chore: bump version to 0.8.16

CHANGELOG.md

@@ -2,20 +2,6 @@
 
 <!-- insert new changelog below this comment -->
 
-## [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/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/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-05-28T00:00:00Z",
+  "updated_at": "2026-05-27T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "aide": {
@@ -2650,8 +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",
@@ -2692,7 +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",

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"]
     }
   }
 }

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 = "0.8.17"
+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 = [

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:
 
@@ -741,7 +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)
@@ -756,19 +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)
@@ -1119,7 +1115,7 @@ def _update_init_options_for_integration(
 @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
@@ -1150,10 +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].")
 
@@ -1226,14 +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)
@@ -1323,7 +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]")
@@ -1375,9 +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:
@@ -1679,18 +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)
@@ -2981,12 +2967,7 @@ 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)
@@ -3620,9 +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)
@@ -3783,9 +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

@@ -439,7 +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.
 
@@ -454,9 +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
@@ -563,15 +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)
@@ -637,56 +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.
@@ -709,28 +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:
@@ -755,7 +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.
 
@@ -765,8 +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
@@ -775,15 +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,
             )
@@ -798,7 +718,6 @@ class CommandRegistrar:
                         project_root,
                         context_note=context_note,
                         _resolved_dir=agent_dir,
-                        link_outputs=link_outputs,
                     )
                     if registered:
                         results[agent_name] = registered
@@ -814,7 +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.
 
@@ -828,8 +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
@@ -839,11 +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,
             )
@@ -857,7 +768,6 @@ class CommandRegistrar:
                         project_root,
                         context_note=context_note,
                         _resolved_dir=agent_dir,
-                        link_outputs=link_outputs,
                     )
                     if registered:
                         results[agent_name] = registered
@@ -906,7 +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/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 ["agy", "--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

@@ -25,12 +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
@@ -1397,53 +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,
@@ -1546,8 +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):
@@ -54,3 +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

@@ -265,13 +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
@@ -285,7 +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("'")
@@ -296,7 +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/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.key, "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/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():

tests/integrations/test_cli.py

@@ -923,23 +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."""
@@ -984,46 +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
@@ -1051,10 +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
@@ -1082,10 +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
@@ -1115,10 +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_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_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)

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

@@ -404,20 +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()
@@ -448,14 +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):
@@ -746,4 +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_hermes.py

@@ -1,347 +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 .hermes/skills/speckit-*/SKILL.md in project dir
-        hermes_skill_files = [f for f in actual if f.startswith(".hermes/skills/speckit-")]
-        assert hermes_skill_files == [], (
-            f"Expected no local 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()
-        )
-        hermes_skill_files = [f for f in actual if f.startswith(".hermes/skills/speckit-")]
-        assert hermes_skill_files == [], (
-            f"Expected no local 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 SKILL.md files in project-local dir
-        local_skills = list((target / ".hermes" / "skills").iterdir())
-        assert local_skills == [], f"Local skills dir should be empty, got: {local_skills}"

tests/integrations/test_integration_subcommand.py

@@ -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.
@@ -1252,7 +1222,7 @@ class TestIntegrationUpgrade:
         assert updated["ai"] == "gemini"
         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/."""

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
@@ -3999,20 +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()
@@ -4034,9 +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']}"