Add Spec Kit Figma extension to community catalog

Add figma extension submitted by @sebastienthibaud to: - extensions/catalog.community.json (alphabetical order) - docs/community/extensions.md community extensions table Closes #3396 Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
fix(cli): exit cleanly on malformed IPv6 URLs in extension/preset/workflow add (#3369 )
2026-07-08 23:59:55 +08:00 · 2026-07-08 12:39:07 +00:00 · 2026-07-07 15:20:13 -05:00 · 2026-07-07 15:14:25 -05:00 · 2026-07-07 15:11:18 -05:00 · 2026-07-07 15:01:43 -05:00
39 changed files with 2121 additions and 114 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,36 @@

 <!-- insert new changelog below this comment -->

+## [0.12.7] - 2026-07-07
+
+### Changed
+
+- fix(bundler): bundle update uninstalls components dropped by new version (#3353)
+- fix(workflows): route run/resume errors to stderr under --json (#3352)
+- fix(workflows): fan-in validate() rejects non-mapping output (#3349)
+- fix(workflows): shell step validate() rejects non-string run (#3348)
+- fix(integrations): agy honors SPECKIT_INTEGRATION_AGY_EXTRA_ARGS (#3347)
+- Add Orchestration Task Context Management extension to community catalog (#3372)
+- Update DocGuard — CDD Enforcement extension to v0.30.0 (#3371)
+- Update Ripple extension to v1.1.0 (#3370)
+- feat(integrations): generalize post-processing to all format types (#3311)
+- chore: release 0.12.6, begin 0.12.7.dev0 development (#3393)
+
+## [0.12.6] - 2026-07-07
+
+### Changed
+
+- fix(bundler): validate catalog URLs in `catalog add` (HTTPS-only, require host) (#3367)
+- Update Ralph Loop extension to v1.2.1 (#3365)
+- fix extension-local script path rewriting (#3364)
+- Add Charter extension to community catalog (#3363)
+- feat(scripts): add Python check-prerequisites PoC (#3302)
+- test: reduce registry manifest test repetition (#3146)
+- fix(integrations): hermes honors SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS (#3346)
+- fix(extensions): coerce non-mapping YAML config roots to {} in ConfigManager (#3345)
+- fix(yaml): pin goose recipe prompt block-scalar indentation (#3343)
+- chore: release 0.12.5, begin 0.12.6.dev0 development (#3381)
+
 ## [0.12.5] - 2026-07-06

