlink_refreshes_existing_cache(
-        self, skills_project, extension_dir, temp_dir
-    ):
-        """Dev-mode skill symlinks should refresh rendered cache content."""
-        if not _can_create_symlink(temp_dir):
-            pytest.skip("Current platform/user cannot create symlinks")
-
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = ExtensionManifest(extension_dir / "extension.yml")
-
-        manager._register_extension_skills(
-            manifest,
-            extension_dir,
-            link_outputs=True,
-        )
-
-        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
-        assert skill_file.is_symlink()
-        assert "Run this to say hello." in skill_file.read_text(encoding="utf-8")
-
-        (extension_dir / "commands" / "hello.md").write_text(
-            "---\n"
-            "description: \"Updated test hello command\"\n"
-            "---\n"
-            "\n"
-            "# Hello Command\n"
-            "\n"
-            "Run this updated hello.\n"
-        )
-
-        written = manager._register_extension_skills(
-            manifest,
-            extension_dir,
-            link_outputs=True,
-        )
-
-        assert "speckit-test-ext-hello" in written
-        assert "Run this updated hello." in skill_file.read_text(encoding="utf-8")
-
-    def test_dev_skill_registration_falls_back_to_copy_when_symlink_fails(
-        self, skills_project, extension_dir, monkeypatch
-    ):
-        """Dev-mode skill registration works when Windows cannot create symlinks."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = ExtensionManifest(extension_dir / "extension.yml")
-
-        def raise_windows_symlink_error(target, link):
-            raise OSError("A required privilege is not held by the client")
-
-        monkeypatch.setattr(
-            "specify_cli.extensions.os.symlink", raise_windows_symlink_error
-        )
-
-        written = manager._register_extension_skills(
-            manifest,
-            extension_dir,
-            link_outputs=True,
-        )
-
-        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
-        assert "speckit-test-ext-hello" in written
-        assert skill_file.exists()
-        assert not skill_file.is_symlink()
-        assert "Run this to say hello." in skill_file.read_text(encoding="utf-8")
-        assert (
-            extension_dir
-            / ".specify-dev"
-            / "extension-skills"
-            / "speckit-test-ext-hello"
-            / "SKILL.md"
-        ).exists()
-
-    def test_dev_skill_registration_falls_back_to_copy_when_relpath_fails(
-        self, skills_project, extension_dir, monkeypatch
-    ):
-        """Dev-mode skill registration stays functional across Windows drive roots."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = ExtensionManifest(extension_dir / "extension.yml")
-
-        def raise_relpath_error(path, start=None):
-            raise ValueError("path is on mount 'D:', start on mount 'C:'")
-
-        monkeypatch.setattr(
-            "specify_cli.extensions.os.path.relpath", raise_relpath_error
-        )
-
-        written = manager._register_extension_skills(
-            manifest,
-            extension_dir,
-            link_outputs=True,
-        )
-
-        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
-        assert "speckit-test-ext-hello" in written
-        assert skill_file.exists()
-        assert not skill_file.is_symlink()
-        assert "Run this to say hello." in skill_file.read_text(encoding="utf-8")
-        assert (
-            extension_dir
-            / ".specify-dev"
-            / "extension-skills"
-            / "speckit-test-ext-hello"
-            / "SKILL.md"
-        ).exists()
-
-    def test_dev_skill_registration_falls_back_to_copy_when_cache_write_fails(
-        self, skills_project, extension_dir, monkeypatch
-    ):
-        """Dev-mode skill registration stays functional when the dev cache is unwritable."""
-        project_dir, skills_dir = skills_project
-        manager = ExtensionManager(project_dir)
-        manifest = ExtensionManifest(extension_dir / "extension.yml")
-        original_write_text = Path.write_text
-
-        def raise_cache_write_error(path, *args, **kwargs):
-            if ".specify-dev" in path.parts:
-                raise OSError("cache is not writable")
-            return original_write_text(path, *args, **kwargs)
-
-        monkeypatch.setattr(Path, "write_text", raise_cache_write_error)
-
-        written = manager._register_extension_skills(
-            manifest,
-            extension_dir,
-            link_outputs=True,
-        )
-
-        skill_file = skills_dir / "speckit-test-ext-hello" / "SKILL.md"
-        assert "speckit-test-ext-hello" in written
-        assert skill_file.exists()
-        assert not skill_file.is_symlink()
-        assert "Run this to say hello." in skill_file.read_text(encoding="utf-8")
-        assert not (
-            extension_dir
-            / ".specify-dev"
-            / "extension-skills"
-            / "speckit-test-ext-hello"
-            / "SKILL.md"
-        ).exists()
-
     def test_registered_skills_in_registry(self, skills_project, extension_dir):
         """Registry should contain registered_skills list."""
         project_dir, skills_dir = skills_project

