chore: bump version to 0.12.5

2026-07-08 23:59:55 +08:00 · 2026-07-06 21:49:33 +00:00
39 changed files with 114 additions and 2113 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,36 +2,6 @@

 <!-- 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
@@ -42,7 +42,6 @@ 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) |
@@ -51,8 +50,7 @@ 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 | 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) |
-| EARS Requirements Syntax | Author, lint, and convert requirements using EARS - the five industry-standard sentence patterns for unambiguous, testable requirements | `docs` | Read+Write | [spec-kit-ears](https://github.com/dhruv-15-03/spec-kit-ears) |
+| 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) |
 | 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) |
@@ -87,7 +85,6 @@ 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-) |
@@ -108,7 +105,7 @@ 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 — surface hidden ripple effects across 9 analysis 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 — delta-anchored analysis across 9 domain-agnostic 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) |
--- a/extensions/catalog.community.json
+++ b/extensions/catalog.community.json
@@ -1,6 +1,6 @@
 {
  "schema_version": "1.0",
-  "updated_at": "2026-07-08T00:00:00Z",
+  "updated_at": "2026-07-01T00:00:00Z",
  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
  "extensions": {
    "aide": {
@@ -670,40 +670,6 @@
      "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",
@@ -1106,10 +1072,10 @@
    "docguard": {
      "name": "DocGuard — CDD Enforcement",
      "id": "docguard",
-      "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.",
+      "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.",
      "author": "raccioly",
-      "version": "0.30.0",
-      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.30.0/spec-kit-docguard-v0.30.0.zip",
+      "version": "0.28.0",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.28.0/spec-kit-docguard-v0.28.0.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",
@@ -1145,7 +1111,7 @@
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-13T00:00:00Z",
-      "updated_at": "2026-07-06T00:00:00Z"
+      "updated_at": "2026-06-23T00:00:00Z"
    },
    "doctor": {
      "name": "Project Health Check",
@@ -1180,39 +1146,6 @@
      "created_at": "2026-03-13T00:00:00Z",
      "updated_at": "2026-03-13T00:00:00Z"
    },
-    "ears": {
-      "name": "EARS Requirements Syntax",
-      "id": "ears",
-      "description": "Author, lint, and convert requirements using EARS (Easy Approach to Requirements Syntax) - the five industry-standard sentence patterns for unambiguous, testable requirements.",
-      "author": "dhruv-15-03",
-      "version": "1.0.0",
-      "download_url": "https://github.com/dhruv-15-03/spec-kit-ears/archive/refs/tags/v1.0.0.zip",
-      "repository": "https://github.com/dhruv-15-03/spec-kit-ears",
-      "homepage": "https://github.com/dhruv-15-03/spec-kit-ears",
-      "documentation": "https://github.com/dhruv-15-03/spec-kit-ears/blob/main/README.md",
-      "changelog": "https://github.com/dhruv-15-03/spec-kit-ears/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "category": "docs",
-      "effect": "read-write",
-      "requires": {
-        "speckit_version": ">=0.9.0"
-      },
-      "provides": {
-        "commands": 3,
-        "hooks": 0
-      },
-      "tags": [
-        "ears",
-        "requirements",
-        "specification",
-        "quality"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-07-08T00:00:00Z",
-      "updated_at": "2026-07-08T00:00:00Z"
-    },
    "extensify": {
      "name": "Extensify",
      "id": "extensify",
@@ -2429,39 +2362,6 @@
      "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",
@@ -2779,8 +2679,8 @@
      "id": "ralph",
      "description": "Autonomous implementation loop using AI agent CLI",
      "author": "Rubiss",
-      "version": "1.2.1",
-      "download_url": "https://github.com/Rubiss-Projects/spec-kit-ralph/archive/refs/tags/v1.2.1.zip",
+      "version": "1.1.1",
+      "download_url": "https://github.com/Rubiss-Projects/spec-kit-ralph/archive/refs/tags/v1.1.1.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",
@@ -2789,7 +2689,7 @@
      "category": "code",
      "effect": "read-write",
      "requires": {
-        "speckit_version": ">=0.8.5",
+        "speckit_version": ">=0.1.0",
        "tools": [
          {
            "name": "copilot",
@@ -2799,10 +2699,6 @@
            "name": "codex",
            "required": false
          },
-          {
-            "name": "claude",
-            "required": false
-          },
          {
            "name": "git",
            "required": true
@@ -2818,14 +2714,13 @@
        "automation",
        "loop",
        "copilot",
-        "codex",
-        "claude"
+        "codex"
      ],
      "verified": false,
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-09T00:00:00Z",
-      "updated_at": "2026-07-06T00:00:00Z"
+      "updated_at": "2026-06-05T03:11:06Z"
    },
    "reconcile": {
      "name": "Reconcile Extension",
@@ -3152,10 +3047,10 @@
    "ripple": {
      "name": "Ripple",
      "id": "ripple",
-      "description": "Detect side effects that tests can't catch after implementation — surface hidden ripple effects across 9 analysis categories",
+      "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",
      "author": "chordpli",
-      "version": "1.1.0",
-      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.1.0.zip",
+      "version": "1.0.0",
+      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.0.0.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",
@@ -3164,13 +3059,7 @@
      "category": "code",
      "effect": "read-write",
      "requires": {
-        "speckit_version": ">=0.2.0",
-        "tools": [
-          {
-            "name": "git",
-            "required": true
-          }
-        ]
+        "speckit_version": ">=0.2.0"
      },
      "provides": {
        "commands": 3,
@@ -3187,7 +3076,7 @@
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-04-20T00:00:00Z",
-      "updated_at": "2026-07-06T00:00:00Z"
+      "updated_at": "2026-04-20T00:00:00Z"
    },
    "roadmap": {
      "name": "Spec Roadmap",
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.12.8.dev0"
+version = "0.12.5"
 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
@@ -1,207 +0,0 @@
-#!/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
@@ -1,210 +0,0 @@
-"""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
@@ -127,14 +127,7 @@ def resolve_github_release_asset_api_url(
    if hostname == "github.com":
        api_base = "https://api.github.com"
    elif is_ghes:
-        # ``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}"
+        authority = hostname if parsed.port is None else f"{hostname}:{parsed.port}"
        api_base = f"{parsed.scheme}://{authority}/api/v3"
    else:
        return None
--- a/src/specify_cli/agents.py
+++ b/src/specify_cli/agents.py
@@ -148,9 +148,7 @@ class CommandRegistrar:
        )
        return f"---\n{yaml_str}---\n"