 ### Changed
--- a/docs/community/extensions.md
+++ b/docs/community/extensions.md
@@ -42,6 +42,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Bugfix Workflow | Structured bugfix workflow — capture bugs, trace to spec artifacts, and patch specs surgically | `process` | Read+Write | [spec-kit-bugfix](https://github.com/Quratulain-bilal/spec-kit-bugfix) |
 | Canon | Adds canon-driven (baseline-driven) workflows: spec-first, code-first, spec-drift. Requires Canon Core preset installation. | `process` | Read+Write | [spec-kit-canon](https://github.com/maximiliamus/spec-kit-canon/tree/master/extension) |
 | Catalog CI | Automated validation for spec-kit community catalog entries — structure, URLs, diffs, and linting | `process` | Read-only | [spec-kit-catalog-ci](https://github.com/Quratulain-bilal/spec-kit-catalog-ci) |
+| Charter | Compose modular project constitutions from shared fragment registries. Centralize governance rules, select per-project fragments, track upstream changes, and keep multi-project setups consistent. | `process` | Read+Write | [spec-kit-charter](https://github.com/Fyloss/spec-kit-charter) |
 | CI Guard | Spec compliance gates for CI/CD — verify specs exist, check drift, and block merges on gaps | `process` | Read-only | [spec-kit-ci-guard](https://github.com/Quratulain-bilal/spec-kit-ci-guard) |
 | Checkpoint Extension | Commit the changes made during the middle of the implementation, so you don't end up with just one very large commit at the end | `code` | Read+Write | [spec-kit-checkpoint](https://github.com/aaronrsun/spec-kit-checkpoint) |
 | Cleanup Extension | Post-implementation quality gate that reviews changes, fixes small issues (scout rule), creates tasks for medium issues, and generates analysis for large issues | `code` | Read+Write | [spec-kit-cleanup](https://github.com/dsrednicki/spec-kit-cleanup) |
@@ -50,7 +51,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Confluence Extension | Create a doc in Confluence summarizing the specifications and planning files | `integration` | Read+Write | [spec-kit-confluence](https://github.com/aaronrsun/spec-kit-confluence) |
 | Cost Tracker | Track real LLM dollar cost across SDD workflows — per-feature budgets, per-integration comparison, and finance-ready exports | `visibility` | Read+Write | [spec-kit-cost](https://github.com/Quratulain-bilal/spec-kit-cost) |
 | Data Model Diagram | Generates Mermaid ER diagrams from Spec Kit data models after planning | `docs` | Read+Write | [spec-kit-data-model-diagram](https://github.com/benizzio/spec-kit-data-model-diagram) |
-| DocGuard — CDD Enforcement | Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. One pinned runtime dependency; pure Node.js otherwise. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| DocGuard — CDD Enforcement | The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
 | Extensify | Create and validate extensions and extension catalogs | `process` | Read+Write | [extensify](https://github.com/mnriem/spec-kit-extensions/tree/main/extensify) |
 | Fix Findings | Automated analyze-fix-reanalyze loop that resolves spec findings until clean | `code` | Read+Write | [spec-kit-fix-findings](https://github.com/Quratulain-bilal/spec-kit-fix-findings) |
 | FixIt Extension | Spec-aware bug fixing — maps bugs to spec artifacts, proposes a plan, applies minimal changes | `code` | Read+Write | [spec-kit-fixit](https://github.com/speckit-community/spec-kit-fixit) |
@@ -85,6 +86,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | .NET Framework to Modern .NET Migration | Orchestrate end-to-end .NET Framework to modern .NET migration across 7 phases, with SDD lifecycle integration | `process` | Read+Write | [spec-kit-fx-to-net](https://github.com/RogerBestMsft/spec-kit-FxToNet) |
 | Onboard | Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step | `process` | Read+Write | [spec-kit-onboard](https://github.com/dmux/spec-kit-onboard) |
 | Optimize | Audit and optimize AI governance for context efficiency — token budgets, rule health, interpretability, compression, coherence, and echo detection | `process` | Read+Write | [spec-kit-optimize](https://github.com/sakitA/spec-kit-optimize) |
+| Orchestration Task Context Management | Adds subagent work-unit orchestration to generated Spec Kit task files | `process` | Read+Write | [spec-kit-orchestration-task-context-management](https://github.com/benizzio/spec-kit-orchestration-task-context-management) |
 | OWASP LLM Threat Model | OWASP Top 10 for LLM Applications 2025 threat analysis on agent artifacts | `code` | Read-only | [spec-kit-threatmodel](https://github.com/NaviaSamal/spec-kit-threatmodel) |
 | Plan Review Gate | Require spec.md and plan.md to be merged via MR/PR before allowing task generation | `process` | Read-only | [spec-kit-plan-review-gate](https://github.com/luno/spec-kit-plan-review-gate) |
 | PR Bridge | Auto-generate pull request descriptions, checklists, and summaries from spec artifacts | `process` | Read-only | [spec-kit-pr-bridge-](https://github.com/Quratulain-bilal/spec-kit-pr-bridge-) |
@@ -105,7 +107,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Retro Extension | Sprint retrospective analysis with metrics, spec accuracy assessment, and improvement suggestions | `process` | Read+Write | [spec-kit-retro](https://github.com/arunt14/spec-kit-retro) |
 | Retrospective Extension | Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates | `docs` | Read+Write | [spec-kit-retrospective](https://github.com/emi-dm/spec-kit-retrospective) |
 | Review Extension | Post-implementation comprehensive code review with specialized agents for code quality, comments, tests, error handling, type design, and simplification | `code` | Read-only | [spec-kit-review](https://github.com/ismaelJimenez/spec-kit-review) |
-| Ripple | Detect side effects that tests can't catch after implementation — delta-anchored analysis across 9 domain-agnostic categories | `code` | Read+Write | [spec-kit-ripple](https://github.com/chordpli/spec-kit-ripple) |
+| Ripple | Detect side effects that tests can't catch after implementation — surface hidden ripple effects across 9 analysis categories | `code` | Read+Write | [spec-kit-ripple](https://github.com/chordpli/spec-kit-ripple) |
 | SDD Utilities | Resume interrupted workflows, validate project health, and verify spec-to-task traceability | `process` | Read+Write | [speckit-utils](https://github.com/mvanhorn/speckit-utils) |
 | Security Review | Full-project secure-by-design security audits plus staged, branch/PR, plan, task, follow-up, and apply reviews | `code` | Read+Write | [spec-kit-security-review](https://github.com/DyanGalih/spec-kit-security-review) |
 | SFSpeckit | Enterprise Salesforce SDLC with 18 commands for the full SDD lifecycle. | `process` | Read+Write | [spec-kit-sf](https://github.com/ysumanth06/spec-kit-sf) |
@@ -114,6 +116,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Spec Critique Extension | Dual-lens critical review of spec and plan from product strategy and engineering risk perspectives | `docs` | Read-only | [spec-kit-critique](https://github.com/arunt14/spec-kit-critique) |
 | Spec Diagram | Auto-generate Mermaid diagrams of SDD workflow state, feature progress, and task dependencies | `visibility` | Read-only | [spec-kit-diagram-](https://github.com/Quratulain-bilal/spec-kit-diagram-) |
 | Spec Kit Discovery Extension | Run technical discovery commands for feasibility, technology selection, scenario-specific technical decisions, legacy codebase assessment, implementation understanding, and proof-of-concept validation | `process` | Read+Write | [spec-kit-discovery](https://github.com/bigsmartben/spec-kit-discovery) |
+| Spec Kit Figma | Agent-agnostic SpecKit extension that grounds spec, plan & task generation in Figma design context — REST + optional MCP, single/mono/multi-repo, macOS/Linux/Windows. | `integration` | Read+Write | [spec-kit-figma](https://github.com/Fyloss/spec-kit-figma) |
 | Spec Kit Preview | Generate evidence-backed low, mid, or high fidelity previews from Spec Kit artifacts as Markdown or self-contained HTML | `docs` | Read+Write | [spec-kit-preview](https://github.com/bigsmartben/spec-kit-preview) |
 | Spec Kit Schedule | Optimal multi-agent task scheduling via CP-SAT — DAG precedence, hallucination-aware caps, file-conflict avoidance, stochastic durations, replanning, and interactive HTML output | `process` | Read+Write | [spec-kit-schedule](https://github.com/jfranc38/spec-kit-schedule) |
 | Spec Kit TLDR | Render a feature's spec.md / plan.md into a review-oriented TLDR (self-contained HTML dashboard + PR-native Markdown) that surfaces risks for faster PR review. | `visibility` | Read+Write | [speckit-tldr](https://github.com/qurore/speckit-tldr) |
--- a/extensions/catalog.community.json
+++ b/extensions/catalog.community.json
@@ -1,6 +1,6 @@
 {
  "schema_version": "1.0",
-  "updated_at": "2026-07-01T00:00:00Z",
+  "updated_at": "2026-07-08T00:00:00Z",
  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
  "extensions": {
    "aide": {
@@ -670,6 +670,40 @@
      "created_at": "2026-04-11T18:00:00Z",
      "updated_at": "2026-04-11T18:00:00Z"
    },
+    "charter": {
+      "name": "Charter",
+      "id": "charter",
+      "description": "Compose modular project constitutions from shared fragment registries. Centralize governance rules, select per-project fragments, track upstream changes, and keep multi-project setups consistent.",
+      "author": "Fyloss",
+      "version": "0.3.1",
+      "download_url": "https://github.com/Fyloss/spec-kit-charter/archive/refs/tags/v0.3.1.zip",
+      "repository": "https://github.com/Fyloss/spec-kit-charter",
+      "homepage": "https://github.com/Fyloss/spec-kit-charter",
+      "documentation": "https://github.com/Fyloss/spec-kit-charter/tree/master/docs",
+      "changelog": "https://github.com/Fyloss/spec-kit-charter/blob/master/CHANGELOG.md",
+      "license": "MIT",
+      "category": "process",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.11.9"
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 1
+      },
+      "tags": [
+        "constitution",
+        "governance",
+        "modular",
+        "fragments",
+        "registry"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-06T00:00:00Z",
+      "updated_at": "2026-07-06T00:00:00Z"
+    },
    "ci-guard": {
      "name": "CI Guard",
      "id": "ci-guard",
@@ -1072,10 +1106,10 @@
    "docguard": {
      "name": "DocGuard — CDD Enforcement",
      "id": "docguard",
-      "description": "Canonical-Driven Development enforcement. Validates, scores, and traces project documentation with automated checks, AI-driven workflows, and spec-kit hooks. One pinned runtime dependency; pure Node.js otherwise.",
+      "description": "The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep.",
      "author": "raccioly",
-      "version": "0.28.0",
-      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.28.0/spec-kit-docguard-v0.28.0.zip",
+      "version": "0.30.0",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.30.0/spec-kit-docguard-v0.30.0.zip",
      "repository": "https://github.com/raccioly/docguard",
      "homepage": "https://www.npmjs.com/package/docguard-cli",
      "documentation": "https://github.com/raccioly/docguard/blob/main/extensions/spec-kit-docguard/README.md",
@@ -1111,7 +1145,7 @@
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-13T00:00:00Z",
-      "updated_at": "2026-06-23T00:00:00Z"
+      "updated_at": "2026-07-06T00:00:00Z"
    },
    "doctor": {
      "name": "Project Health Check",
@@ -1179,6 +1213,47 @@
      "created_at": "2026-03-18T00:00:00Z",
      "updated_at": "2026-04-23T00:00:00Z"
    },
+    "figma": {
+      "name": "Spec Kit Figma",
+      "id": "figma",
+      "description": "Agent-agnostic SpecKit extension that grounds spec, plan & task generation in Figma design context — REST + optional MCP, single/mono/multi-repo, macOS/Linux/Windows.",
+      "author": "Fyloss",
+      "version": "1.6.0",
+      "download_url": "https://github.com/Fyloss/spec-kit-figma/archive/refs/tags/v1.6.0.zip",
+      "repository": "https://github.com/Fyloss/spec-kit-figma",
+      "homepage": "https://github.com/Fyloss/spec-kit-figma",
+      "documentation": "https://github.com/Fyloss/spec-kit-figma/blob/main/docs/INSTALL.md",
+      "changelog": "https://github.com/Fyloss/spec-kit-figma/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "integration",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.1.0",
+        "tools": [
+          { "name": "git", "required": true },
+          { "name": "bash", "required": false },
+          { "name": "curl", "required": false },
+          { "name": "jq", "required": false },
+          { "name": "pwsh", "required": false }
+        ]
+      },
+      "provides": {
+        "commands": 5,
+        "hooks": 6
+      },
+      "tags": [
+        "figma",
+        "design",
+        "frontend",
+        "ui",
+        "design-system"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-08T00:00:00Z",
+      "updated_at": "2026-07-08T00:00:00Z"
+    },
    "fix-findings": {
      "name": "Fix Findings",
      "id": "fix-findings",
@@ -2362,6 +2437,39 @@
      "created_at": "2026-04-03T00:00:00Z",
      "updated_at": "2026-04-03T00:00:00Z"
    },
+    "orchestration-task-context-management": {
+      "name": "Orchestration Task Context Management",
+      "id": "orchestration-task-context-management",
+      "description": "Adds subagent work-unit orchestration to generated Spec Kit task files",
+      "author": "Igor Benicio de Mesquita",
+      "version": "0.0.0",
+      "download_url": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/archive/refs/tags/v0.0.0.zip",
+      "repository": "https://github.com/benizzio/spec-kit-orchestration-task-context-management",
+      "homepage": "https://github.com/benizzio/spec-kit-orchestration-task-context-management",
+      "documentation": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/blob/main/README.md",
+      "changelog": "https://github.com/benizzio/spec-kit-orchestration-task-context-management/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "category": "process",
+      "effect": "read-write",
+      "requires": {
+        "speckit_version": ">=0.7.2"
+      },
+      "provides": {
+        "commands": 2,
+        "hooks": 2
+      },
+      "tags": [
+        "agent",
+        "orchestration",
+        "tasks",
+        "context"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-07-06T00:00:00Z",
+      "updated_at": "2026-07-06T00:00:00Z"
+    },
    "orchestrator": {
      "name": "Spec Orchestrator",
      "id": "orchestrator",
@@ -2679,8 +2787,8 @@
      "id": "ralph",
      "description": "Autonomous implementation loop using AI agent CLI",
      "author": "Rubiss",
-      "version": "1.1.1",
-      "download_url": "https://github.com/Rubiss-Projects/spec-kit-ralph/archive/refs/tags/v1.1.1.zip",
+      "version": "1.2.1",
+      "download_url": "https://github.com/Rubiss-Projects/spec-kit-ralph/archive/refs/tags/v1.2.1.zip",
      "repository": "https://github.com/Rubiss-Projects/spec-kit-ralph",
      "homepage": "https://github.com/Rubiss-Projects/spec-kit-ralph",
      "documentation": "https://github.com/Rubiss-Projects/spec-kit-ralph/blob/main/README.md",
@@ -2689,7 +2797,7 @@
      "category": "code",
      "effect": "read-write",
      "requires": {
-        "speckit_version": ">=0.1.0",
+        "speckit_version": ">=0.8.5",
        "tools": [
          {
            "name": "copilot",
@@ -2699,6 +2807,10 @@
            "name": "codex",
            "required": false
          },
+          {
+            "name": "claude",
+            "required": false
+          },
          {
            "name": "git",
            "required": true
@@ -2714,13 +2826,14 @@
        "automation",
        "loop",
        "copilot",
-        "codex"
+        "codex",
+        "claude"
      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-09T00:00:00Z",
-      "updated_at": "2026-06-05T03:11:06Z"
+      "updated_at": "2026-07-06T00:00:00Z"
    },
    "reconcile": {
      "name": "Reconcile Extension",
@@ -3047,10 +3160,10 @@
    "ripple": {
      "name": "Ripple",
      "id": "ripple",
-      "description": "Detect side effects that tests can't catch after implementation — delta-anchored analysis across 9 domain-agnostic categories with fix-induced side effect detection",
+      "description": "Detect side effects that tests can't catch after implementation — surface hidden ripple effects across 9 analysis categories",
      "author": "chordpli",
-      "version": "1.0.0",
-      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.0.0.zip",
+      "version": "1.1.0",
+      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.1.0.zip",
      "repository": "https://github.com/chordpli/spec-kit-ripple",
      "homepage": "https://github.com/chordpli/spec-kit-ripple",
      "documentation": "https://github.com/chordpli/spec-kit-ripple/blob/main/README.md",
@@ -3059,7 +3172,13 @@
      "category": "code",
      "effect": "read-write",
      "requires": {
-        "speckit_version": ">=0.2.0"
+        "speckit_version": ">=0.2.0",
+        "tools": [
+          {
+            "name": "git",
+            "required": true
+          }
+        ]
      },
      "provides": {
        "commands": 3,
@@ -3076,7 +3195,7 @@
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-04-20T00:00:00Z",
-      "updated_at": "2026-04-20T00:00:00Z"
+      "updated_at": "2026-07-06T00:00:00Z"
    },
    "roadmap": {
      "name": "Spec Roadmap",
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.12.5"
+version = "0.12.8.dev0"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 readme = "README.md"
 requires-python = ">=3.11"
--- a/scripts/python/check_prerequisites.py
+++ b/scripts/python/check_prerequisites.py
@@ -0,0 +1,207 @@
+#!/usr/bin/env python3
+"""Consolidated prerequisite checking script."""
+
+from __future__ import annotations
+
+import json
+import sys
+from dataclasses import dataclass
+from pathlib import Path
+
+try:
+    from common import FeaturePaths, format_speckit_command, get_feature_paths
+except ImportError:  # pragma: no cover - direct execution from unusual cwd
+    sys.path.insert(0, str(Path(__file__).resolve().parent))
+    from common import FeaturePaths, format_speckit_command, get_feature_paths
+
+
+def _json_line(payload: object) -> str:
+    return json.dumps(payload, ensure_ascii=False, separators=(",", ":")) + "\n"
+
+
+HELP_TEXT = """Usage: check_prerequisites.py [OPTIONS]
+
+Consolidated prerequisite checking for Spec-Driven Development workflow.
+
+OPTIONS:
+  --json              Output in JSON format
+  --require-tasks     Require tasks.md to exist (for implementation phase)
+  --include-tasks     Include tasks.md in AVAILABLE_DOCS list
+  --paths-only        Only output path variables (no prerequisite validation)
+  --help, -h          Show this help message
+
+EXAMPLES:
+  # Check task prerequisites (plan.md required)
+  ./check_prerequisites.py --json
+
+  # Check implementation prerequisites (plan.md + tasks.md required)
+  ./check_prerequisites.py --json --require-tasks --include-tasks
+
+  # Get feature paths only (no validation)
+  ./check_prerequisites.py --paths-only
+
+"""
+
+
+@dataclass(frozen=True)
+class Args:
+    json_mode: bool = False
+    require_tasks: bool = False
+    include_tasks: bool = False
+    paths_only: bool = False
+
+
+def _parse_args(argv: list[str]) -> Args:
+    json_mode = False
+    require_tasks = False
+    include_tasks = False
+    paths_only = False
+
+    for arg in argv:
+        if arg == "--json":
+            json_mode = True
+        elif arg == "--require-tasks":
+            require_tasks = True
+        elif arg == "--include-tasks":
+            include_tasks = True
+        elif arg == "--paths-only":
+            paths_only = True
+        elif arg in {"--help", "-h"}:
+            sys.stdout.write(HELP_TEXT)
+            raise SystemExit(0)
+        else:
+            print(
+                f"ERROR: Unknown option '{arg}'. Use --help for usage information.",
+                file=sys.stderr,
+            )
+            raise SystemExit(1)
+
+    return Args(
+        json_mode=json_mode,
+        require_tasks=require_tasks,
+        include_tasks=include_tasks,
+        paths_only=paths_only,
+    )
+
+
+def _dir_has_entries(path: Path) -> bool:
+    try:
+        return path.is_dir() and any(path.iterdir())
+    except OSError:
+        return False
+
+
+def _available_docs(paths: FeaturePaths, include_tasks: bool) -> list[str]:
+    docs: list[str] = []
+    if paths.research.is_file():
+        docs.append("research.md")
+    if paths.data_model.is_file():
+        docs.append("data-model.md")
+    if _dir_has_entries(paths.contracts_dir):
+        docs.append("contracts/")
+    if paths.quickstart.is_file():
+        docs.append("quickstart.md")
+    if include_tasks and paths.tasks.is_file():
+        docs.append("tasks.md")
+    return docs
+
+
+def _print_paths_only(paths: FeaturePaths, json_mode: bool) -> None:
+    if json_mode:
+        sys.stdout.write(
+            _json_line(
+                {
+                    "REPO_ROOT": str(paths.repo_root),
+                    "BRANCH": paths.current_branch,
+                    "FEATURE_DIR": str(paths.feature_dir),
+                    "FEATURE_SPEC": str(paths.feature_spec),
+                    "IMPL_PLAN": str(paths.impl_plan),
+                    "TASKS": str(paths.tasks),
+                }
+            )
+        )
+        return
+
+    print(f"REPO_ROOT: {paths.repo_root}")
+    print(f"BRANCH: {paths.current_branch}")
+    print(f"FEATURE_DIR: {paths.feature_dir}")
+    print(f"FEATURE_SPEC: {paths.feature_spec}")
+    print(f"IMPL_PLAN: {paths.impl_plan}")
+    print(f"TASKS: {paths.tasks}")
+
+
+def _check_file(path: Path, description: str) -> None:
+    marker = "✓" if path.is_file() else "✗"
+    print(f"  {marker} {description}")
+
+
+def _check_dir(path: Path, description: str) -> None:
+    marker = "✓" if _dir_has_entries(path) else "✗"
+    print(f"  {marker} {description}")
+
+
+def _print_text_results(paths: FeaturePaths, include_tasks: bool) -> None:
+    print(f"FEATURE_DIR:{paths.feature_dir}")
+    print("AVAILABLE_DOCS:")
+    _check_file(paths.research, "research.md")
+    _check_file(paths.data_model, "data-model.md")
+    _check_dir(paths.contracts_dir, "contracts/")
+    _check_file(paths.quickstart, "quickstart.md")
+    if include_tasks:
+        _check_file(paths.tasks, "tasks.md")
+
+
+def main(argv: list[str] | None = None) -> int:
+    args = _parse_args(list(argv if argv is not None else sys.argv[1:]))
+
+    try:
+        paths = get_feature_paths(
+            no_persist=args.paths_only,
+            script_file=Path(__file__),
+        )
+    except SystemExit as exc:
+        if exc.code == 0:
+            return 0
+        print("ERROR: Failed to resolve feature paths", file=sys.stderr)
+        return int(exc.code) if isinstance(exc.code, int) else 1
+
+    if args.paths_only:
+        _print_paths_only(paths, args.json_mode)
+        return 0
+
+    if not paths.feature_dir.is_dir():
+        print(f"ERROR: Feature directory not found: {paths.feature_dir}", file=sys.stderr)
+        print(
+            f"Run {format_speckit_command('specify', paths.repo_root)} first to create the feature structure.",
+            file=sys.stderr,
+        )
+        return 1
+
+    if not paths.impl_plan.is_file():
+        print(f"ERROR: plan.md not found in {paths.feature_dir}", file=sys.stderr)
+        print(
+            f"Run {format_speckit_command('plan', paths.repo_root)} first to create the implementation plan.",
+            file=sys.stderr,
+        )
+        return 1
+
+    if args.require_tasks and not paths.tasks.is_file():
+        print(f"ERROR: tasks.md not found in {paths.feature_dir}", file=sys.stderr)
+        print(
+            f"Run {format_speckit_command('tasks', paths.repo_root)} first to create the task list.",
+            file=sys.stderr,
+        )
+        return 1
+
+    docs = _available_docs(paths, args.include_tasks)
+    if args.json_mode:
+        sys.stdout.write(
+            _json_line({"FEATURE_DIR": str(paths.feature_dir), "AVAILABLE_DOCS": docs})
+        )
+    else:
+        _print_text_results(paths, args.include_tasks)
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())
--- a/scripts/python/common.py
+++ b/scripts/python/common.py
@@ -0,0 +1,210 @@
+"""Shared helpers for Spec Kit Python scripts."""
+
+from __future__ import annotations
+
+import json
+import os
+import sys
+from dataclasses import dataclass
+from pathlib import Path
+
+
+def _trim_trailing_separators(value: Path) -> str:
+    text = str(value)
+    while len(text) > 1 and text.endswith((os.sep, "/")):
+        text = text[:-1]
+    return text
+
+
+def find_specify_root(start_dir: Path | None = None) -> Path | None:
+    current = (start_dir or Path.cwd()).resolve()
+    while True:
+        if (current / ".specify").is_dir():
+            return current
+        parent = current.parent
+        if parent == current:
+            return None
+        current = parent
+
+
+def resolve_specify_init_dir() -> Path:
+    raw = os.environ.get("SPECIFY_INIT_DIR", "")
+    candidate = Path(raw)
+    if not candidate.is_absolute():
+        candidate = Path.cwd() / candidate
+    try:
+        init_root = candidate.resolve(strict=True)
+    except OSError:
+        print(
+            f"ERROR: SPECIFY_INIT_DIR does not point to an existing directory: {raw}",
+            file=sys.stderr,
+        )
+        raise SystemExit(1)
+    if not init_root.is_dir():
+        print(
+            f"ERROR: SPECIFY_INIT_DIR does not point to an existing directory: {raw}",
+            file=sys.stderr,
+        )
+        raise SystemExit(1)
+    if not (init_root / ".specify").is_dir():
+        print(
+            "ERROR: SPECIFY_INIT_DIR is not a Spec Kit project "
+            f"(no .specify/ directory): {init_root}",
+            file=sys.stderr,
+        )
+        raise SystemExit(1)
+    return init_root
+
+
+def get_repo_root(script_file: Path | None = None) -> Path:
+    if os.environ.get("SPECIFY_INIT_DIR"):
+        return resolve_specify_init_dir()
+
+    specify_root = find_specify_root()
+    if specify_root is not None:
+        return specify_root
+
+    if script_file is not None:
+        script_root = find_specify_root(script_file.resolve().parent)
+        if script_root is not None:
+            return script_root
+
+        # Installed scripts live at .specify/scripts/python/<script>.py.
+        return script_file.resolve().parents[3]
+    return Path.cwd().resolve()
+
+
+def get_current_branch() -> str:
+    return os.environ.get("SPECIFY_FEATURE", "")
+
+
+def read_feature_json_feature_directory(repo_root: Path) -> str:
+    feature_json = repo_root / ".specify" / "feature.json"
+    if not feature_json.is_file():
+        return ""
+    try:
+        data = json.loads(feature_json.read_text(encoding="utf-8"))
+    except (OSError, json.JSONDecodeError):
+        return ""
+    value = data.get("feature_directory") if isinstance(data, dict) else None
+    return value if isinstance(value, str) else ""
+
+
+def _json_dump(data: dict[str, str]) -> str:
+    return json.dumps(data, ensure_ascii=False, separators=(",", ":")) + "\n"
+
+
+def persist_feature_json(repo_root: Path, feature_dir_value: str) -> None:
+    value = feature_dir_value
+    try:
+        relative = Path(value)
+        if relative.is_absolute():
+            try:
+                value = relative.resolve().relative_to(repo_root.resolve()).as_posix()
+            except ValueError:
+                value = str(relative)
+    except OSError:
+        pass
+
+    current = read_feature_json_feature_directory(repo_root)
+    if current == value:
+        return
+
+    specify_dir = repo_root / ".specify"
+    specify_dir.mkdir(parents=True, exist_ok=True)
+    (specify_dir / "feature.json").write_text(
+        _json_dump({"feature_directory": value}),
+        encoding="utf-8",
+    )
+
+
+@dataclass(frozen=True)
+class FeaturePaths:
+    repo_root: Path
+    current_branch: str
+    feature_dir: Path
+    feature_spec: Path
+    impl_plan: Path
+    tasks: Path
+    research: Path
+    data_model: Path
+    quickstart: Path
+    contracts_dir: Path
+
+
+def get_feature_paths(
+    *, no_persist: bool = False, script_file: Path | None = None
+) -> FeaturePaths:
+    repo_root = get_repo_root(script_file)
+    current_branch = get_current_branch()
+
+    feature_dir_raw = os.environ.get("SPECIFY_FEATURE_DIRECTORY", "")
+    if feature_dir_raw:
+        feature_dir = Path(feature_dir_raw)
+        if not feature_dir.is_absolute():
+            feature_dir = repo_root / feature_dir
+        if not no_persist:
+            persist_feature_json(repo_root, feature_dir_raw)
+    elif (repo_root / ".specify" / "feature.json").is_file():
+        stored = read_feature_json_feature_directory(repo_root)
+        if not stored:
+            print(
+                "ERROR: Feature directory not found. Set SPECIFY_FEATURE_DIRECTORY "
+                "or ensure .specify/feature.json contains feature_directory.",
+                file=sys.stderr,
+            )
+            raise SystemExit(1)
+        feature_dir = Path(stored)
+        if not feature_dir.is_absolute():
+            feature_dir = repo_root / feature_dir
+    else:
+        print(
+            "ERROR: Feature directory not found. Set SPECIFY_FEATURE_DIRECTORY "
+            "or run the specify command to create .specify/feature.json.",
+            file=sys.stderr,
+        )
+        raise SystemExit(1)
+
+    if not current_branch:
+        current_branch = Path(_trim_trailing_separators(feature_dir)).name
+
+    return FeaturePaths(
+        repo_root=repo_root,
+        current_branch=current_branch,
+        feature_dir=feature_dir,
+        feature_spec=feature_dir / "spec.md",
+        impl_plan=feature_dir / "plan.md",
+        tasks=feature_dir / "tasks.md",
+        research=feature_dir / "research.md",
+        data_model=feature_dir / "data-model.md",
+        quickstart=feature_dir / "quickstart.md",
+        contracts_dir=feature_dir / "contracts",
+    )
+
+
+def get_invoke_separator(repo_root: Path) -> str:
+    integration_json = repo_root / ".specify" / "integration.json"
+    if not integration_json.is_file():
+        return "."
+    try:
+        state = json.loads(integration_json.read_text(encoding="utf-8"))
+        key = state.get("default_integration") or state.get("integration") or ""
+        settings = state.get("integration_settings")
+        if isinstance(key, str) and isinstance(settings, dict):
+            entry = settings.get(key)
+            if isinstance(entry, dict) and entry.get("invoke_separator") in {".", "-"}:
+                return entry["invoke_separator"]
+    except (OSError, json.JSONDecodeError):
+        pass
+    return "."
+
+
+def format_speckit_command(command_name: str, repo_root: Path) -> str:
+    separator = get_invoke_separator(repo_root)
+    name = command_name.lstrip("/")
+    if name.startswith("speckit."):
+        name = name[len("speckit.") :]
+    elif name.startswith("speckit-"):
+        name = name[len("speckit-") :]
+    name = name.replace(".", separator)
+    return f"/speckit{separator}{name}"
--- a/src/specify_cli/_github_http.py
+++ b/src/specify_cli/_github_http.py
@@ -127,7 +127,14 @@ def resolve_github_release_asset_api_url(
    if hostname == "github.com":
        api_base = "https://api.github.com"
    elif is_ghes:
-        authority = hostname if parsed.port is None else f"{hostname}:{parsed.port}"
+        # ``parsed.port`` raises ValueError on a malformed port (e.g.
+        # ``host:notaport``); the function's contract is to return None for
+        # anything it can't resolve, not to raise.
+        try:
+            port = parsed.port
+        except ValueError:
+            return None
+        authority = hostname if port is None else f"{hostname}:{port}"
        api_base = f"{parsed.scheme}://{authority}/api/v3"
    else:
        return None
--- a/src/specify_cli/agents.py
+++ b/src/specify_cli/agents.py
@@ -148,7 +148,9 @@ class CommandRegistrar:
        )
        return f"---\n{yaml_str}---\n"

-    def _adjust_script_paths(self, frontmatter: dict) -> dict:
+    def _adjust_script_paths(
+        self, frontmatter: dict, extension_id: Optional[str] = None
+    ) -> dict:
        """Normalize script paths in frontmatter to generated project locations.