tests/test_extensions.py

@@ -11,7 +11,6 @@ Tests cover:
 
 import pytest
 import json
-import os
 import platform
 import tempfile
 import shutil
@@ -37,18 +36,6 @@ from specify_cli.extensions import (
 )
 
 
-def can_create_symlink(tmp_path: Path) -> bool:
-    """Return True when the current platform/user can create file symlinks."""
-    target = tmp_path / "symlink-target.txt"
-    link = tmp_path / "symlink-link.txt"
-    target.write_text("ok", encoding="utf-8")
-    try:
-        os.symlink(target, link)
-    except OSError:
-        return False
-    return link.is_symlink()
-
-
 # ===== Fixtures =====
 
 @pytest.fixture
@@ -1735,168 +1722,6 @@ Run {SCRIPT}
         assert "description: Test hello command" in content
         assert "test-ext" in content
 
-    def test_dev_register_commands_symlinks_rendered_copilot_agent(
-        self, extension_dir, project_dir, temp_dir
-    ):
-        """Dev-mode registration should symlink agent files to rendered outputs."""
-        if not can_create_symlink(temp_dir):
-            pytest.skip("Current platform/user cannot create symlinks")
-
-        agents_dir = project_dir / ".github" / "agents"
-        agents_dir.mkdir(parents=True)
-
-        manifest = ExtensionManifest(extension_dir / "extension.yml")
-        registrar = CommandRegistrar()
-        registered = registrar.register_commands_for_agent(
-            "copilot",
-            manifest,
-            extension_dir,
-            project_dir,
-            link_outputs=True,
-        )
-
-        assert registered == ["speckit.test-ext.hello"]
-
-        cmd_file = agents_dir / "speckit.test-ext.hello.agent.md"
-        assert cmd_file.is_symlink()
-
-        target = cmd_file.resolve()
-        assert ".specify-dev" in target.parts
-        assert target.is_file()
-        assert "Extension: test-ext" in cmd_file.read_text(encoding="utf-8")
-
-    def test_dev_register_commands_falls_back_to_copy_when_symlink_fails(
-        self, extension_dir, project_dir, monkeypatch
-    ):
-        """Dev-mode registration stays functional when symlinks are unavailable."""
-        agents_dir = project_dir / ".github" / "agents"
-        agents_dir.mkdir(parents=True)
-
-        def raise_symlink_error(target, link):
-            raise OSError("symlink unavailable")
-
-        monkeypatch.setattr("specify_cli.agents.os.symlink", raise_symlink_error)
-
-        manifest = ExtensionManifest(extension_dir / "extension.yml")
-        registrar = CommandRegistrar()
-        registrar.register_commands_for_agent(
-            "copilot",
-            manifest,
-            extension_dir,
-            project_dir,
-            link_outputs=True,
-        )
-
-        cmd_file = agents_dir / "speckit.test-ext.hello.agent.md"
-        assert cmd_file.exists()
-        assert not cmd_file.is_symlink()
-        assert "Extension: test-ext" in cmd_file.read_text(encoding="utf-8")
-        assert (
-            extension_dir
-            / ".specify-dev"
-            / "agent-commands"
-            / "copilot"
-            / "speckit.test-ext.hello.agent.md"
-        ).exists()
-
-    def test_dev_register_commands_falls_back_to_copy_when_relpath_fails(
-        self, extension_dir, project_dir, monkeypatch
-    ):
-        """Dev-mode registration stays functional across Windows drive roots."""
-        agents_dir = project_dir / ".github" / "agents"
-        agents_dir.mkdir(parents=True)
-
-        def raise_relpath_error(path, start=None):