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

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

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

        Returns:
            Modified frontmatter with normalized project paths
@@ -171,15 +168,11 @@ 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, extension_id=extension_id
-                    )
+                    scripts[key] = self.rewrite_project_relative_paths(script_path)
        return frontmatter

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

-        # 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/"
-        )
+        # Only rewrite top-level style references so extension-local paths like
+        # ".specify/extensions/<ext>/scripts/..." remain intact.
        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?memory/', r"\1.specify/memory/", text)
-        text = re.sub(
-            r'(^|[\s`"\'(])(?:\.?/)?scripts/', rf"\1{scripts_replacement}", text
-        )
+        text = re.sub(r'(^|[\s`"\'(])(?:\.?/)?scripts/', r"\1.specify/scripts/", text)
        text = re.sub(
            r'(^|[\s`"\'(])(?:\.?/)?templates/', r"\1.specify/templates/", text
        )
@@ -327,7 +312,6 @@ 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.

@@ -347,7 +331,7 @@ 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, extension_id=extension_id
+                agent_name, frontmatter, body, project_root
            )

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

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

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

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

    def _convert_argument_placeholder(
        self, content: str, from_placeholder: str, to_placeholder: str
@@ -550,7 +528,6 @@ 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.

@@ -568,7 +545,6 @@ 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
@@ -638,9 +614,7 @@ class CommandRegistrar:
                        frontmatter[key] = core_frontmatter[key]
                frontmatter.pop("strategy", None)

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

            for key in agent_config.get("strip_frontmatter_keys", []):
                frontmatter.pop(key, None)
@@ -679,11 +653,10 @@ 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, extension_id=extension_id
+                    agent_name, frontmatter, body, project_root
                )
                body = self._convert_argument_placeholder(
                    body, "$ARGUMENTS", agent_config["args"]
@@ -693,7 +666,7 @@ class CommandRegistrar:
                )
            elif agent_config["format"] == "toml":
                body = self.resolve_skill_placeholders(
-                    agent_name, frontmatter, body, project_root, extension_id=extension_id
+                    agent_name, frontmatter, body, project_root
                )
                body = self._convert_argument_placeholder(
                    body, "$ARGUMENTS", agent_config["args"]
@@ -706,17 +679,6 @@ 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)
@@ -759,7 +721,6 @@ class CommandRegistrar:
                            source_id,
                            cmd_file,
                            project_root,
-                            extension_id=extension_id,
                        )
                    elif agent_config["format"] == "markdown":
                        alias_output = self.render_markdown_command(
@@ -777,9 +738,6 @@ 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
@@ -792,7 +750,6 @@ class CommandRegistrar:
                            source_id,
                            cmd_file,
                            project_root,
-                            extension_id=extension_id,
                        )

                alias_file = (
@@ -924,7 +881,6 @@ 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.