        Rewrites known repo-relative and top-level script paths under the
@@ -158,6 +160,7 @@ class CommandRegistrar:

        Args:
            frontmatter: Frontmatter dictionary
+            extension_id: Extension id when rendering extension-owned commands.

        Returns:
            Modified frontmatter with normalized project paths
@@ -168,11 +171,15 @@ class CommandRegistrar:
        if isinstance(scripts, dict):
            for key, script_path in scripts.items():
                if isinstance(script_path, str):
-                    scripts[key] = self.rewrite_project_relative_paths(script_path)
+                    scripts[key] = self.rewrite_project_relative_paths(
+                        script_path, extension_id=extension_id
+                    )
        return frontmatter

    @staticmethod
-    def rewrite_project_relative_paths(text: str) -> str:
+    def rewrite_project_relative_paths(
+        text: str, extension_id: Optional[str] = None
+    ) -> str:
        """Rewrite repo-relative paths to their generated project locations."""
        if not isinstance(text, str) or not text:
            return text
@@ -184,10 +191,18 @@ class CommandRegistrar:
        ):
            text = text.replace(old, new)

-        # Only rewrite top-level style references so extension-local paths like
-        # ".specify/extensions/<ext>/scripts/..." remain intact.
+        # Only rewrite top-level style references so existing generated paths
+        # like ".specify/extensions/<ext>/scripts/..." remain intact. When
+        # rendering extension commands, top-level "scripts/" is extension-local.
+        scripts_replacement = (
+            f".specify/extensions/{extension_id}/scripts/"
+            if extension_id
+            else ".specify/scripts/"
+        )
        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?memory/', r"\1.specify/memory/", text)
-        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?scripts/', r"\1.specify/scripts/", text)
+        text = re.sub(
+            r'(^|[\s`"\'(])(?:\.?/)?scripts/', rf"\1{scripts_replacement}", text
+        )
        text = re.sub(
            r'(^|[\s`"\'(])(?:\.?/)?templates/', r"\1.specify/templates/", text
        )
@@ -312,6 +327,7 @@ class CommandRegistrar:
        source_id: str,
        source_file: str,
        project_root: Path,
+        extension_id: Optional[str] = None,
    ) -> str:
        """Render a command override as a SKILL.md file.

@@ -331,7 +347,7 @@ class CommandRegistrar:
        agent_config = self.AGENT_CONFIGS.get(agent_name, {})
        if agent_config.get("extension") == "/SKILL.md":
            body = self.resolve_skill_placeholders(
-                agent_name, frontmatter, body, project_root
+                agent_name, frontmatter, body, project_root, extension_id=extension_id
            )

        description = frontmatter.get(
@@ -393,7 +409,11 @@ class CommandRegistrar:

    @staticmethod
    def resolve_skill_placeholders(
-        agent_name: str, frontmatter: dict, body: str, project_root: Path
+        agent_name: str,
+        frontmatter: dict,
+        body: str,
+        project_root: Path,
+        extension_id: Optional[str] = None,
    ) -> str:
        """Resolve script placeholders for skills-backed agents."""
        if not isinstance(frontmatter, dict):
@@ -433,7 +453,9 @@ class CommandRegistrar:

        body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)

-        return CommandRegistrar.rewrite_project_relative_paths(body)
+        return CommandRegistrar.rewrite_project_relative_paths(
+            body, extension_id=extension_id
+        )

    def _convert_argument_placeholder(
        self, content: str, from_placeholder: str, to_placeholder: str
@@ -528,6 +550,7 @@ class CommandRegistrar:
        context_note: str = None,
        _resolved_dir: Path = None,
        link_outputs: bool = False,
+        extension_id: Optional[str] = None,
    ) -> List[str]:
        """Register commands for a specific agent.

@@ -545,6 +568,7 @@ class CommandRegistrar:
            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.
+            extension_id: Extension id when rendering extension-owned commands.

        Returns:
            List of registered command names
@@ -614,7 +638,9 @@ class CommandRegistrar:
                        frontmatter[key] = core_frontmatter[key]
                frontmatter.pop("strategy", None)

-            frontmatter = self._adjust_script_paths(frontmatter)
+            frontmatter = self._adjust_script_paths(
+                frontmatter, extension_id=extension_id
+            )

            for key in agent_config.get("strip_frontmatter_keys", []):
                frontmatter.pop(key, None)
@@ -653,10 +679,11 @@ class CommandRegistrar:
                    source_id,
                    cmd_file,
                    project_root,
+                    extension_id=extension_id,
                )
            elif agent_config["format"] == "markdown":
                body = self.resolve_skill_placeholders(
-                    agent_name, frontmatter, body, project_root
+                    agent_name, frontmatter, body, project_root, extension_id=extension_id
                )
                body = self._convert_argument_placeholder(
                    body, "$ARGUMENTS", agent_config["args"]
@@ -666,7 +693,7 @@ class CommandRegistrar:
                )
            elif agent_config["format"] == "toml":
                body = self.resolve_skill_placeholders(
-                    agent_name, frontmatter, body, project_root
+                    agent_name, frontmatter, body, project_root, extension_id=extension_id
                )
                body = self._convert_argument_placeholder(
                    body, "$ARGUMENTS", agent_config["args"]
@@ -679,6 +706,17 @@ class CommandRegistrar:
            else:
                raise ValueError(f"Unsupported format: {agent_config['format']}")

+            # -- Post-process for non-skills agents -----------------------
+            _integration = None
+            if agent_config["extension"] != "/SKILL.md":
+                from specify_cli.integrations import (  # noqa: PLC0415
+                    get_integration,
+                )
+
+                _integration = get_integration(agent_name)
+                if _integration is not None:
+                    output = _integration.post_process_command_content(output)
+
            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)
@@ -721,6 +759,7 @@ class CommandRegistrar:
                            source_id,
                            cmd_file,
                            project_root,
+                            extension_id=extension_id,
                        )
                    elif agent_config["format"] == "markdown":
                        alias_output = self.render_markdown_command(
@@ -738,6 +777,9 @@ class CommandRegistrar:
                        raise ValueError(
                            f"Unsupported format: {agent_config['format']}"
                        )
+
+                    if agent_config["extension"] != "/SKILL.md" and _integration is not None:
+                        alias_output = _integration.post_process_command_content(alias_output)
                else:
                    # For other agents, reuse the primary output
                    alias_output = output
@@ -750,6 +792,7 @@ class CommandRegistrar:
                            source_id,
                            cmd_file,
                            project_root,
+                            extension_id=extension_id,
                        )

                alias_file = (
@@ -881,6 +924,7 @@ class CommandRegistrar:
        context_note: str = None,
        link_outputs: bool = False,
        create_missing_active_skills_dir: bool = False,
+        extension_id: Optional[str] = None,
    ) -> Dict[str, List[str]]:
        """Register commands for all detected agents in the project.

@@ -897,6 +941,7 @@ class CommandRegistrar:
                Recovery requires active skills mode (or Kimi's existing native
                skills directory) and is skipped when safe resolution or
                creation fails.
+            extension_id: Extension id when rendering extension-owned commands.

        Returns:
            Dictionary mapping agent names to list of registered commands
@@ -999,6 +1044,7 @@ class CommandRegistrar:
                        context_note=context_note,
                        _resolved_dir=agent_dir,
                        link_outputs=link_outputs,
+                        extension_id=extension_id,
                    )
                    if registered:
                        results[agent_name] = registered
@@ -1023,6 +1069,7 @@ class CommandRegistrar:
        project_root: Path,
        context_note: Optional[str] = None,
        link_outputs: bool = False,
+        extension_id: Optional[str] = None,
    ) -> Dict[str, List[str]]:
        """Register commands for all non-skill agents in the project.

@@ -1038,6 +1085,7 @@ class CommandRegistrar:
            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.
+            extension_id: Extension id when rendering extension-owned commands.

        Returns:
            Dictionary mapping agent names to list of registered commands
@@ -1066,6 +1114,7 @@ class CommandRegistrar:
                        context_note=context_note,
                        _resolved_dir=agent_dir,
                        link_outputs=link_outputs,
+                        extension_id=extension_id,
                    )
                    if registered:
                        results[agent_name] = registered
--- a/src/specify_cli/authentication/http.py
+++ b/src/specify_cli/authentication/http.py
@@ -73,6 +73,13 @@ class _StripAuthOnRedirect(urllib.request.HTTPRedirectHandler):
        self._redirect_validator = redirect_validator

    def redirect_request(self, req, fp, code, msg, headers, newurl):
+        try:
+            new_parsed = urlparse(newurl)
+        except ValueError as exc:
+            # Malformed redirect target (e.g. unterminated IPv6 bracket).
+            # Surface as URLError so callers' download error handling applies.
+            raise urllib.error.URLError(f"malformed redirect URL: {exc}") from exc
+
        if self._redirect_validator is not None:
            self._redirect_validator(req.full_url, newurl)

@@ -83,7 +90,6 @@ class _StripAuthOnRedirect(urllib.request.HTTPRedirectHandler):
        new_req = super().redirect_request(req, fp, code, msg, headers, newurl)
        if new_req is not None:
            old_scheme = urlparse(req.full_url).scheme
-            new_parsed = urlparse(newurl)
            hostname = (new_parsed.hostname or "").lower()
            is_https_downgrade = old_scheme == "https" and new_parsed.scheme != "https"
            if _hostname_in_hosts(hostname, self._hosts) and not is_https_downgrade:
--- a/src/specify_cli/bundler/commands_impl/catalog_config.py
+++ b/src/specify_cli/bundler/commands_impl/catalog_config.py
@@ -95,7 +95,11 @@ def _is_local_path(url: str) -> bool:
    """True when *url* denotes a local filesystem path rather than a URL."""
    if _WINDOWS_DRIVE_RE.match(url):
        return True
-    scheme = urlparse(url).scheme.lower()
+    try:
+        scheme = urlparse(url).scheme.lower()
+    except ValueError:
+        # Malformed URLs (e.g. an unclosed IPv6 bracket) are not local paths.
+        return False
    return scheme not in _REMOTE_SCHEMES


@@ -137,7 +141,10 @@ def add_source(
    url = url.strip()
    if not url:
        raise BundlerError("A catalog url is required.")
-    parsed = urlparse(url)
+    try:
+        parsed = urlparse(url)
+    except ValueError as exc:
+        raise BundlerError(f"Invalid catalog url: '{url}'.") from exc
    if not (parsed.scheme or parsed.path):
        raise BundlerError(f"Invalid catalog url: '{url}'.")
    # Reject unsupported URL schemes (e.g. ssh://, ftp://) up front so they are
@@ -148,6 +155,20 @@ def add_source(
            f"Unsupported catalog url scheme '{parsed.scheme}://' in '{url}'. "
            "Use http(s)://, file://, builtin://, or a local path."
        )
+    if parsed.scheme.lower() in {"http", "https"}:
+        # Mirror specify_cli.catalogs._validate_catalog_url (#3209/#3210):
+        # HTTPS only (HTTP just for localhost), and check hostname, not
+        # netloc — netloc is truthy for host-less URLs like "https://:8080"
+        # or "https://user@". Validating here keeps junk out of
+        # bundle-catalogs.yml instead of failing later at fetch time.
+        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
+        if parsed.scheme.lower() != "https" and not is_localhost:
+            raise BundlerError(
+                f"Catalog url must use HTTPS (got {parsed.scheme}://). "
+                "HTTP is only allowed for localhost."
+            )
+        if not parsed.hostname:
+            raise BundlerError(f"Catalog url must be a valid URL with a host: {url}")

    url = _canonicalize_url(url)
    install_policy = InstallPolicy.parse(policy)
--- a/src/specify_cli/bundler/services/installer.py
+++ b/src/specify_cli/bundler/services/installer.py
@@ -130,6 +130,28 @@ def install_bundle(
            done.append(component)
            result.installed.append(component)
            contributed.append(component)
+
+        # On update (refresh), uninstall components this bundle used to own
+        # that the new version no longer ships. Otherwise they are dropped
+        # from the record below (contributed only holds plan.components) yet
+        # left on disk — permanently orphaned, since no bundle record can
+        # ever remove them. A stale component still owned by another bundle
+        # is kept installed and simply de-attributed here (it stays in that
+        # bundle's record). Mirrors remove_bundle's refcount logic.
+        if refresh and existing is not None:
+            planned = {(c.kind, c.id) for c in plan.components}
+            still_needed = components_still_needed(
+                records, exclude_bundle_id=plan.bundle_id
+            )
+            for component in existing.contributed_components:
+                key = (component.kind, component.id)
+                if key in planned:
+                    continue
+                if key in still_needed:
+                    continue
+                if installer.is_installed(project_root, component):
+                    installer.remove(project_root, component)
+                    result.uninstalled.append(component)
    except BundlerError:
        _rollback(project_root, installer, done)
        raise
--- a/src/specify_cli/extensions/init.py
+++ b/src/specify_cli/extensions/init.py
@@ -1075,9 +1075,11 @@ class ExtensionManager:
                        pass  # best-effort cleanup
                continue
            frontmatter, body = registrar.parse_frontmatter(content)
-            frontmatter = registrar._adjust_script_paths(frontmatter)
+            frontmatter = registrar._adjust_script_paths(
+                frontmatter, extension_id=manifest.id
+            )
            body = registrar.resolve_skill_placeholders(
-                selected_ai, frontmatter, body, self.project_root
+                selected_ai, frontmatter, body, self.project_root, extension_id=manifest.id
            )

            original_desc = frontmatter.get("description", "")
@@ -1958,6 +1960,7 @@ class CommandRegistrar:
            project_root,
            context_note=context_note,
            link_outputs=link_outputs,
+            extension_id=manifest.id,
        )

    def register_commands_for_all_agents(
@@ -1978,6 +1981,7 @@ class CommandRegistrar:
            context_note=context_note,
            link_outputs=link_outputs,
            create_missing_active_skills_dir=create_missing_active_skills_dir,
+            extension_id=manifest.id,
        )

    def unregister_commands(
@@ -2688,7 +2692,12 @@ class ConfigManager:
            return {}

        try:
-            return yaml.safe_load(file_path.read_text(encoding="utf-8")) or {}
+            data = yaml.safe_load(file_path.read_text(encoding="utf-8"))
+            # Coerce a non-mapping root (list/scalar, or None for an empty
+            # file) to {} so callers that iterate/merge the result — e.g.
+            # _merge_configs' .items() — never crash. Mirrors the same
+            # non-dict-root guard in get_project_config().
+            return data if isinstance(data, dict) else {}
        except (yaml.YAMLError, OSError, UnicodeError):
            return {}

--- a/src/specify_cli/extensions/_commands.py
+++ b/src/specify_cli/extensions/_commands.py
@@ -426,7 +426,11 @@ def extension_add(
    if from_url and not dev:
        from urllib.parse import urlparse

-        parsed = urlparse(from_url)
+        try:
+            parsed = urlparse(from_url)
+        except ValueError:
+            console.print(f"[red]Error:[/red] Invalid URL: {_escape_markup(from_url)}")
+            raise typer.Exit(1)
        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")

        if parsed.scheme != "https" and not (parsed.scheme == "http" and is_localhost):
--- a/src/specify_cli/integrations/agy/init.py
+++ b/src/specify_cli/integrations/agy/init.py
@@ -89,7 +89,11 @@ class AgyIntegration(SkillsIntegration):
        output_json: bool = True,
    ) -> list[str] | None:
        # agy does not support --model or JSON output; both params are ignored
-        return [self._resolve_executable(), "--print", prompt]
+        args = [self._resolve_executable(), "--print", prompt]
+        # Honor SPECKIT_INTEGRATION_AGY_EXTRA_ARGS (operator-supplied flags),
+        # appended after the positional prompt like the devin integration.
+        self._apply_extra_args_env_var(args)
+        return args

    def setup(
        self,
--- a/src/specify_cli/integrations/base.py
+++ b/src/specify_cli/integrations/base.py
@@ -123,6 +123,19 @@ class IntegrationBase(ABC):
    integration that sets this flag.
    """