-            raise ValueError("path is on mount 'D:', start on mount 'C:'")
-
-        monkeypatch.setattr("specify_cli.agents.os.path.relpath", raise_relpath_error)
-
-        manifest = ExtensionManifest(extension_dir / "extension.yml")
-        registrar = CommandRegistrar()
-        registrar.register_commands_for_agent(
-            "copilot",
-            manifest,
-            extension_dir,
-            project_dir,
-            link_outputs=True,
-        )
-
-        cmd_file = agents_dir / "speckit.test-ext.hello.agent.md"
-        assert cmd_file.exists()
-        assert not cmd_file.is_symlink()
-        assert "Extension: test-ext" in cmd_file.read_text(encoding="utf-8")
-        assert (
-            extension_dir
-            / ".specify-dev"
-            / "agent-commands"
-            / "copilot"
-            / "speckit.test-ext.hello.agent.md"
-        ).exists()
-
-    def test_dev_register_commands_falls_back_to_copy_when_cache_write_fails(
-        self, extension_dir, project_dir, monkeypatch
-    ):
-        """Dev-mode registration stays functional when the dev cache is unwritable."""
-        agents_dir = project_dir / ".github" / "agents"
-        agents_dir.mkdir(parents=True)
-        original_write_text = Path.write_text
-
-        def raise_cache_write_error(path, *args, **kwargs):
-            if ".specify-dev" in path.parts:
-                raise OSError("cache is not writable")
-            return original_write_text(path, *args, **kwargs)
-
-        monkeypatch.setattr(Path, "write_text", raise_cache_write_error)
-
-        manifest = ExtensionManifest(extension_dir / "extension.yml")
-        registrar = CommandRegistrar()
-        registrar.register_commands_for_agent(
-            "copilot",
-            manifest,
-            extension_dir,
-            project_dir,
-            link_outputs=True,
-        )
-
-        cmd_file = agents_dir / "speckit.test-ext.hello.agent.md"
-        assert cmd_file.exists()
-        assert not cmd_file.is_symlink()
-        assert "Extension: test-ext" in cmd_file.read_text(encoding="utf-8")
-        assert not (
-            extension_dir
-            / ".specify-dev"
-            / "agent-commands"
-            / "copilot"
-            / "speckit.test-ext.hello.agent.md"
-        ).exists()
-
-    def test_dev_register_commands_rejects_cache_path_traversal(self, temp_dir):
-        """Dev-mode cache writes must stay inside the agent cache root."""
-        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
-
-        source_dir = temp_dir / "extension"
-        source_dir.mkdir()
-        commands_dir = temp_dir / "commands"
-        commands_dir.mkdir()
-
-        with pytest.raises(ValueError, match="escapes directory"):
-            AgentCommandRegistrar._write_registered_output(
-                commands_dir / "safe.md",
-                "content",
-                source_dir,
-                "copilot",
-                "../escaped",
-                ".md",
-                True,
-            )
-
-        assert not (
-            source_dir
-            / ".specify-dev"
-            / "agent-commands"
-            / "escaped.md"
-        ).exists()
-
     def test_copilot_companion_prompt_created(self, extension_dir, project_dir):
         """Test that companion .prompt.md files are created in .github/prompts/."""
         agents_dir = project_dir / ".github" / "agents"
@@ -3633,86 +3458,6 @@ class TestExtensionIgnore:
 class TestExtensionAddCLI:
     """CLI integration tests for extension add command."""
 