@@ -941,7 +897,6 @@ 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
@@ -1044,7 +999,6 @@ class CommandRegistrar:
                        context_note=context_note,
                        _resolved_dir=agent_dir,
                        link_outputs=link_outputs,
-                        extension_id=extension_id,
                    )
                    if registered:
                        results[agent_name] = registered
@@ -1069,7 +1023,6 @@ 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.

@@ -1085,7 +1038,6 @@ 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
@@ -1114,7 +1066,6 @@ 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
@@ -73,13 +73,6 @@ 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)

@@ -90,6 +83,7 @@ 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
@@ -95,11 +95,7 @@ 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
-    try:
-        scheme = urlparse(url).scheme.lower()
-    except ValueError:
-        # Malformed URLs (e.g. an unclosed IPv6 bracket) are not local paths.
-        return False
+    scheme = urlparse(url).scheme.lower()
    return scheme not in _REMOTE_SCHEMES


@@ -141,10 +137,7 @@ def add_source(
    url = url.strip()
    if not url:
        raise BundlerError("A catalog url is required.")
-    try:
-        parsed = urlparse(url)
-    except ValueError as exc:
-        raise BundlerError(f"Invalid catalog url: '{url}'.") from exc
+    parsed = urlparse(url)
    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
@@ -155,20 +148,6 @@ 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
@@ -130,28 +130,6 @@ 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
@@ -1075,11 +1075,9 @@ class ExtensionManager:
                        pass  # best-effort cleanup
                continue
            frontmatter, body = registrar.parse_frontmatter(content)
-            frontmatter = registrar._adjust_script_paths(
-                frontmatter, extension_id=manifest.id
-            )
+            frontmatter = registrar._adjust_script_paths(frontmatter)
            body = registrar.resolve_skill_placeholders(
-                selected_ai, frontmatter, body, self.project_root, extension_id=manifest.id
+                selected_ai, frontmatter, body, self.project_root
            )

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

    def register_commands_for_all_agents(
@@ -1981,7 +1978,6 @@ 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(
@@ -2692,12 +2688,7 @@ class ConfigManager:
            return {}

        try:
-            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 {}
+            return yaml.safe_load(file_path.read_text(encoding="utf-8")) or {}
        except (yaml.YAMLError, OSError, UnicodeError):
            return {}

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

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

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

    def setup(
        self,
--- a/src/specify_cli/integrations/base.py
+++ b/src/specify_cli/integrations/base.py
@@ -123,19 +123,6 @@ 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
@@ -1191,18 +1178,12 @@ class YamlIntegration(IntegrationBase):
            default_flow_style=False,
        ).strip()

-        # 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.
+        # Indent the body for YAML block scalar
        indented = "\n".join(f"  {line}" for line in body.split("\n"))

        lines = [
            header_yaml,
-            "prompt: |2",
+            "prompt: |",
            indented,
            "",
            f"# Source: {source_id}",
--- a/src/specify_cli/integrations/hermes/init.py
+++ b/src/specify_cli/integrations/hermes/init.py
@@ -253,11 +253,6 @@ 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
@@ -309,14 +309,7 @@ class IntegrationManifest:
            if abs_path.is_symlink() or not abs_path.is_file():
                modified.append(rel)
                continue
-            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:
+            if _sha256(abs_path) != expected_hash:
                modified.append(rel)
        return modified

@@ -365,17 +358,9 @@ class IntegrationManifest:
                    skipped.append(path)
                    continue
            else:
-                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
+                if not force and _sha256(path) != expected_hash:
+                    skipped.append(path)
+                    continue
            try:
                path.unlink()
            except OSError:
--- a/src/specify_cli/presets/_commands.py
+++ b/src/specify_cli/presets/_commands.py
@@ -104,13 +104,7 @@ def preset_add(
            from ipaddress import ip_address
            from urllib.parse import urlparse as _urlparse

-            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)
+            _parsed = _urlparse(from_url)

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

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


-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]:
+def _parse_input_values(input_values: list[str] | None) -> dict[str, Any]:
    """Parse repeated ``key=value`` CLI inputs into a dict.