+    def post_process_command_content(self, content: str) -> str:
+        """Transform command content after format rendering.
+
+        Called by ``register_commands()`` for non-skills format types
+        (Markdown, TOML, YAML) after the command has been rendered into
+        its target format and before writing to disk.  Skills-format
+        agents use ``post_process_skill_content()`` instead.
+
+        Subclasses may override to inject agent-specific content.
+        The default implementation returns *content* unchanged.
+        """
+        return content
+
    # -- Public API -------------------------------------------------------

    @classmethod
@@ -1178,12 +1191,18 @@ class YamlIntegration(IntegrationBase):
            default_flow_style=False,
        ).strip()

-        # Indent the body for YAML block scalar
+        # Indent the body for YAML block scalar. Use an explicit indentation
+        # indicator ("|2") rather than a bare "|": YAML infers a plain block
+        # scalar's indentation from its first non-empty line, so a body whose
+        # first line is itself indented (e.g. a markdown code block or a nested
+        # list item) would make the parser expect that deeper indent for the
+        # whole block and reject the later, less-indented lines. Pinning the
+        # indent to 2 keeps the recipe parseable whatever the body looks like.
        indented = "\n".join(f"  {line}" for line in body.split("\n"))

        lines = [
            header_yaml,
-            "prompt: |",
+            "prompt: |2",
            indented,
            "",
            f"# Source: {source_id}",
--- a/src/specify_cli/integrations/hermes/init.py
+++ b/src/specify_cli/integrations/hermes/init.py
@@ -253,6 +253,11 @@ class HermesIntegration(SkillsIntegration):
        """
        args = [self._resolve_executable(), "chat", "-Q"]

+        # Operator-supplied SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS go here —
+        # after the base command but before Spec Kit's canonical -m/--json/-s/-q
+        # flags — so they can't displace or clobber them (mirrors opencode).
+        self._apply_extra_args_env_var(args)
+
        if model:
            args.extend(["-m", model])
        if output_json:
--- a/src/specify_cli/integrations/manifest.py
+++ b/src/specify_cli/integrations/manifest.py
@@ -309,7 +309,14 @@ class IntegrationManifest:
            if abs_path.is_symlink() or not abs_path.is_file():
                modified.append(rel)
                continue
-            if _sha256(abs_path) != expected_hash:
+            try:
+                changed = _sha256(abs_path) != expected_hash
+            except OSError:
+                # Unreadable regular file (e.g. permission denied): treat as
+                # modified, consistent with the symlink / non-regular-file
+                # handling above, rather than letting the OSError escape.
+                changed = True
+            if changed:
                modified.append(rel)
        return modified

@@ -358,9 +365,17 @@ class IntegrationManifest:
                    skipped.append(path)
                    continue
            else:
-                if not force and _sha256(path) != expected_hash:
-                    skipped.append(path)
-                    continue
+                if not force:
+                    try:
+                        matches = _sha256(path) == expected_hash
+                    except OSError:
+                        # Unreadable: can't verify it's ours, so preserve it
+                        # (mirrors the path.unlink() OSError guard below).
+                        skipped.append(path)
+                        continue
+                    if not matches:
+                        skipped.append(path)
+                        continue
            try:
                path.unlink()
            except OSError:
--- a/src/specify_cli/presets/_commands.py
+++ b/src/specify_cli/presets/_commands.py
@@ -104,7 +104,13 @@ def preset_add(
            from ipaddress import ip_address
            from urllib.parse import urlparse as _urlparse

-            _parsed = _urlparse(from_url)
+            try:
+                _parsed = _urlparse(from_url)
+            except ValueError:
+                from rich.markup import escape as _escape_markup
+
+                console.print(f"[red]Error:[/red] Invalid URL: {_escape_markup(from_url)}")
+                raise typer.Exit(1)

            def _is_allowed_download_url(parsed_url):
                host = parsed_url.hostname
@@ -135,7 +141,9 @@ def preset_add(
                )
                raise typer.Exit(1)

-            console.print(f"Installing preset from [cyan]{from_url}[/cyan]...")
+            from rich.markup import escape as _esc
+
+            console.print(f"Installing preset from [cyan]{_esc(from_url)}[/cyan]...")
            import urllib.error
            import tempfile
            import shutil
--- a/src/specify_cli/workflows/_commands.py
+++ b/src/specify_cli/workflows/_commands.py
@@ -50,7 +50,17 @@ workflow_step_catalog_app = typer.Typer(
 workflow_step_app.add_typer(workflow_step_catalog_app, name="catalog")


-def _parse_input_values(input_values: list[str] | None) -> dict[str, Any]:
+def _error_console(json_output: bool):
+    """Console for error text: stderr under ``--json`` so the JSON stdout
+    stream stays parseable, the normal console otherwise. Mirrors the
+    stderr-only error routing already used by ``specify bundle``.
+    """
+    return err_console if json_output else console
+
+
+def _parse_input_values(
+    input_values: list[str] | None, *, json_output: bool = False
+) -> dict[str, Any]:
    """Parse repeated ``key=value`` CLI inputs into a dict.

    Shared by ``workflow run`` and ``workflow resume``. Exits with an error
@@ -59,7 +69,9 @@ def _parse_input_values(input_values: list[str] | None) -> dict[str, Any]:
    inputs: dict[str, Any] = {}
    for kv in input_values or []:
        if "=" not in kv:
-            console.print(f"[red]Error:[/red] Invalid input format: {kv!r} (expected key=value)")
+            _error_console(json_output).print(
+                f"[red]Error:[/red] Invalid input format: {kv!r} (expected key=value)"
+            )
            raise typer.Exit(1)
        key, _, value = kv.partition("=")
        inputs[key.strip()] = value.strip()
@@ -335,25 +347,26 @@ def workflow_run(
    if not json_output:
        engine.on_step_start = lambda sid, label: console.print(f"  \u25b8 [{sid}] {label} \u2026")

+    err = _error_console(json_output)
    try:
        definition = engine.load_workflow(source_path if is_file_source else source)
    except FileNotFoundError:
-        console.print(f"[red]Error:[/red] Workflow not found: {source}")
+        err.print(f"[red]Error:[/red] Workflow not found: {source}")
        raise typer.Exit(1)
    except ValueError as exc:
-        console.print(f"[red]Error:[/red] Invalid workflow: {exc}")
+        err.print(f"[red]Error:[/red] Invalid workflow: {exc}")
        raise typer.Exit(1)

    # Validate
    errors = engine.validate(definition)
    if errors:
-        console.print("[red]Workflow validation failed:[/red]")
-        for err in errors:
-            console.print(f"  • {err}")
+        err.print("[red]Workflow validation failed:[/red]")
+        for verr in errors:
+            err.print(f"  • {verr}")
        raise typer.Exit(1)

    # Parse inputs
-    inputs = _parse_input_values(input_values)
+    inputs = _parse_input_values(input_values, json_output=json_output)

    if not json_output:
        console.print(f"\n[bold cyan]Running workflow:[/bold cyan] {definition.name} ({definition.id})")
@@ -363,10 +376,10 @@ def workflow_run(
        with _stdout_to_stderr_when(json_output):
            state = engine.execute(definition, inputs)
    except ValueError as exc:
-        console.print(f"[red]Error:[/red] {exc}")
+        err.print(f"[red]Error:[/red] {exc}")
        raise typer.Exit(1)
    except Exception as exc:
-        console.print(f"[red]Workflow failed:[/red] {exc}")
+        err.print(f"[red]Workflow failed:[/red] {exc}")
        raise typer.Exit(1)

    if json_output:
@@ -411,19 +424,20 @@ def workflow_resume(
    if not json_output:
        engine.on_step_start = lambda sid, label: console.print(f"  \u25b8 [{sid}] {label} \u2026")

-    inputs = _parse_input_values(input_values)
+    inputs = _parse_input_values(input_values, json_output=json_output)
+    err = _error_console(json_output)

    try:
        with _stdout_to_stderr_when(json_output):
            state = engine.resume(run_id, inputs or None)
    except FileNotFoundError:
-        console.print(f"[red]Error:[/red] Run not found: {run_id}")
+        err.print(f"[red]Error:[/red] Run not found: {run_id}")
        raise typer.Exit(1)
    except ValueError as exc:
-        console.print(f"[red]Error:[/red] {exc}")
+        err.print(f"[red]Error:[/red] {exc}")
        raise typer.Exit(1)
    except Exception as exc:
-        console.print(f"[red]Resume failed:[/red] {exc}")
+        err.print(f"[red]Resume failed:[/red] {exc}")
        raise typer.Exit(1)

    if json_output:
@@ -617,7 +631,11 @@ def workflow_add(
        from urllib.parse import urlparse
        from specify_cli.authentication.http import open_url as _open_url

-        parsed_src = urlparse(source)
+        try:
+            parsed_src = urlparse(source)
+        except ValueError:
+            console.print(f"[red]Error:[/red] Invalid URL: {_escape_markup(source)}")
+            raise typer.Exit(1)
        src_host = parsed_src.hostname or ""
        src_loopback = src_host == "localhost"
        if not src_loopback:
--- a/src/specify_cli/workflows/steps/fan_in/init.py
+++ b/src/specify_cli/workflows/steps/fan_in/init.py
@@ -58,4 +58,13 @@ class FanInStep(StepBase):
                f"Fan-in step {config.get('id', '?')!r}: "
                f"'wait_for' must be a non-empty list of step IDs."
            )
+        output = config.get("output")
+        if output is not None and not isinstance(output, dict):
+            # execute() silently coerces a non-mapping output to {}, so the
+            # author's declared aggregation keys would vanish with no error.
+            # Reject at validation, mirroring the command-step (#3262) fix.
+            errors.append(
+                f"Fan-in step {config.get('id', '?')!r}: 'output' must be a "
+                f"mapping of key -> expression, got {type(output).__name__}."
+            )
        return errors
--- a/src/specify_cli/workflows/steps/shell/init.py
+++ b/src/specify_cli/workflows/steps/shell/init.py
@@ -90,6 +90,16 @@ class ShellStep(StepBase):
            errors.append(
                f"Shell step {config.get('id', '?')!r} is missing 'run' field."
            )
+        elif not isinstance(config["run"], str):
+            # execute() str()-coerces run and invokes it under shell=True, so a
+            # null or list 'run' would run the Python repr ('None', "['echo']")
+            # as a command. Reject non-strings at validation, mirroring the
+            # command-step input/options and gate options type checks. An
+            # expression like "{{ ... }}" is still a str, so it stays valid.
+            errors.append(
+                f"Shell step {config.get('id', '?')!r}: 'run' must be a string, "
+                f"got {type(config['run']).__name__}."
+            )
        output_format = config.get("output_format")
        if output_format is not None and output_format != "json":
            errors.append(
--- a/tests/integration/test_bundler_install_flow.py
+++ b/tests/integration/test_bundler_install_flow.py
@@ -220,3 +220,68 @@ def test_pre_existing_component_is_not_attributed_or_removed(tmp_path: Path):

    remove_bundle(tmp_path, "demo-bundle", installer)
    assert ("extensions", "ext-a") in installer.installed
+
+
+def _bundle(manifest_id, ext_ids, *, version="1.0.0"):
+    data = valid_manifest_dict()
+    data["bundle"]["id"] = manifest_id
+    data["bundle"]["version"] = version
+    data["provides"] = {
+        "extensions": [{"id": e, "version": version} for e in ext_ids]
+    }
+    return BundleManifest.from_dict(data)
+
+
+def test_update_uninstalls_components_dropped_by_new_version(tmp_path: Path):
+    """`bundle update` must uninstall components the new version no longer
+    ships, instead of orphaning them (installed on disk, tracked by nothing)."""
+    make_project(tmp_path)
+    installer = FakeInstaller()
+
+    man_v1 = _bundle("demo", ["ext-a", "ext-b"])
+    install_bundle(tmp_path, _plan(man_v1), installer, manifest=man_v1)
+    assert ("extensions", "ext-b") in installer.installed
+
+    man_v2 = _bundle("demo", ["ext-a"], version="2.0.0")
+    result = install_bundle(
+        tmp_path, _plan(man_v2), installer, manifest=man_v2, refresh=True
+    )
+
+    # ext-b was dropped by v2 -> uninstalled and reported.
+    assert ("extensions", "ext-b") in installer.remove_calls
+    assert ("extensions", "ext-b") in {(c.kind, c.id) for c in result.uninstalled}
+    assert ("extensions", "ext-b") not in installer.installed
+    assert ("extensions", "ext-a") in installer.installed
+
+    # The saved record lists only ext-a.
+    rec = next(r for r in load_records(tmp_path) if r.bundle_id == "demo")
+    keys = {(c.kind, c.id) for c in rec.contributed_components}
+    assert ("extensions", "ext-a") in keys
+    assert ("extensions", "ext-b") not in keys
+
+
+def test_update_keeps_component_still_needed_by_sibling_bundle(tmp_path: Path):
+    """A dropped component still owned by another bundle stays installed."""
+    make_project(tmp_path)
+    installer = FakeInstaller()
+
+    man_sib = _bundle("sibling", ["ext-b"])
+    install_bundle(tmp_path, _plan(man_sib), installer, manifest=man_sib)
+
+    man_v1 = _bundle("demo", ["ext-a", "ext-b"])
+    install_bundle(tmp_path, _plan(man_v1), installer, manifest=man_v1)
+
+    man_v2 = _bundle("demo", ["ext-a"], version="2.0.0")
+    install_bundle(
+        tmp_path, _plan(man_v2), installer, manifest=man_v2, refresh=True
+    )
+
+    # ext-b is still needed by 'sibling' -> not removed, stays installed.
+    assert ("extensions", "ext-b") not in installer.remove_calls
+    assert ("extensions", "ext-b") in installer.installed
+
+    # But demo's record no longer attributes it.
+    rec = next(r for r in load_records(tmp_path) if r.bundle_id == "demo")
+    assert ("extensions", "ext-b") not in {
+        (c.kind, c.id) for c in rec.contributed_components
+    }
--- a/tests/integrations/conftest.py
+++ b/tests/integrations/conftest.py
@@ -1,8 +1,24 @@
 """Shared test helpers for integration tests."""

+import pytest
+
 from specify_cli.integrations.base import MarkdownIntegration


+@pytest.fixture(autouse=True)
+def _isolate_integration_home(monkeypatch: pytest.MonkeyPatch, tmp_path):
+    """Keep integration tests from reading or writing the real user home."""
+    home = tmp_path / "home"
+    for path in (home, home / ".cache", home / ".config", home / ".local" / "share"):
+        path.mkdir(parents=True, exist_ok=True)
+
+    monkeypatch.setenv("HOME", str(home))
+    monkeypatch.setenv("USERPROFILE", str(home))
+    monkeypatch.setenv("XDG_CACHE_HOME", str(home / ".cache"))
+    monkeypatch.setenv("XDG_CONFIG_HOME", str(home / ".config"))
+    monkeypatch.setenv("XDG_DATA_HOME", str(home / ".local" / "share"))
+
+
 class StubIntegration(MarkdownIntegration):
    """Minimal concrete integration for testing."""