-    def test_add_dev_links_copilot_agent_when_supported(
-        self, extension_dir, project_dir, temp_dir
-    ):
-        """extension add --dev should link generated agent files when possible."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        (project_dir / ".github" / "agents").mkdir(parents=True)
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir):
-            result = runner.invoke(
-                app,
-                ["extension", "add", str(extension_dir), "--dev"],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 0, result.output
-
-        agent_file = (
-            project_dir
-            / ".github"
-            / "agents"
-            / "speckit.test-ext.hello.agent.md"
-        )
-        assert agent_file.exists()
-        if can_create_symlink(temp_dir):
-            assert agent_file.is_symlink()
-            assert ".specify-dev" in agent_file.resolve().parts
-        else:
-            assert not agent_file.is_symlink()
-
-    def test_add_dev_falls_back_to_copy_when_windows_symlinks_unavailable(
-        self, extension_dir, project_dir, monkeypatch
-    ):
-        """extension add --dev should work when Windows cannot create symlinks."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        (project_dir / ".github" / "agents").mkdir(parents=True)
-
-        def raise_windows_symlink_error(target, link):
-            raise OSError("A required privilege is not held by the client")
-
-        monkeypatch.setattr(
-            "specify_cli.agents.os.symlink", raise_windows_symlink_error
-        )
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir):
-            result = runner.invoke(
-                app,
-                ["extension", "add", str(extension_dir), "--dev"],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 0, result.output
-
-        agent_file = (
-            project_dir
-            / ".github"
-            / "agents"
-            / "speckit.test-ext.hello.agent.md"
-        )
-        assert agent_file.exists()
-        assert not agent_file.is_symlink()
-        assert "Extension: test-ext" in agent_file.read_text(encoding="utf-8")
-        assert (
-            project_dir
-            / ".specify"
-            / "extensions"
-            / "test-ext"
-            / ".specify-dev"
-            / "agent-commands"
-            / "copilot"
-            / "speckit.test-ext.hello.agent.md"
-        ).exists()
-
     def test_add_by_display_name_uses_resolved_id_for_download(self, tmp_path):
         """extension add by display name should use resolved ID for download_extension()."""
         from typer.testing import CliRunner
@@ -3807,67 +3552,6 @@ class TestExtensionAddCLI:
         assert "bundled with spec-kit" in result.output
         assert "reinstall" in result.output.lower()
 
-    def test_add_from_url_prompts_before_spinner(self, tmp_path):
-        """Confirm prompt for --from <url> must fire before the console.status spinner.
-
-        Regression test for #2783: typer.confirm() inside console.status()
-        was overwritten by the Rich spinner, making the command appear hung.
-        """
-        from typer.testing import CliRunner
-        from unittest.mock import patch, MagicMock
-        from specify_cli import app
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        call_order: list[str] = []
-
-        original_status = MagicMock()
-
-        def record_status(*args, **kwargs):
-            call_order.append("spinner")
-            return original_status
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch("specify_cli.console.status", side_effect=record_status), \
-             patch("typer.confirm", side_effect=lambda *a, **kw: (call_order.append("confirm"), False)[-1]):
-            result = runner.invoke(
-                app,
-                ["extension", "add", "my-ext", "--from", "https://example.com/ext.zip"],
-                catch_exceptions=True,
-            )
-
-        assert "confirm" in call_order, "confirm prompt was never called"
-        # The confirm must fire BEFORE the spinner is entered
-        if "spinner" in call_order:
-            assert call_order.index("confirm") < call_order.index("spinner"), \
-                f"confirm must precede spinner, got: {call_order}"
-        assert result.exit_code == 0  # user declined → clean exit
-
-    def test_add_from_url_cancel_exits_cleanly(self, tmp_path):
-        """Declining the --from <url> confirmation should exit with code 0."""
-        from typer.testing import CliRunner
-        from unittest.mock import patch
-        from specify_cli import app
-
-        project_dir = tmp_path / "test-project"
-        project_dir.mkdir()
-        (project_dir / ".specify").mkdir()
-
-        runner = CliRunner()
-        with patch.object(Path, "cwd", return_value=project_dir), \
-             patch("typer.confirm", return_value=False):
-            result = runner.invoke(
-                app,
-                ["extension", "add", "my-ext", "--from", "https://example.com/ext.zip"],
-                catch_exceptions=True,
-            )
-
-        assert result.exit_code == 0
-        assert "Cancelled" in result.output
-
 
 class TestDownloadExtensionBundled:
     """Tests for download_extension handling of bundled extensions."""
@@ -4060,20 +3744,13 @@ class TestExtensionUpdateCLI:
         ).read_text()
         assert restored_config_content == original_config_content
 