    Shared by ``workflow run`` and ``workflow resume``. Exits with an error
@@ -69,9 +59,7 @@ def _parse_input_values(
    inputs: dict[str, Any] = {}
    for kv in input_values or []:
        if "=" not in kv:
-            _error_console(json_output).print(
-                f"[red]Error:[/red] Invalid input format: {kv!r} (expected key=value)"
-            )
+            console.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()
@@ -347,26 +335,25 @@ 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:
-        err.print(f"[red]Error:[/red] Workflow not found: {source}")
+        console.print(f"[red]Error:[/red] Workflow not found: {source}")
        raise typer.Exit(1)
    except ValueError as exc:
-        err.print(f"[red]Error:[/red] Invalid workflow: {exc}")
+        console.print(f"[red]Error:[/red] Invalid workflow: {exc}")
        raise typer.Exit(1)

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

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

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

    if json_output:
@@ -424,20 +411,19 @@ 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, json_output=json_output)
-    err = _error_console(json_output)
+    inputs = _parse_input_values(input_values)

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

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

-        try:
-            parsed_src = urlparse(source)
-        except ValueError:
-            console.print(f"[red]Error:[/red] Invalid URL: {_escape_markup(source)}")
-            raise typer.Exit(1)
+        parsed_src = urlparse(source)
        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
@@ -58,13 +58,4 @@ 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
@@ -90,16 +90,6 @@ 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
@@ -220,68 +220,3 @@ 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
@@ -1,24 +1,8 @@
 """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
@@ -1,21 +0,0 @@
-"""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
@@ -81,26 +81,6 @@ 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
@@ -184,23 +184,6 @@ 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
@@ -353,38 +353,3 @@ 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
@@ -481,40 +481,3 @@ 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
@@ -48,19 +48,6 @@ 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
@@ -100,6 +87,16 @@ 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)
@@ -165,15 +162,6 @@ 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), (
@@ -199,77 +187,62 @@ class TestMultiInstallSafeContracts:
            f"{_integration_commands_dir(second)!r}"
        )

-    @pytest.mark.parametrize(
-        "ordered_keys",
-        _multi_install_safe_orders(),
-        ids=_multi_install_safe_order_id,
-    )
+    @pytest.mark.parametrize(("first", "second"), _multi_install_safe_pairs())
    def test_safe_integrations_have_disjoint_manifests(
        self,
        tmp_path,
-        ordered_keys,
+        first,
+        second,
    ):
-        # 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}"
-        )
+        for initial, additional in ((first, second), (second, first)):
+            project_root = tmp_path / f"project-{initial}-{additional}"
+            project_root.mkdir()
+            runner = CliRunner()

-        project_root = tmp_path / "project"
-        project_root.mkdir()
-        runner = CliRunner()
+            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

-        # 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", key, "--script", "sh"],
+                    ["integration", "install", additional, "--script", "sh"],
                    catch_exceptions=False,
                )
                assert install_result.exit_code == 0, install_result.output
-        finally:
-            os.chdir(original_cwd)
+            finally:
+                os.chdir(original_cwd)

-        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")
+            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")
            )
-            files = manifest.get("files", {})
-            assert isinstance(files, dict), f"{key} manifest files must be an object"
-            manifests[key] = set(files.keys())

-        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)}"
+            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)}"
            )


--- a/tests/test_authentication.py
+++ b/tests/test_authentication.py
@@ -845,22 +845,6 @@ 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
@@ -1,339 +0,0 @@
-"""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
@@ -850,67 +850,6 @@ 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
@@ -31,7 +31,6 @@ from specify_cli.extensions import (
    ExtensionRegistry,
    ExtensionManager,
    CommandRegistrar,
-    ConfigManager,
    HookExecutor,
    ExtensionCatalog,
    ExtensionError,
@@ -1147,12 +1146,10 @@ 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(
@@ -1166,7 +1163,6 @@ 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."""
@@ -1698,29 +1694,6 @@ $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
@@ -1735,24 +1708,6 @@ $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
@@ -5441,29 +5396,6 @@ 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
@@ -7560,52 +7492,3 @@ 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
@@ -233,23 +233,6 @@ 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
@@ -1,245 +0,0 @@
-"""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
@@ -4538,27 +4538,6 @@ 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
@@ -322,87 +322,3 @@ 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
@@ -1266,26 +1266,6 @@ 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
@@ -2202,27 +2182,6 @@ 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)."""
@@ -5593,23 +5552,6 @@ 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
@@ -222,39 +222,3 @@ 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")