--- a/tests/integrations/test_home_isolation.py
+++ b/tests/integrations/test_home_isolation.py
@@ -0,0 +1,21 @@
+"""Regression tests for integration-test environment isolation."""
+
+from __future__ import annotations
+
+import os
+from pathlib import Path
+
+
+def test_integration_tests_use_tmp_home(tmp_path: Path) -> None:
+    home = tmp_path / "home"
+
+    assert Path(os.environ["HOME"]) == home
+    assert Path(os.environ["USERPROFILE"]) == home
+    assert Path(os.environ["XDG_CACHE_HOME"]) == home / ".cache"
+    assert Path(os.environ["XDG_CONFIG_HOME"]) == home / ".config"
+    assert Path(os.environ["XDG_DATA_HOME"]) == home / ".local" / "share"
+
+    assert home.is_dir()
+    assert (home / ".cache").is_dir()
+    assert (home / ".config").is_dir()
+    assert (home / ".local" / "share").is_dir()
--- a/tests/integrations/test_integration_agy.py
+++ b/tests/integrations/test_integration_agy.py
@@ -81,6 +81,26 @@ class TestAgyBuildExecArgs:
        result = i.build_exec_args("my prompt", output_json=False)
        assert result == ["agy", "--print", "my prompt"]

+    def test_build_exec_args_honors_extra_args(self, monkeypatch):
+        """SPECKIT_INTEGRATION_AGY_EXTRA_ARGS must be appended after the prompt.
+
+        agy previously skipped _apply_extra_args_env_var entirely, so the
+        documented per-integration extra-args hook was silently ignored
+        (same class as the merged cursor-agent fix #3265).
+        """
+        from specify_cli.integrations import get_integration
+        monkeypatch.setenv("SPECKIT_INTEGRATION_AGY_EXTRA_ARGS", "--verbose")
+        i = get_integration("agy")
+        assert i.build_exec_args("my prompt") == [
+            "agy", "--print", "my prompt", "--verbose",
+        ]
+
+    def test_build_exec_args_honors_executable_override(self, monkeypatch):
+        from specify_cli.integrations import get_integration
+        monkeypatch.setenv("SPECKIT_INTEGRATION_AGY_EXECUTABLE", "/custom/agy")
+        i = get_integration("agy")
+        assert i.build_exec_args("my prompt")[0] == "/custom/agy"
+

 class TestAgyHookCommandNote:
    """Verify dot-to-hyphen normalization note is injected into hook sections."""
--- a/tests/integrations/test_integration_base_yaml.py
+++ b/tests/integrations/test_integration_base_yaml.py
@@ -184,6 +184,23 @@ class YamlIntegrationTests:
        assert "scripts:" not in parsed["prompt"]
        assert "---" not in parsed["prompt"]

+    def test_yaml_prompt_with_indented_first_line_stays_valid(self):
+        """A body whose first line is indented must still parse.
+
+        A bare ``|`` block scalar infers its indentation from the first
+        non-empty line, so a body starting with an indented line (e.g. a
+        markdown code block or nested list item) made the parser expect that
+        deeper indent for the whole block and reject the later, shallower
+        lines. The explicit ``|2`` indicator pins the indent so it parses."""
+        body = "    indented first line\nback to normal\n    indented again"
+        rendered = YamlIntegration._render_yaml("Title", "Desc", body, "src")
+
+        yaml_lines = [
+            ln for ln in rendered.split("\n") if not ln.startswith("# Source:")
+        ]
+        parsed = yaml.safe_load("\n".join(yaml_lines))
+        assert parsed["prompt"].rstrip("\n") == body
+
    def test_plan_command_has_no_context_placeholder(self, tmp_path):
        """The generated plan command must not carry a context-file placeholder.

--- a/tests/integrations/test_integration_hermes.py
+++ b/tests/integrations/test_integration_hermes.py
@@ -353,3 +353,38 @@ class TestHermesInitFlow:
            if "agent-context" not in d.name
        ]
        assert local_skills == [], f"Local skills dir should be empty, got: {local_skills}"
+
+
+class TestHermesBuildExecArgs:
+    """CLI dispatch argv, including the operator extra-args env hook."""
+
+    def test_build_exec_args_default_shape(self):
+        i = get_integration("hermes")
+        assert i.build_exec_args("/speckit-plan hi", output_json=True) == [
+            "hermes", "chat", "-Q", "--json", "-s", "speckit-plan", "-q", "hi",
+        ]
+
+    def test_build_exec_args_honors_extra_args(self, monkeypatch):
+        """SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS is injected before the
+        canonical -m/--json/-s/-q flags (same env hook as codex/opencode/
+        devin; hermes previously skipped _apply_extra_args_env_var entirely).
+        """
+        monkeypatch.setenv(
+            "SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS", "--temperature 0.2"
+        )
+        i = get_integration("hermes")
+        args = i.build_exec_args("/speckit-plan hi", output_json=True)
+        assert args == [
+            "hermes", "chat", "-Q", "--temperature", "0.2",
+            "--json", "-s", "speckit-plan", "-q", "hi",
+        ]
+        # Injected before the canonical flags so it can't displace them.
+        assert args.index("--temperature") < args.index("--json")
+        assert args.index("--temperature") < args.index("-s")
+
+    def test_build_exec_args_honors_executable_override(self, monkeypatch):
+        monkeypatch.setenv(
+            "SPECKIT_INTEGRATION_HERMES_EXECUTABLE", "/custom/hermes"
+        )
+        i = get_integration("hermes")
+        assert i.build_exec_args("/speckit-plan hi")[0] == "/custom/hermes"
--- a/tests/integrations/test_manifest.py
+++ b/tests/integrations/test_manifest.py
@@ -481,3 +481,40 @@ class TestRecordExistingNewGuards:
        m = IntegrationManifest("test", tmp_path)
        with pytest.raises(ValueError, match=r"canonical|'\.\.' segments"):
            m.record_existing("dir/../file.txt")
+
+
+class TestManifestUnreadableFile:
+    """A managed file that is unreadable (e.g. PermissionError) must not crash
+    check_modified()/uninstall() — the CLI handlers surfaced a raw traceback."""
+
+    def _mk(self, tmp_path):
+        m = IntegrationManifest("test", tmp_path)
+        m.record_file("sub/f.md", "content")
+        return m
+
+    def test_check_modified_treats_unreadable_as_modified(self, tmp_path, monkeypatch):
+        m = self._mk(tmp_path)
+
+        def raise_perm(_path):
+            raise PermissionError("unreadable")
+
+        monkeypatch.setattr(
+            "specify_cli.integrations.manifest._sha256", raise_perm
+        )
+        # Before the fix this raised PermissionError.
+        assert m.check_modified() == ["sub/f.md"]
+
+    def test_uninstall_preserves_unreadable_file(self, tmp_path, monkeypatch):
+        m = self._mk(tmp_path)
+
+        def raise_perm(_path):
+            raise PermissionError("unreadable")
+
+        monkeypatch.setattr(
+            "specify_cli.integrations.manifest._sha256", raise_perm
+        )
+        removed, skipped = m.uninstall(force=False)
+        # Can't verify ownership => preserve, don't crash and don't delete.
+        assert removed == []
+        assert (tmp_path / "sub" / "f.md") in skipped
+        assert (tmp_path / "sub" / "f.md").exists()
--- a/tests/integrations/test_registry.py
+++ b/tests/integrations/test_registry.py
@@ -48,6 +48,19 @@ def _multi_install_safe_pairs() -> list[tuple[str, str]]:
    ]


+def _multi_install_safe_orders() -> list[list[str]]:
+    safe_keys = _multi_install_safe_keys()
+    if len(safe_keys) < 2:
+        return [safe_keys]
+    return [safe_keys[index:] + safe_keys[:index] for index in range(len(safe_keys))]
+
+
+def _multi_install_safe_order_id(ordered_keys: list[str]) -> str:
+    if not ordered_keys:
+        return "no-safe-integrations"
+    return f"init-{ordered_keys[0]}"
+
+
 def _posix_path(value: str | None) -> str | None:
    if not value:
        return None
@@ -87,16 +100,6 @@ def _paths_overlap(first: str | None, second: str | None) -> bool:
        return False


-def _path_is_inside(path: str | None, directory: str | None) -> bool:
-    if not path or not directory:
-        return False
-    try:
-        PurePosixPath(path).relative_to(PurePosixPath(directory))
-        return True
-    except ValueError:
-        return False
-
-
 class TestRegistry:
    def test_registry_is_dict(self):
        assert isinstance(INTEGRATION_REGISTRY, dict)
@@ -162,6 +165,15 @@ class TestRegistrarKeyAlignment:
 class TestMultiInstallSafeContracts:
    """Declared safe integrations must stay isolated from each other."""

+    def test_safe_install_orders_rotate_each_integration_through_init(self):
+        safe_keys = _multi_install_safe_keys()
+        orders = _multi_install_safe_orders()
+
+        assert len(safe_keys) >= 2
+        assert [order[0] for order in orders] == safe_keys
+        assert len({tuple(order) for order in orders}) == len(safe_keys)
+        assert all(sorted(order) == safe_keys for order in orders)
+
    @pytest.mark.parametrize("key", _multi_install_safe_keys())
    def test_safe_integrations_have_static_isolated_paths(self, key):
        assert _integration_root_dir(key), (
@@ -187,62 +199,77 @@ class TestMultiInstallSafeContracts:
            f"{_integration_commands_dir(second)!r}"
        )

-    @pytest.mark.parametrize(("first", "second"), _multi_install_safe_pairs())
+    @pytest.mark.parametrize(
+        "ordered_keys",
+        _multi_install_safe_orders(),
+        ids=_multi_install_safe_order_id,
+    )
    def test_safe_integrations_have_disjoint_manifests(
        self,
        tmp_path,
-        first,
-        second,
+        ordered_keys,
    ):
-        for initial, additional in ((first, second), (second, first)):
-            project_root = tmp_path / f"project-{initial}-{additional}"
-            project_root.mkdir()
-            runner = CliRunner()
+        # The pairwise disjointness contract is only meaningful with at least
+        # two safe integrations. Guard so a shrunken registry fails loudly here
+        # rather than passing vacuously (or tripping over ordered_keys[0] below).
+        assert len(ordered_keys) >= 2, (
+            f"expected at least two multi-install-safe integrations, got {ordered_keys}"
+        )

-            original_cwd = os.getcwd()
-            try:
-                os.chdir(project_root)
-                init_result = runner.invoke(
-                    app,
-                    [
-                        "init",
-                        "--here",
-                        "--integration",
-                        initial,
-                        "--script",
-                        "sh",
-                        "--ignore-agent-tools",
-                    ],
-                    catch_exceptions=False,
-                )
-                assert init_result.exit_code == 0, init_result.output
+        project_root = tmp_path / "project"
+        project_root.mkdir()
+        runner = CliRunner()

+        # Install every safe integration once into a single project, then assert
+        # pairwise manifest isolation. Each safe integration writes only to its
+        # own (disjoint) directories and always records what it writes, so a
+        # manifest's contents are independent of install order and of which other
+        # integrations are co-installed. The parametrized rotations keep the
+        # aggregate setup while placing each safe integration first once, so each
+        # one still exercises the `specify init --integration ...` path.
+        original_cwd = os.getcwd()
+        try:
+            os.chdir(project_root)
+            init_result = runner.invoke(
+                app,
+                [
+                    "init",
+                    "--here",
+                    "--integration",
+                    ordered_keys[0],
+                    "--script",
+                    "sh",
+                    "--ignore-agent-tools",
+                ],
+                catch_exceptions=False,
+            )
+            assert init_result.exit_code == 0, init_result.output
+
+            for key in ordered_keys[1:]:
                install_result = runner.invoke(
                    app,
-                    ["integration", "install", additional, "--script", "sh"],
+                    ["integration", "install", key, "--script", "sh"],
                    catch_exceptions=False,
                )
                assert install_result.exit_code == 0, install_result.output
-            finally:
-                os.chdir(original_cwd)
+        finally:
+            os.chdir(original_cwd)

-            initial_manifest = json.loads(
-                (
-                    project_root / ".specify" / "integrations" / f"{initial}.manifest.json"
-                ).read_text(encoding="utf-8")
-            )
-            additional_manifest = json.loads(
-                (
-                    project_root / ".specify" / "integrations" / f"{additional}.manifest.json"
-                ).read_text(encoding="utf-8")
+        integrations_dir = project_root / ".specify" / "integrations"
+        manifests = {}
+        for key in ordered_keys:
+            manifest = json.loads(
+                (integrations_dir / f"{key}.manifest.json").read_text(encoding="utf-8")
            )
+            files = manifest.get("files", {})
+            assert isinstance(files, dict), f"{key} manifest files must be an object"
+            manifests[key] = set(files.keys())

-            initial_files = set(initial_manifest.get("files", {}))
-            additional_files = set(additional_manifest.get("files", {}))
-
-            assert initial_files.isdisjoint(additional_files), (
-                f"{initial} and {additional} are declared multi-install safe but both manage "
-                f"these files: {sorted(initial_files & additional_files)}"
+        for first, second in _multi_install_safe_pairs():
+            overlap = manifests[first] & manifests[second]
+            assert not overlap, (
+                f"{first} and {second} are declared multi-install safe but both manage "
+                f"these files: {sorted(overlap)}"
            )


--- a/tests/test_authentication.py
+++ b/tests/test_authentication.py
@@ -845,6 +845,22 @@ class TestRedirectStripping:
        auth3 = req3.get_header("Authorization") or req3.unredirected_hdrs.get("Authorization")
        assert auth3 == "Bearer tok"

+    def test_malformed_redirect_url_raises_urlerror_not_valueerror(self):
+        """A redirect to a malformed URL (unterminated IPv6 bracket) surfaces
+        as URLError, which download paths already handle, rather than an
+        unhandled ValueError traceback."""
+        import urllib.error
+        from specify_cli.authentication.http import _StripAuthOnRedirect
+        from urllib.request import Request
+        import io
+
+        handler = _StripAuthOnRedirect(("github.com",))
+        req = Request("https://github.com/org/repo")
+
+        with pytest.raises(urllib.error.URLError):
+            handler.redirect_request(req, io.BytesIO(b""), 302, "Found", {},
+                                     "https://[::1/asset")
+