-    def test_update_failure_rolls_back_registry_hooks_and_commands(self, tmp_path, monkeypatch):
+    def test_update_failure_rolls_back_registry_hooks_and_commands(self, tmp_path):
         """Failed update should restore original registry, hooks, and command files."""
         from typer.testing import CliRunner
         from unittest.mock import patch
         from specify_cli import app
         import yaml
 
-        # Isolate home directory so Hermes' global ~/.hermes/skills/ doesn't
-        # interfere — without a real skills dir, Hermes is skipped during
-        # command registration, keeping the test focused on Claude/Codex/etc.
-        fake_home = tmp_path / "home"
-        fake_home.mkdir()
-        monkeypatch.setattr(Path, "home", lambda: fake_home)
-
         runner = CliRunner()
         project_dir = tmp_path / "project"
         project_dir.mkdir()
@@ -4095,9 +3772,7 @@ class TestExtensionUpdateCLI:
             if agent_name not in agent_registrar.AGENT_CONFIGS:
                 continue
             agent_cfg = agent_registrar.AGENT_CONFIGS[agent_name]
-            commands_dir = AgentRegistrar._resolve_agent_dir(
-                agent_name, agent_cfg, project_dir
-            )
+            commands_dir = project_dir / agent_cfg["dir"]
             for cmd_name in cmd_names:
                 output_name = AgentRegistrar._compute_output_name(agent_name, cmd_name, agent_cfg)
                 cmd_path = commands_dir / f"{output_name}{agent_cfg['extension']}"

tests/test_workflows.py

@@ -2332,48 +2332,6 @@ steps:
         assert state.status == RunStatus.COMPLETED
         assert state.step_results["only-step"]["output"]["stdout"].strip() == "hello"
 
-    def test_run_id_uses_speckit_workflow_run_id_env_override(self, project_dir, monkeypatch):
-        """When no run_id argument is provided, SPECKIT_WORKFLOW_RUN_ID overrides the auto-generated run ID."""
-        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
-
-        monkeypatch.setenv("SPECKIT_WORKFLOW_RUN_ID", "env-run-123")
-        definition = WorkflowDefinition.from_string("""
-schema_version: "1.0"
-workflow:
-  id: "env-run-id"
-  name: "Env Run Id"
-  version: "1.0.0"
-steps:
-  - id: stamp
-    type: shell
-    run: "echo {{ context.run_id }}"
-""")
-        state = WorkflowEngine(project_dir).execute(definition)
-
-        assert state.run_id == "env-run-123"
-        assert state.step_results["stamp"]["output"]["stdout"].strip() == "env-run-123"
-
-    def test_run_id_arg_takes_precedence_over_env_override(self, project_dir, monkeypatch):
-        """Explicit run_id keeps existing precedence over SPECKIT_WORKFLOW_RUN_ID."""
-        from specify_cli.workflows.engine import WorkflowDefinition, WorkflowEngine
-
-        monkeypatch.setenv("SPECKIT_WORKFLOW_RUN_ID", "env-run-123")
-        definition = WorkflowDefinition.from_string("""
-schema_version: "1.0"
-workflow:
-  id: "explicit-run-id"
-  name: "Explicit Run Id"
-  version: "1.0.0"
-steps:
-  - id: stamp
-    type: shell
-    run: "echo {{ context.run_id }}"
-""")
-        state = WorkflowEngine(project_dir).execute(definition, run_id="explicit-456")
-
-        assert state.run_id == "explicit-456"
-        assert state.step_results["stamp"]["output"]["stdout"].strip() == "explicit-456"
-
 
 # ===== State Persistence Tests =====