 # ---------------------------------------------------------------------------
 # _fetch_latest_release_tag delegation
--- a/tests/test_check_prerequisites_python_parity.py
+++ b/tests/test_check_prerequisites_python_parity.py
@@ -0,0 +1,339 @@
+"""Parity tests for the Python check-prerequisites PoC."""
+
+from __future__ import annotations
+
+import json
+import os
+import shutil
+import subprocess
+import sys
+from pathlib import Path
+
+import pytest
+
+from tests.conftest import requires_bash
+
+PROJECT_ROOT = Path(__file__).resolve().parent.parent
+COMMON_SH = PROJECT_ROOT / "scripts" / "bash" / "common.sh"
+CHECK_PREREQS_SH = PROJECT_ROOT / "scripts" / "bash" / "check-prerequisites.sh"
+COMMON_PS = PROJECT_ROOT / "scripts" / "powershell" / "common.ps1"
+CHECK_PREREQS_PS = PROJECT_ROOT / "scripts" / "powershell" / "check-prerequisites.ps1"
+COMMON_PY = PROJECT_ROOT / "scripts" / "python" / "common.py"
+CHECK_PREREQS_PY = PROJECT_ROOT / "scripts" / "python" / "check_prerequisites.py"
+
+HAS_PWSH = shutil.which("pwsh") is not None
+_WINDOWS_POWERSHELL = (
+    shutil.which("powershell.exe") or shutil.which("powershell")
+) if os.name == "nt" else None
+
+
+def _install_scripts(repo: Path) -> None:
+    bash_dir = repo / ".specify" / "scripts" / "bash"
+    bash_dir.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_SH, bash_dir / "common.sh")
+    shutil.copy(CHECK_PREREQS_SH, bash_dir / "check-prerequisites.sh")
+
+    ps_dir = repo / ".specify" / "scripts" / "powershell"
+    ps_dir.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_PS, ps_dir / "common.ps1")
+    shutil.copy(CHECK_PREREQS_PS, ps_dir / "check-prerequisites.ps1")
+
+    py_dir = repo / ".specify" / "scripts" / "python"
+    py_dir.mkdir(parents=True, exist_ok=True)
+    shutil.copy(COMMON_PY, py_dir / "common.py")
+    shutil.copy(CHECK_PREREQS_PY, py_dir / "check_prerequisites.py")
+
+
+def _write_feature_json(
+    repo: Path, feature_directory: str = "specs/001-my-feature"
+) -> None:
+    (repo / ".specify" / "feature.json").write_text(
+        json.dumps({"feature_directory": feature_directory}, separators=(",", ":"))
+        + "\n",
+        encoding="utf-8",
+    )
+
+
+def _clean_env() -> dict[str, str]:
+    env = os.environ.copy()
+    for key in list(env):
+        if key.startswith("SPECIFY_"):
+            env.pop(key)
+    return env
+
+
+def _git_init(repo: Path) -> None:
+    subprocess.run(["git", "init", "-q"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "config", "user.email", "test@example.com"], cwd=repo, check=True
+    )
+    subprocess.run(["git", "config", "user.name", "Test User"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "commit", "--allow-empty", "-m", "init", "-q"], cwd=repo, check=True
+    )
+
+
+@pytest.fixture
+def prereq_repo(tmp_path: Path) -> Path:
+    repo = tmp_path / "proj"
+    repo.mkdir()
+    _git_init(repo)
+    (repo / ".specify").mkdir()
+    _install_scripts(repo)
+    return repo
+
+
+def _py_cmd(repo: Path, *args: str) -> list[str]:
+    script = repo / ".specify" / "scripts" / "python" / "check_prerequisites.py"
+    return [sys.executable, str(script), *args]
+
+
+def _repo_copy_py_cmd(repo: Path, *args: str) -> list[str]:
+    script = repo / "scripts" / "python" / "check_prerequisites.py"
+    return [sys.executable, str(script), *args]
+
+
+def _bash_cmd(repo: Path, *args: str) -> list[str]:
+    script = repo / ".specify" / "scripts" / "bash" / "check-prerequisites.sh"
+    return ["bash", str(script), *args]
+
+
+def _ps_cmd(repo: Path, *args: str) -> list[str]:
+    script = repo / ".specify" / "scripts" / "powershell" / "check-prerequisites.ps1"
+    exe = "pwsh" if HAS_PWSH else _WINDOWS_POWERSHELL
+    return [exe, "-NoProfile", "-File", str(script), *args]
+
+
+def _run(
+    cmd: list[str], repo: Path, env: dict[str, str] | None = None
+) -> subprocess.CompletedProcess[str]:
+    return subprocess.run(
+        cmd,
+        cwd=repo,
+        capture_output=True,
+        text=True,
+        check=False,
+        env=env or _clean_env(),
+    )
+
+
+def _json_stdout(result: subprocess.CompletedProcess[str]) -> object:
+    return json.loads(result.stdout)
+
+
+def _normalize_status_text(text: str) -> str:
+    return (
+        text.replace("  ✓ ", "  [OK] ")
+        .replace("  ✗ ", "  [FAIL] ")
+        .replace("\r\n", "\n")
+    )
+
+
+def _normalize_help_text(text: str) -> str:
+    normalized = text.replace("\r\n", "\n").replace(
+        "check-prerequisites.sh", "check_prerequisites.py"
+    )
+    return "\n".join("" if not line.strip() else line for line in normalized.split("\n"))
+
+
+@requires_bash
+@pytest.mark.parametrize(
+    "args",
+    [
+        ("--json",),
+        ("--json", "--include-tasks"),
+        ("--json", "--require-tasks", "--include-tasks"),
+        ("--json", "--paths-only"),
+    ],
+)
+def test_python_json_output_matches_bash(prereq_repo: Path, args: tuple[str, ...]) -> None:
+    feat = prereq_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True)
+    (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
+    (feat / "tasks.md").write_text("# tasks\n", encoding="utf-8")
+    (feat / "research.md").write_text("# research\n", encoding="utf-8")
+    (feat / "data-model.md").write_text("# model\n", encoding="utf-8")
+    (feat / "quickstart.md").write_text("# quickstart\n", encoding="utf-8")
+    (feat / "contracts" / "v1").mkdir(parents=True)
+    _write_feature_json(prereq_repo)
+
+    bash = _run(_bash_cmd(prereq_repo, *args), prereq_repo)
+    py = _run(_py_cmd(prereq_repo, *args), prereq_repo)
+
+    assert py.returncode == bash.returncode == 0
+    assert py.stderr == bash.stderr == ""
+    assert _json_stdout(py) == _json_stdout(bash)
+
+
+@requires_bash
+def test_python_text_output_matches_bash(prereq_repo: Path) -> None:
+    feat = prereq_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True)
+    (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
+    (feat / "contracts").mkdir()
+    _write_feature_json(prereq_repo)
+
+    bash = _run(_bash_cmd(prereq_repo, "--include-tasks"), prereq_repo)
+    py = _run(_py_cmd(prereq_repo, "--include-tasks"), prereq_repo)
+
+    assert py.returncode == bash.returncode == 0
+    assert py.stderr == bash.stderr == ""
+    assert _normalize_status_text(py.stdout) == _normalize_status_text(bash.stdout)
+
+
+@requires_bash
+def test_python_help_output_matches_bash(prereq_repo: Path) -> None:
+    bash = _run(_bash_cmd(prereq_repo, "--help"), prereq_repo)
+    py = _run(_py_cmd(prereq_repo, "--help"), prereq_repo)
+
+    assert py.returncode == bash.returncode == 0
+    assert py.stderr == bash.stderr == ""
+    assert _normalize_help_text(py.stdout) == _normalize_help_text(bash.stdout)
+
+
+@requires_bash
+def test_python_unknown_option_matches_bash_error_shape(prereq_repo: Path) -> None:
+    bash = _run(_bash_cmd(prereq_repo, "--bogus"), prereq_repo)
+    py = _run(_py_cmd(prereq_repo, "--bogus"), prereq_repo)
+
+    assert py.returncode == bash.returncode == 1
+    assert py.stdout == bash.stdout == ""
+    assert py.stderr == bash.stderr
+
+
+@pytest.mark.skipif(not (HAS_PWSH or _WINDOWS_POWERSHELL), reason="no PowerShell available")
+@pytest.mark.parametrize(
+    ("py_args", "ps_args"),
+    [
+        (("--json",), ("-Json",)),
+        (("--json", "--include-tasks"), ("-Json", "-IncludeTasks")),
+        (
+            ("--json", "--require-tasks", "--include-tasks"),
+            ("-Json", "-RequireTasks", "-IncludeTasks"),
+        ),
+        (("--json", "--paths-only"), ("-Json", "-PathsOnly")),
+    ],
+    ids=[
+        "json",
+        "json_include_tasks",
+        "json_require_tasks_include_tasks",
+        "json_paths_only",
+    ],
+)
+def test_python_json_output_matches_powershell(
+    prereq_repo: Path, py_args: tuple[str, ...], ps_args: tuple[str, ...]
+) -> None:
+    feat = prereq_repo / "specs" / "001-my-feature"
+    feat.mkdir(parents=True)
+    (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
+    (feat / "tasks.md").write_text("# tasks\n", encoding="utf-8")
+    (feat / "research.md").write_text("# research\n", encoding="utf-8")
+    (feat / "data-model.md").write_text("# model\n", encoding="utf-8")
+    (feat / "quickstart.md").write_text("# quickstart\n", encoding="utf-8")
+    (feat / "contracts" / "v1").mkdir(parents=True)
+    _write_feature_json(prereq_repo)
+
+    ps = _run(_ps_cmd(prereq_repo, *ps_args), prereq_repo)
+    py = _run(_py_cmd(prereq_repo, *py_args), prereq_repo)
+
+    assert py.returncode == ps.returncode == 0
+    assert py.stderr == ps.stderr == ""
+    assert _json_stdout(py) == _json_stdout(ps)
+
+
+def test_python_repo_copy_script_file_fallback_finds_repo_root(tmp_path: Path) -> None:
+    repo = tmp_path / "proj"
+    outside = tmp_path / "outside"
+    repo.mkdir()
+    outside.mkdir()
+    _git_init(repo)
+    (repo / ".specify").mkdir()
+    _write_feature_json(repo)
+    (repo / "specs" / "001-my-feature").mkdir(parents=True)
+
+    py_dir = repo / "scripts" / "python"
+    py_dir.mkdir(parents=True)
+    shutil.copy(COMMON_PY, py_dir / "common.py")
+    shutil.copy(CHECK_PREREQS_PY, py_dir / "check_prerequisites.py")
+
+    py = _run(_repo_copy_py_cmd(repo, "--json", "--paths-only"), outside)
+
+    assert py.returncode == 0, py.stderr
+    assert Path(_json_stdout(py)["REPO_ROOT"]) == repo
+
+
+def test_python_paths_only_does_not_persist_feature_json(prereq_repo: Path) -> None:
+    (prereq_repo / "specs" / "001-my-feature").mkdir(parents=True)
+    (prereq_repo / "specs" / "002-other").mkdir(parents=True)
+    _write_feature_json(prereq_repo, "specs/001-my-feature")
+    feature_json = prereq_repo / ".specify" / "feature.json"
+    before = feature_json.read_text(encoding="utf-8")
+    env = _clean_env()
+    env["SPECIFY_FEATURE_DIRECTORY"] = "specs/002-other"
+
+    py = _run(_py_cmd(prereq_repo, "--json", "--paths-only"), prereq_repo, env=env)
+
+    assert py.returncode == 0, py.stderr
+    assert "002-other" in _json_stdout(py)["FEATURE_DIR"]
+    assert feature_json.read_text(encoding="utf-8") == before
+
+
+def test_python_normal_mode_persists_feature_json(prereq_repo: Path) -> None:
+    (prereq_repo / "specs" / "001-my-feature").mkdir(parents=True)
+    feat = prereq_repo / "specs" / "002-other"
+    feat.mkdir(parents=True)
+    (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
+    _write_feature_json(prereq_repo, "specs/001-my-feature")
+    env = _clean_env()
+    env["SPECIFY_FEATURE_DIRECTORY"] = "specs/002-other"
+
+    py = _run(_py_cmd(prereq_repo, "--json"), prereq_repo, env=env)
+
+    assert py.returncode == 0, py.stderr
+    data = json.loads(
+        (prereq_repo / ".specify" / "feature.json").read_text(encoding="utf-8")
+    )
+    assert data["feature_directory"] == "specs/002-other"
+
+
+@pytest.mark.parametrize(
+    ("args", "expected"),
+    [
+        (("--json",), "Feature directory not found"),
+        (("--json",), "plan.md not found"),
+        (("--json", "--require-tasks"), "tasks.md not found"),
+    ],
+    ids=["missing_feature_context", "missing_plan", "missing_tasks"],
+)
+def test_python_negative_errors_are_stderr_only(
+    tmp_path: Path, args: tuple[str, ...], expected: str
+) -> None:
+    repo = tmp_path / "proj"
+    repo.mkdir()
+    _git_init(repo)
+    (repo / ".specify").mkdir()
+    _install_scripts(repo)
+
+    if expected in {"plan.md not found", "tasks.md not found"}:
+        feat = repo / "specs" / "001-my-feature"
+        feat.mkdir(parents=True)
+        _write_feature_json(repo)
+        if expected == "tasks.md not found":
+            (feat / "plan.md").write_text("# plan\n", encoding="utf-8")
+
+    py = _run(_py_cmd(repo, *args), repo)
+
+    assert py.returncode != 0
+    assert expected in py.stderr
+    assert expected not in py.stdout
+    assert py.stdout.strip() == ""
+
+
+def test_python_branch_falls_back_to_feature_dir_basename(prereq_repo: Path) -> None:
+    (prereq_repo / "specs" / "001-my-feature").mkdir(parents=True)
+    _write_feature_json(prereq_repo)
+
+    py = _run(_py_cmd(prereq_repo, "--json", "--paths-only"), prereq_repo)
+
+    assert py.returncode == 0, py.stderr
+    assert _json_stdout(py)["BRANCH"] == "001-my-feature"
--- a/tests/test_extension_skills.py
+++ b/tests/test_extension_skills.py
@@ -850,6 +850,67 @@ class TestExtensionSkillRegistration:
        assert ".specify/templates/checklist.md" in content
        assert ".specify/memory/constitution.md" in content

+    def test_skill_registration_uses_extension_local_script_paths(self, project_dir, temp_dir):
+        """Auto-registered skills should not rewrite extension scripts into core scripts."""
+        _create_init_options(project_dir, ai="claude", ai_skills=True)
+        skills_dir = _create_skills_dir(project_dir, ai="claude")
+
+        ext_dir = temp_dir / "scripted-ext"
+        ext_dir.mkdir()
+        manifest_data = {
+            "schema_version": "1.0",
+            "extension": {
+                "id": "scripted-ext",
+                "name": "Scripted Extension",
+                "version": "1.0.0",
+                "description": "Test",
+            },
+            "requires": {"speckit_version": ">=0.1.0"},
+            "provides": {
+                "commands": [
+                    {
+                        "name": "speckit.scripted-ext.check",
+                        "file": "commands/check.md",
+                        "description": "Scripted check command",
+                    }
+                ]
+            },
+        }
+        with open(ext_dir / "extension.yml", "w") as f:
+            yaml.safe_dump(manifest_data, f)
+
+        (ext_dir / "commands").mkdir()
+        (ext_dir / "scripts" / "bash").mkdir(parents=True)
+        (ext_dir / "scripts" / "bash" / "resolve-skill.sh").write_text(
+            "#!/usr/bin/env bash\n"
+        )
+        (ext_dir / "scripts" / "bash" / "ensure-skills.sh").write_text(
+            "#!/usr/bin/env bash\n"
+        )
+        (ext_dir / "commands" / "check.md").write_text(
+            "---\n"
+            "description: Scripted check command\n"
+            "scripts:\n"
+            '  sh: scripts/bash/resolve-skill.sh "{ARGS}"\n'
+            "---\n\n"
+            "Run {SCRIPT}\n"
+            "Then run scripts/bash/ensure-skills.sh.\n"
+        )
+
+        manager = ExtensionManager(project_dir)
+        manager.install_from_directory(ext_dir, "0.1.0", register_commands=False)
+
+        content = (skills_dir / "speckit-scripted-ext-check" / "SKILL.md").read_text()
+        assert "{SCRIPT}" not in content
+        assert "{ARGS}" not in content
+        assert (
+            '.specify/extensions/scripted-ext/scripts/bash/resolve-skill.sh "$ARGUMENTS"'
+            in content
+        )
+        assert ".specify/extensions/scripted-ext/scripts/bash/ensure-skills.sh" in content
+        assert ".specify/scripts/bash/resolve-skill.sh" not in content
+        assert ".specify/scripts/bash/ensure-skills.sh" not in content
+
    def test_missing_command_file_skipped(self, skills_project, temp_dir):
        """Commands with missing source files should be skipped gracefully."""
        project_dir, skills_dir = skills_project
--- a/tests/test_extensions.py
+++ b/tests/test_extensions.py
@@ -31,6 +31,7 @@ from specify_cli.extensions import (
    ExtensionRegistry,
    ExtensionManager,
    CommandRegistrar,
+    ConfigManager,
    HookExecutor,
    ExtensionCatalog,
    ExtensionError,
@@ -1146,10 +1147,12 @@ class TestExtensionManager:
            context_note=None,
            link_outputs=False,
            create_missing_active_skills_dir=False,
+            extension_id=None,
        ):
            captured["create_missing_active_skills_dir"] = (
                create_missing_active_skills_dir
            )
+            captured["extension_id"] = extension_id
            return {}

        monkeypatch.setattr(
@@ -1163,6 +1166,7 @@ class TestExtensionManager:
        registrar.register_commands_for_all_agents(manifest, extension_dir, project_dir)

        assert captured["create_missing_active_skills_dir"] is False
+        assert captured["extension_id"] == manifest.id

    def test_install_duplicate(self, extension_dir, project_dir):
        """Test installing already installed extension."""
@@ -1694,6 +1698,29 @@ $ARGUMENTS
        assert adjusted["scripts"]["sh"] == ".specify/extensions/test-ext/scripts/setup.sh {ARGS}"
        assert adjusted["scripts"]["ps"] == ".specify/scripts/powershell/setup-plan.ps1 {ARGS}"

+    def test_adjust_script_paths_rewrites_extension_top_level_scripts(self):
+        """Extension command-local scripts should resolve under the installed extension."""
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        registrar = AgentCommandRegistrar()
+        original = {
+            "scripts": {
+                "sh": "scripts/bash/resolve-skill.sh {ARGS}",
+                "ps": "../../scripts/powershell/setup-plan.ps1 -Json",
+            }
+        }
+
+        adjusted = registrar._adjust_script_paths(original, extension_id="test-ext")
+
+        assert (
+            adjusted["scripts"]["sh"]
+            == ".specify/extensions/test-ext/scripts/bash/resolve-skill.sh {ARGS}"
+        )
+        assert (
+            adjusted["scripts"]["ps"]
+            == ".specify/scripts/powershell/setup-plan.ps1 -Json"
+        )
+
    def test_rewrite_project_relative_paths_preserves_extension_local_body_paths(self):
        """Body rewrites should preserve extension-local assets while fixing top-level refs."""
        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
@@ -1708,6 +1735,24 @@ $ARGUMENTS
        assert ".specify/extensions/test-ext/templates/spec.md" in rewritten
        assert ".specify/scripts/bash/setup-plan.sh" in rewritten

+    def test_rewrite_project_relative_paths_uses_extension_context_for_scripts(self):
+        """Extension source bodies treat top-level scripts/ as extension-local."""
+        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
+
+        body = (
+            "Run scripts/bash/ensure-skills.sh\n"
+            "Fallback ../../scripts/bash/setup-plan.sh\n"
+            "Read templates/checklist.md\n"
+        )
+
+        rewritten = AgentCommandRegistrar.rewrite_project_relative_paths(
+            body, extension_id="test-ext"
+        )
+
+        assert ".specify/extensions/test-ext/scripts/bash/ensure-skills.sh" in rewritten
+        assert ".specify/scripts/bash/setup-plan.sh" in rewritten
+        assert ".specify/templates/checklist.md" in rewritten
+
    def test_render_toml_command_handles_embedded_triple_double_quotes(self):
        """TOML renderer should stay valid when body includes triple double-quotes."""
        from specify_cli.agents import CommandRegistrar as AgentCommandRegistrar
@@ -5396,6 +5441,29 @@ class TestExtensionAddCLI:
                f"confirm must precede spinner, got: {call_order}"
        assert result.exit_code == 0  # user declined → clean exit

+    def test_add_from_malformed_ipv6_url_exits_cleanly(self, tmp_path):
+        """A malformed IPv6 URL must produce a clean error, not a ValueError traceback."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        project_dir = tmp_path / "test-project"
+        project_dir.mkdir()
+        (project_dir / ".specify").mkdir()
+
+        runner = CliRunner()
+        with patch.object(Path, "cwd", return_value=project_dir):
+            result = runner.invoke(
+                app,
+                ["extension", "add", "my-ext", "--from", "https://[::1/ext.zip"],
+                catch_exceptions=True,
+            )
+
+        assert result.exit_code == 1
+        assert result.exception is None or isinstance(result.exception, SystemExit)
+        plain = strip_ansi(result.output)
+        assert "Invalid URL" in plain
+
    def test_add_status_escapes_extension_markup(self, tmp_path):
        """User-controlled extension names must not be parsed as Rich markup."""
        from rich.markup import escape as escape_markup
@@ -7492,3 +7560,52 @@ def test_extension_wrapper_resolves_ghes_asset_when_host_configured(tmp_path, mo
    )
    assert resolved == "https://ghes.example/api/v3/repos/o/r/releases/assets/7"
    assert captured == ["https://ghes.example/api/v3/repos/o/r/releases/tags/v1"]
+
+
+class TestConfigManagerNonMappingYaml:
+    """A non-mapping YAML config root must not crash config/hook resolution."""
+
+    def _make(self, tmp_path, body: str):
+        ext_dir = tmp_path / ".specify" / "extensions" / "jira"
+        ext_dir.mkdir(parents=True)
+        (ext_dir / "jira-config.yml").write_text(body, encoding="utf-8")
+        return ConfigManager(tmp_path, "jira")
+
+    def test_get_config_coerces_list_root(self, tmp_path):
+        """A YAML list root previously raised AttributeError in _merge_configs."""
+        cm = self._make(tmp_path, "- foo\n- bar\n")
+        assert cm.get_config() == {}
+
+    def test_get_config_coerces_scalar_root(self, tmp_path):
+        cm = self._make(tmp_path, "just a string\n")
+        assert cm.get_config() == {}
+
+    def test_has_value_and_get_value_do_not_raise(self, tmp_path):
+        cm = self._make(tmp_path, "- foo\n")
+        assert cm.has_value("anything") is False
+        assert cm.get_value("anything") is None
+
+    def test_valid_local_config_layers_over_list_root_project_config(self, tmp_path):
+        """A malformed project config must not block a valid local config."""
+        ext_dir = tmp_path / ".specify" / "extensions" / "jira"
+        ext_dir.mkdir(parents=True)
+        (ext_dir / "jira-config.yml").write_text("- foo\n- bar\n", encoding="utf-8")
+        (ext_dir / "local-config.yml").write_text(
+            "notifications:\n  enabled: true\n", encoding="utf-8"
+        )
+        cm = ConfigManager(tmp_path, "jira")
+        assert cm.get_value("notifications.enabled") is True
+
+    def test_hook_condition_returns_false_without_raising(self, tmp_path):
+        """`config.x is set` on a scalar-root config must evaluate cleanly.
+
+        Before the fix, _merge_configs raised AttributeError and the
+        exception was swallowed by should_execute_hook, silently disabling
+        every config-based hook for the extension. Assert on
+        _evaluate_condition directly so the crash isn't masked.
+        """
+        ext_dir = tmp_path / ".specify" / "extensions" / "jira"
+        ext_dir.mkdir(parents=True)
+        (ext_dir / "jira-config.yml").write_text("just a string\n", encoding="utf-8")
+        executor = HookExecutor(tmp_path)
+        assert executor._evaluate_condition("config.x is set", "jira") is False
--- a/tests/test_github_http.py
+++ b/tests/test_github_http.py
@@ -233,6 +233,23 @@ class TestResolveGitHubReleaseAssetApiUrl:
        assert result is None
        assert called == []

+    def test_returns_none_on_malformed_ghes_port(self):
+        """A malformed port on an allowlisted GHES host returns None, not a
+        ValueError (contract: resolve or return None, never raise)."""
+        called = []
+
+        def open_never(url, timeout=None, extra_headers=None):
+            called.append(url)
+            raise AssertionError("open_url_fn must not be called")
+
+        result = resolve_github_release_asset_api_url(
+            "https://ghes.example:notaport/o/r/releases/download/v1/ext.zip",
+            open_never,
+            github_hosts=("ghes.example",),
+        )
+        assert result is None
+        assert called == []
+
    def test_passthrough_for_unlisted_ghes_api_asset_url(self):
        """A direct GHES /api/v3 asset URL passes through even when the host is
        not allowlisted: passthrough issues no API request, and the download
--- a/tests/test_post_process.py
+++ b/tests/test_post_process.py
@@ -0,0 +1,245 @@
+"""Tests for post_process_command_content() hook on IntegrationBase.
+
+Verifies that the generalized post-processing hook:
+- Runs for non-skills format types (Markdown, TOML, YAML)
+- Does NOT run for skills-format agents
+- Default no-op returns content unchanged
+- Exceptions propagate to caller
+"""
+
+from __future__ import annotations
+
+from unittest.mock import patch
+
+import pytest
+
+from specify_cli.agents import CommandRegistrar
+from specify_cli.integrations.base import IntegrationBase
+
+
+@pytest.fixture
+def registrar():
+    return CommandRegistrar()
+
+
+@pytest.fixture
+def ext_dir(tmp_path):
+    """Create a mock extension with a simple command template."""
+    ext = tmp_path / "extension"
+    ext.mkdir()
+    cmd_dir = ext / "commands"
+    cmd_dir.mkdir()
+    return ext, cmd_dir
+
+
+def _write_cmd(cmd_dir, name="review.md", body="Review the code.\n"):
+    cmd_file = cmd_dir / name
+    cmd_file.write_text(
+        f"---\ndescription: Test command\n---\n\n{body}",
+        encoding="utf-8",
+    )
+    return cmd_file
+
+
+class TestDefaultNoOp:
+    def test_returns_content_unchanged(self):
+        base = IntegrationBase()
+        content = "Some command content\nwith multiple lines."
+        assert base.post_process_command_content(content) == content
+
+    def test_empty_string(self):
+        base = IntegrationBase()
+        assert base.post_process_command_content("") == ""
+
+
+class TestMarkdownAgentPostProcess:
+    def test_opencode_post_process_applied(
+        self, tmp_path, registrar, ext_dir, monkeypatch
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        opencode = get_integration("opencode")
+        marker = "<!-- POST_PROCESSED -->"
+
+        def _inject_marker(self, content):
+            return content + marker
+
+        monkeypatch.setattr(
+            opencode.__class__, "post_process_command_content", _inject_marker
+        )
+
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+        registrar.register_commands(
+            "opencode", commands, "test-ext", ext, tmp_path
+        )
+
+        cmd_output = tmp_path / ".opencode" / "commands" / "speckit.test.review.md"
+        assert cmd_output.exists()
+        content = cmd_output.read_text(encoding="utf-8")
+        assert marker in content
+
+
+class TestTomlAgentPostProcess:
+    def test_gemini_post_process_applied(
+        self, tmp_path, registrar, ext_dir, monkeypatch
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        gemini = get_integration("gemini")
+        marker = "# POST_PROCESSED"
+
+        def _inject_marker(self, content):
+            return content + f"\n{marker}\n"
+
+        monkeypatch.setattr(
+            gemini.__class__, "post_process_command_content", _inject_marker
+        )
+
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+        registrar.register_commands(
+            "gemini", commands, "test-ext", ext, tmp_path
+        )
+
+        cmd_output = tmp_path / ".gemini" / "commands" / "speckit.test.review.toml"
+        assert cmd_output.exists()
+        content = cmd_output.read_text(encoding="utf-8")
+        assert marker in content
+
+
+class TestYamlAgentPostProcess:
+    def test_goose_post_process_applied(
+        self, tmp_path, registrar, ext_dir, monkeypatch
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        goose = get_integration("goose")
+        marker = "# POST_PROCESSED"
+
+        def _inject_marker(self, content):
+            return content + f"\n{marker}\n"
+
+        monkeypatch.setattr(
+            goose.__class__, "post_process_command_content", _inject_marker
+        )
+
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+        registrar.register_commands(
+            "goose", commands, "test-ext", ext, tmp_path
+        )
+
+        cmd_output = tmp_path / ".goose" / "recipes" / "speckit.test.review.yaml"
+        assert cmd_output.exists()
+        content = cmd_output.read_text(encoding="utf-8")
+        assert marker in content
+
+
+class TestSkillsAgentExcluded:
+    def test_claude_post_process_not_called(
+        self, tmp_path, registrar, ext_dir, monkeypatch
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        claude = get_integration("claude")
+        marker = "<!-- SHOULD_NOT_APPEAR -->"
+
+        def _inject_marker(self, content):
+            return content + marker
+
+        monkeypatch.setattr(
+            claude.__class__, "post_process_command_content", _inject_marker
+        )
+
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+        registrar.register_commands(
+            "claude", commands, "test-ext", ext, tmp_path
+        )
+
+        skill_file = (
+            tmp_path / ".claude" / "skills" / "speckit-test-review" / "SKILL.md"
+        )
+        assert skill_file.exists()
+        content = skill_file.read_text(encoding="utf-8")
+        assert marker not in content
+
+    def test_skills_agent_method_never_called(
+        self, tmp_path, registrar, ext_dir
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        claude = get_integration("claude")
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+
+        with patch.object(
+            claude.__class__, "post_process_command_content", wraps=claude.post_process_command_content
+        ) as mock_method:
+            registrar.register_commands(
+                "claude", commands, "test-ext", ext, tmp_path
+            )
+            mock_method.assert_not_called()
+
+
+class TestExceptionPropagation:
+    def test_hook_exception_propagates(
+        self, tmp_path, registrar, ext_dir, monkeypatch
+    ):
+        ext, cmd_dir = ext_dir
+        _write_cmd(cmd_dir)
+
+        from specify_cli.integrations import get_integration
+
+        opencode = get_integration("opencode")
+
+        def _raise(self, content):
+            raise RuntimeError("Hook failed")
+
+        monkeypatch.setattr(
+            opencode.__class__, "post_process_command_content", _raise
+        )
+
+        commands = [{"name": "speckit.test.review", "file": "commands/review.md"}]
+        with pytest.raises(RuntimeError, match="Hook failed"):
+            registrar.register_commands(
+                "opencode", commands, "test-ext", ext, tmp_path
+            )
+
+
+class TestRegressionPlainTemplate:
+    @pytest.mark.parametrize(
+        "agent,path_pattern",
+        [
+            ("claude", ".claude/skills/speckit-test-plain/SKILL.md"),
+            ("opencode", ".opencode/commands/speckit.test.plain.md"),
+        ],
+        ids=["skills", "markdown"],
+    )
+    def test_plain_template_unchanged(
+        self, tmp_path, registrar, ext_dir, agent, path_pattern
+    ):
+        ext, cmd_dir = ext_dir
+        body_text = "This is a plain command with no special content.\n"
+        _write_cmd(cmd_dir, name="plain.md", body=body_text)
+
+        commands = [{"name": "speckit.test.plain", "file": "commands/plain.md"}]
+        registrar.register_commands(
+            agent, commands, "test-ext", ext, tmp_path
+        )
+
+        output_file = tmp_path / path_pattern
+        assert output_file.exists(), f"Output file missing for {agent}"
+        content = output_file.read_text(encoding="utf-8")
+        assert body_text.strip() in content, f"Body text missing in {agent} output"
--- a/tests/test_presets.py
+++ b/tests/test_presets.py
@@ -4538,6 +4538,27 @@ class TestBundledPresetLocator:
        assert "got https://" not in output
        open_url.assert_not_called()

+    def test_preset_add_from_malformed_ipv6_url_exits_cleanly(self, project_dir):
+        """A malformed IPv6 URL must produce a clean error, not a ValueError traceback."""
+        from typer.testing import CliRunner
+        from unittest.mock import patch
+        from specify_cli import app
+
+        runner = CliRunner()
+        with patch.object(Path, "cwd", return_value=project_dir), \
+             patch("specify_cli.authentication.http.open_url") as open_url:
+            result = runner.invoke(
+                app,
+                ["preset", "add", "--from", "https://[::1/preset.zip"],
+                catch_exceptions=True,
+            )
+
+        assert result.exit_code == 1
+        assert result.exception is None or isinstance(result.exception, SystemExit)
+        output = strip_ansi(result.output)
+        assert "Invalid URL" in output
+        open_url.assert_not_called()
+
    def test_preset_add_from_url_redirect_error_describes_disallowed_url(self, project_dir, monkeypatch, capsys):
        """Redirect rejection message covers hostless HTTPS, not only non-HTTPS URLs."""
        import typer
--- a/tests/test_workflow_run_without_project.py
+++ b/tests/test_workflow_run_without_project.py
@@ -322,3 +322,87 @@ class TestWorkflowRunWithoutProject:

        assert result.exit_code != 0
        assert ".specify path exists but is not a directory" in result.output
+
+
+class TestWorkflowRunJsonErrorStream:
+    """Under --json, error text must go to stderr so stdout stays parseable."""
+
+    def _bad_workflow(self, tmp_path):
+        wf = tmp_path / "bad.yml"
+        wf.write_text(
+            yaml.dump(
+                {
+                    "schema_version": "1.0",
+                    "workflow": {
+                        "id": "bad-wf",
+                        "name": "Bad",
+                        "version": "1.0.0",
+                        "description": "fails validation",
+                    },
+                    # shell step missing required 'run' -> validation error
+                    "steps": [{"id": "s", "type": "shell"}],
+                }
+            ),
+            encoding="utf-8",
+        )
+        return wf
+
+    def test_run_json_validation_error_not_on_stdout(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        wf = self._bad_workflow(tmp_path)
+        runner = CliRunner()
+        old = os.getcwd()
+        try:
+            os.chdir(tmp_path)
+            result = runner.invoke(
+                app, ["workflow", "run", str(wf), "--json"], catch_exceptions=False
+            )
+        finally:
+            os.chdir(old)
+
+        assert result.exit_code == 1
+        # stdout must carry only JSON (here: nothing) — never human error text.
+        assert "validation failed" not in result.stdout
+        assert "Error" not in result.stdout
+        # The message is routed to stderr instead.
+        assert "validation failed" in result.stderr
+
+    def test_run_json_invalid_input_not_on_stdout(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        # A valid single-shell workflow so we get past load/validate to
+        # _parse_input_values, which rejects the malformed --input.
+        wf = tmp_path / "ok.yml"
+        wf.write_text(
+            yaml.dump(
+                {
+                    "schema_version": "1.0",
+                    "workflow": {
+                        "id": "ok-wf",
+                        "name": "OK",
+                        "version": "1.0.0",
+                        "description": "x",
+                    },
+                    "steps": [{"id": "s", "type": "shell", "run": "echo hi"}],
+                }
+            ),
+            encoding="utf-8",
+        )
+        runner = CliRunner()
+        old = os.getcwd()
+        try:
+            os.chdir(tmp_path)
+            result = runner.invoke(
+                app,
+                ["workflow", "run", str(wf), "--json", "--input", "no-equals"],
+                catch_exceptions=False,
+            )
+        finally:
+            os.chdir(old)
+
+        assert result.exit_code == 1
+        assert "Invalid input format" not in result.stdout
+        assert "Invalid input format" in result.stderr
--- a/tests/test_workflows.py
+++ b/tests/test_workflows.py
@@ -1266,6 +1266,26 @@ class TestShellStep:
        errors = step.validate({"id": "test"})
        assert any("missing 'run'" in e for e in errors)

+    @pytest.mark.parametrize("bad_run", [None, ["echo", "hi"], 42])
+    def test_validate_rejects_non_string_run(self, bad_run):
+        """A non-string 'run' must be rejected at validation.
+
+        execute() str()-coerces run and invokes it under shell=True, so a
+        null or list run would otherwise run the Python repr as a command.
+        """
+        from specify_cli.workflows.steps.shell import ShellStep
+
+        step = ShellStep()
+        errors = step.validate({"id": "s", "run": bad_run})
+        assert any("'run' must be a string" in e for e in errors)
+
+    def test_validate_accepts_string_and_expression_run(self):
+        from specify_cli.workflows.steps.shell import ShellStep
+
+        step = ShellStep()
+        assert step.validate({"id": "s", "run": "echo hi"}) == []
+        assert step.validate({"id": "s", "run": "{{ steps.x.output }}"}) == []
+

    def test_output_format_json_exposes_data(self, tmp_path):
        from specify_cli.workflows.steps.shell import ShellStep
@@ -2182,6 +2202,27 @@ class TestFanInStep:
        errors = step.validate({"id": "test", "wait_for": "not-a-list"})
        assert any("non-empty list" in e for e in errors)

+    @pytest.mark.parametrize("bad_output", [["{{ fan_in.results }}"], "{{ x }}", 42])
+    def test_validate_rejects_non_mapping_output(self, bad_output):
+        """A non-mapping 'output' must be rejected: execute() would otherwise
+        silently coerce it to {} and drop the declared aggregation keys."""
+        from specify_cli.workflows.steps.fan_in import FanInStep
+
+        step = FanInStep()
+        errors = step.validate(
+            {"id": "j", "wait_for": ["a"], "output": bad_output}
+        )
+        assert any("'output' must be a mapping" in e for e in errors)
+
+    def test_validate_accepts_mapping_or_absent_output(self):
+        from specify_cli.workflows.steps.fan_in import FanInStep
+
+        step = FanInStep()
+        assert step.validate(
+            {"id": "j", "wait_for": ["a"], "output": {"joined": "{{ x }}"}}
+        ) == []
+        assert step.validate({"id": "j", "wait_for": ["a"]}) == []
+

 class TestFanOutConcurrency:
    """Fan-out honors max_concurrency (WorkflowEngine._run_fan_out)."""
@@ -5552,6 +5593,23 @@ class TestWorkflowRemoveGuard:


 class TestWorkflowAddSymlinkGuard:
+    def test_add_malformed_ipv6_url_exits_cleanly(self, temp_dir, monkeypatch):
+        """A malformed IPv6 URL must produce a clean error, not a ValueError traceback."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        (temp_dir / ".specify").mkdir(exist_ok=True)
+        monkeypatch.chdir(temp_dir)
+        result = CliRunner().invoke(
+            app,
+            ["workflow", "add", "https://[::1/wf.yaml"],
+            catch_exceptions=True,
+        )
+
+        assert result.exit_code == 1
+        assert result.exception is None or isinstance(result.exception, SystemExit)
+        assert "Invalid URL" in result.output
+
    @pytest.mark.skipif(not hasattr(os, "symlink"), reason="symlinks are unavailable")
    def test_add_refuses_symlinked_specify(self, temp_dir, monkeypatch):
        """workflow add must refuse a symlinked .specify (writes could escape root)."""
--- a/tests/unit/test_bundler_catalog_config.py
+++ b/tests/unit/test_bundler_catalog_config.py
@@ -222,3 +222,39 @@ def test_add_source_allows_local_path_with_colon(tmp_path: Path, monkeypatch):
    # A relative path containing ':' but no '://' is still a local path.
    source = cc.add_source(project, "weird:name.json", policy="install-allowed", priority=50)
    assert source.url.endswith("weird:name.json") or "weird" in source.url
+
+
+def test_add_source_rejects_plain_http_for_non_localhost(tmp_path: Path):
+    project = tmp_path / "proj"
+    (project / ".specify").mkdir(parents=True)
+    with pytest.raises(BundlerError, match="HTTPS"):
+        cc.add_source(project, "http://example.com/catalog.json", policy="install-allowed", priority=50)
+
+
+def test_add_source_allows_http_for_localhost(tmp_path: Path):
+    project = tmp_path / "proj"
+    (project / ".specify").mkdir(parents=True)
+    source = cc.add_source(project, "http://localhost:8080/c.json", policy="install-allowed", priority=50)
+    assert source.url == "http://localhost:8080/c.json"
+
+
+def test_add_source_rejects_host_less_remote_urls(tmp_path: Path):
+    project = tmp_path / "proj"
+    (project / ".specify").mkdir(parents=True)
+    for url in ("https://:8080", "https://user@"):
+        with pytest.raises(BundlerError, match="host"):
+            cc.add_source(project, url, policy="install-allowed", priority=50)
+
+
+def test_add_source_wraps_invalid_ipv6_as_bundler_error(tmp_path: Path):
+    project = tmp_path / "proj"
+    (project / ".specify").mkdir(parents=True)
+    with pytest.raises(BundlerError, match="Invalid catalog url"):
+        cc.add_source(project, "https://[::1/c.json", policy="install-allowed", priority=50)
+
+
+def test_remove_source_does_not_crash_on_invalid_ipv6(tmp_path: Path):
+    project = tmp_path / "proj"
+    (project / ".specify").mkdir(parents=True)
+    with pytest.raises(BundlerError, match="No project-scoped catalog source"):
+        cc.remove_source(project, "https://[::1/c.json")
Author	SHA1	Message	Date
github-actions[bot]	786a2f415c	Add Spec Kit Figma extension to community catalog Add figma extension submitted by @sebastienthibaud to: - extensions/catalog.community.json (alphabetical order) - docs/community/extensions.md community extensions table Closes #3396 Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>	2026-07-08 12:39:07 +00:00
Marsel Safin	882e1e90d0	fix(cli): exit cleanly on malformed IPv6 URLs in `extension`/`preset`/`workflow add` (#3369 ) * fix(cli): exit cleanly on malformed IPv6 URLs in extension/preset/workflow add extension add --from, preset add --from, and workflow add <url> parsed the user-supplied URL with a bare urlparse before their HTTPS/host validation, so an unclosed IPv6 bracket escaped as a raw ValueError traceback. Wrap each parse and emit the surrounding validation's clean error style + typer.Exit(1) instead. Fixes #3368 Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * fix(cli): convert malformed redirect URLs to URLError in shared redirect handler Parse the redirect target once in _StripAuthOnRedirect.redirect_request before the validator and stdlib handler run, converting ValueError into URLError which every download path already catches. Also escape from_url in the preset install message so IPv6 brackets don't break Rich markup. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>	2026-07-07 15:20:13 -05:00
Ali jawwad	a307894709	fix(github-http): return None on malformed GHES port instead of raising (#3379 ) resolve_github_release_asset_api_url's is_ghes branch built the authority with 'parsed.port', which raises ValueError on a malformed port (e.g. host:notaport). The function's contract is to resolve or return None, never raise — every other unresolvable case returns None. An allowlisted GHES host with a bad port therefore crashed the caller. Read parsed.port defensively and return None on ValueError. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-07 15:14:25 -05:00
Ali jawwad	10d4bca64c	fix(integrations): guard _sha256 against unreadable managed files (#3376 ) manifest.py::_sha256 does an unguarded open(). check_modified() and uninstall() both call it on a readable-but-unopenable regular file (e.g. permission denied) without catching OSError, so 'specify integration upgrade/uninstall/switch' surface a raw PermissionError traceback. Guard both call sites: in check_modified() treat an unreadable file as modified (consistent with the adjacent symlink / non-regular-file handling); in uninstall() treat it as skipped and preserve it (mirroring the existing path.unlink() OSError guard just below). The force short-circuit is unchanged. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-07 15:11:18 -05:00
Manfred Riem	f1a8d8f95b	chore: release 0.12.7, begin 0.12.8.dev0 development (#3398 ) * chore: bump version to 0.12.7 * chore: begin 0.12.8.dev0 development --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>	2026-07-07 15:01:43 -05:00
Ali jawwad	d5ba062eab	fix(bundler): bundle update uninstalls components dropped by new version (#3353 ) On refresh (bundle update), install_bundle iterated only the new plan's components, so a component the previous version owned but the new one no longer ships was left installed on disk while being dropped from the rewritten record (contributed only holds plan.components). With no record referencing it, remove_bundle could never clean it up — permanently orphaned, violating the provenance invariant (FR-022). After the component loop, when refresh and a prior record exists, uninstall each previously-owned component absent from the new plan — unless another bundle still needs it (components_still_needed refcount, mirroring remove_bundle), in which case it stays installed and is simply de-attributed. Runs inside the existing try so a failed removal takes the same no-record-written rollback path. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-07 14:59:27 -05:00
Ali jawwad	12faf7b5b5	fix(workflows): route run/resume errors to stderr under --json (#3352 ) workflow run/resume --json is contracted to emit a single JSON object on stdout, but every error path (workflow-not-found, invalid workflow, validation failure, execute/resume failure, and the shared _parse_input_values invalid-input error) used console.print, landing the human error text on stdout and corrupting the machine-readable stream. Route those messages through err_console when --json is set (a no-op for normal text mode), mirroring the stderr-only error routing already used by 'specify bundle' (_fail) and err_console elsewhere in this module. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-07 14:52:36 -05:00
Ali jawwad	220e6fcc4e	fix(workflows): fan-in validate() rejects non-mapping output (#3349 ) FanInStep.validate() only checked wait_for, so a non-mapping 'output' (a list or scalar) validated clean; execute() then silently coerces it to {}, so the author's declared aggregation keys vanish with COMPLETED status and no diagnostic. Reject a non-mapping output at validation, mirroring the command-step (#3262) non-mapping fix. execute()'s defensive coercion is left in place for unvalidated callers. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-07 14:49:29 -05:00
Ali jawwad	fb796c2a39	fix(workflows): shell step validate() rejects non-string run (#3348 ) ShellStep.validate() only checked that 'run' was present, so run: (null) or a GitHub-Actions-style list validated clean; execute() then str()-coerces the value and invokes it under shell=True, literally running 'None' or "['echo', 'hi']" as a command. Add a type check after the presence check, mirroring the command-step (#3262) and gate options validation. Expression strings ('{{ ... }}') are strings, so they stay valid. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-07 14:48:26 -05:00
Ali jawwad	0151d239b5	fix(integrations): agy honors SPECKIT_INTEGRATION_AGY_EXTRA_ARGS (#3347 ) AgyIntegration.build_exec_args returned [exe, '--print', prompt] without calling _apply_extra_args_env_var(), so the documented per-integration extra-args env hook was silently dropped for agy — same class as the cursor-agent fix #3265. Append the hook after the positional prompt, matching the devin integration's shape. agy still ignores model/output as before. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-07 14:38:36 -05:00
github-actions[bot]	f764270d06	Add Orchestration Task Context Management extension to community catalog (#3372 ) Add orchestration-task-context-management extension submitted by @benizzio to: - extensions/catalog.community.json (alphabetical order) - docs/community/extensions.md community extensions table Closes #3356 Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>	2026-07-07 12:56:34 -05:00
github-actions[bot]	7839acce86	Update DocGuard — CDD Enforcement extension to v0.30.0 (#3371 ) Update docguard extension submitted by @raccioly: - extensions/catalog.community.json (version, download_url, description, updated_at) - docs/community/extensions.md community extensions table Closes #3355 Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>	2026-07-07 12:30:29 -05:00
github-actions[bot]	1935cf7e48	Update Ripple extension to v1.1.0 (#3370 ) Update ripple extension submitted by @chordpli: - extensions/catalog.community.json (version, download_url, description, requires.tools) - docs/community/extensions.md community extensions table Closes #3354 Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>	2026-07-07 12:25:54 -05:00
Roland Huss	d4e7d2b888	feat(integrations): generalize post-processing to all format types (#3311 ) * feat(integrations): add post_process_command_content() hook for all format types Add post_process_command_content(self, content: str) -> str to IntegrationBase with a no-op default. Wire it into register_commands() for non-skills format types (Markdown, TOML, YAML) after format rendering, before writing to disk. Also applies to aliases rendered via the inject_name path (cline, forge). Skills-format agents are excluded to preserve the existing post_process_skill_content() path and avoid double-processing. This gives extension authors a clean per-agent content transformation seam for all 21 non-skills integrations that previously had no post-processing hook. Ref: #3303 Assisted-By: 🤖 Claude Code * fix: initialize _integration before conditional branch Prevents potential UnboundLocalError if the non-skills guard is refactored without updating the alias path reference. Assisted-By: 🤖 Claude Code	2026-07-07 11:35:43 -05:00
Manfred Riem	abaed10d00	chore: release 0.12.6, begin 0.12.7.dev0 development (#3393 ) * chore: bump version to 0.12.6 * chore: begin 0.12.7.dev0 development --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>	2026-07-07 11:05:13 -05:00
Marsel Safin	2b5e175440	fix(bundler): validate catalog URLs in `catalog add` (HTTPS-only, require host) (#3367 ) * fix(bundler): validate catalog URLs in `catalog add` (HTTPS-only, require host) add_source persisted remote catalog URLs without the HTTPS/host checks that specify_cli.catalogs (#3210) and the bundler adapters (#3333) enforce, and an unclosed IPv6 bracket escaped as a raw ValueError. Mirror the catalogs.py validation for http(s) schemes and wrap urlparse so malformed input raises BundlerError. Fixes #3366 Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * docs: correct config filename and validation reference in comment Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>	2026-07-07 11:01:46 -05:00
github-actions[bot]	0e40438903	Update Ralph Loop extension to v1.2.1 (#3365 ) Update ralph extension submitted by @Rubiss: - extensions/catalog.community.json (version, download_url, speckit_version, tools, tags, updated_at) Closes #3337 Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>	2026-07-07 10:55:18 -05:00
Zhiyao Wen	1930f89d17	fix extension-local script path rewriting (#3364 ) Co-authored-by: Zhiyao <zhiyao@ZhiyaodeMacBook-Air.local>	2026-07-07 10:51:50 -05:00
github-actions[bot]	4bb5166445	Add Charter extension to community catalog (#3363 ) Add charter extension submitted by @Huljo to: - extensions/catalog.community.json (alphabetical order) - docs/community/extensions.md community extensions table Closes #3322 Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>	2026-07-07 09:53:05 -05:00
WOLIKIMCHENG	73f77c200f	feat(scripts): add Python check-prerequisites PoC (#3302 ) * feat(scripts): add Python check-prerequisites PoC * fix(scripts): address check-prerequisites parity feedback * test(scripts): label PowerShell prerequisite parity cases --------- Co-authored-by: root <kinsonnee@gmail.com>	2026-07-06 17:54:31 -05:00
Pascal THUET	b8d27e472f	test: reduce registry manifest test repetition (#3146 ) * test: isolate integration test home Assisted-by: Codex (model: GPT-5, autonomous) * test: reduce registry manifest test repetition Assisted-by: Codex (model: GPT-5, autonomous) * test: clarify disjoint-manifest order rationale and guard safe set Add a >=2 precondition, explain why two install orders are tested (manifests are order-independent; the orders only vary the init path), and build the manifest map with a comprehension. * test: rotate init coverage for manifest isolation Assisted-by: Codex (model: GPT-5, autonomous) * test: assert integration home isolation Assisted-by: Codex (model: GPT-5, autonomous) * test: guard multi-install manifest rotations Assisted-by: Codex (model: GPT-5, autonomous)	2026-07-06 17:50:33 -05:00
Ali jawwad	587b1859fa	fix(integrations): hermes honors SPECKIT_INTEGRATION_HERMES_EXTRA_ARGS (#3346 ) HermesIntegration.build_exec_args routed argv[0] through _resolve_executable() but never called _apply_extra_args_env_var(), so the documented per-integration extra-args env hook was silently dropped for hermes — the same class of bug fixed for cursor-agent in #3265. Insert the hook after the base 'chat -Q' command and before Spec Kit's canonical -m/--json/-s/-q flags (mirrors opencode), so operator args can't displace or clobber the canonical flags. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-06 17:38:39 -05:00
Ali jawwad	52480ee50f	fix(extensions): coerce non-mapping YAML config roots to {} in ConfigManager (#3345 ) ConfigManager._load_yaml_config returned yaml.safe_load(...) or {}, which only guards falsy roots — a truthy non-mapping root (a YAML list or scalar) flows straight into _merge_configs, whose .items() raises AttributeError. get_config()/has_value()/get_value() then crash, and via should_execute_hook's blanket 'except Exception: return False' every config-based hook condition for that extension is silently disabled. Coerce a non-dict root to {}, mirroring the existing non-dict-root guard in get_project_config(). Hardens all three call sites in one place. Co-authored-by: Claude Fable 5 <noreply@anthropic.com>	2026-07-06 17:36:35 -05:00
Quratulain-bilal	d3e7b06fa7	fix(yaml): pin goose recipe prompt block-scalar indentation (#3343 ) the goose recipe renderer emitted the prompt body under a bare '\|' block scalar. yaml infers a plain block scalar's indentation from its first non-empty line, so a command body whose first line is itself indented (a markdown code block, a nested list item) made the parser expect that deeper indent for the whole block and reject the later, shallower lines - the generated .goose recipe then failed to parse. use an explicit '\|2' indentation indicator so the block is always read at 2 spaces regardless of the body. added a regression test that round-trips an indented-first-line body through the yaml parser.	2026-07-06 17:34:16 -05:00
Manfred Riem	de6a04eaad	chore: release 0.12.5, begin 0.12.6.dev0 development (#3381 ) * chore: bump version to 0.12.5 * chore: begin 0.12.6.dev0 development --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>	2026-07-06 16:51:18 -05:00