chore: bump version to 0.12.13

2026-08-15 14:02:04 +02:00 · 2026-07-13 18:08:07 +00:00
32 changed files with 331 additions and 8399 deletions
@@ -2,37 +2,6 @@

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

-## [0.12.15] - 2026-07-14
-
-### Changed
-
- Update Autonomous Run Governance preset to v0.1.4 (#3511)
- fix(workflows): raise catalog error, not raw ValueError, on a malformed catalog URL (#3484)
- fix(workflows): evaluate 'in'/'not in' safely on a non-iterable right operand (#3447) (#3468)
- fix: add trailing newline to init-options.json output (#3509)
- feat(workflows): align workflow CLI with extension command surface (#3419)
- fix(extensions): stop env-var config leaking across prefix-colliding extension IDs (#3497)
- fix(integrations): escape control characters in goose recipe YAML renderer (#3384)
- [extension] Update DocGuard — CDD Enforcement extension to v0.32.0 (#3489)
- [extension] Add Multi-Repo Branch Sync extension to community catalog (#3411)
- chore: release 0.12.14, begin 0.12.15.dev0 development (#3506)
-
-## [0.12.14] - 2026-07-13
-
-### Changed
-
- [extension] Add Spec Kit Memory extension to community catalog (#3455)
- Add Test-First Governance preset to community catalog (#3504)
- Add Autonomous Run Governance preset to community catalog (#3501)
- fix(workflows): validate command step input/options are mappings (#3262)
- fix(presets): resolve() honors manifest-declared file: for installed presets (#3351)
- fix(init): don't block on confirmation for 'init --here' without a TTY (#3236)
- [extension] Add Quality Gates (Enforcement Layer) extension to community catalog (#3431)
- fix(integrations): exit cleanly on unbalanced quote in --integration-options (#3457) (#3466)
- fix(integrations): declare kiro-cli multi-install safe (#3471) (#3485)
- fix(workflows): fail fan-in step on non-list wait_for instead of crashing (#3482)
- chore: release 0.12.13, begin 0.12.14.dev0 development (#3498)
-
 ## [0.12.13] - 2026-07-13

 ### Changed
@@ -51,7 +51,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | Confluence Extension | Create a doc in Confluence summarizing the specifications and planning files | `integration` | Read+Write | [spec-kit-confluence](https://github.com/aaronrsun/spec-kit-confluence) |
 | Cost Tracker | Track real LLM dollar cost across SDD workflows — per-feature budgets, per-integration comparison, and finance-ready exports | `visibility` | Read+Write | [spec-kit-cost](https://github.com/Quratulain-bilal/spec-kit-cost) |
 | Data Model Diagram | Generates Mermaid ER diagrams from Spec Kit data models after planning | `docs` | Read+Write | [spec-kit-data-model-diagram](https://github.com/benizzio/spec-kit-data-model-diagram) |
-| DocGuard — CDD Enforcement | Doc-integrity engine with MCP server, SARIF output, and zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, spec-kit hooks. Pure Node.js. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
+| DocGuard — CDD Enforcement | The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep. | `docs` | Read+Write | [spec-kit-docguard](https://github.com/raccioly/docguard) |
 | 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) |
 | 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) |
@@ -84,7 +84,6 @@ The following community-contributed extensions are available in [`catalog.commun
 | MemoryLint | Evidence-driven instruction drift checker: audits agent memory files for boundary, reality, conflict, and redundancy drift. | `process` | Read+Write | [memorylint](https://github.com/RbBtSn0w/spec-kit-extensions/tree/main/memorylint) |
 | Microsoft 365 Integration | Fetch Teams messages, meeting transcripts, and SharePoint/OneDrive files as local Markdown for spec generation | `integration` | Read+Write | [spec-kit-m365](https://github.com/BenBtg/spec-kit-m365) |
 | Multi-Model Review | Cross-model Spec Kit handoffs for spec authoring, implementation routing, and review. | `process` | Read+Write | [multi-model-review](https://github.com/formin/multi-model-review) |
-| Multi-Repo Branch Sync | Creates the feature branch in affected sub-repositories and git submodules via plan/tasks hooks | `process` | Read+Write | [multi-repo-sync](https://github.com/fyloss/spec-kit-multi-repo-sync) |
 | Multi-Sites Spec Kit | Multi-site aware specify command with per-site spec folders, auto-increment, and Drupal support | `process` | Read+Write | [spec-kit-multi-sites](https://github.com/teeyo/spec-kit-multi-sites) |
 | .NET Framework to Modern .NET Migration | Orchestrate end-to-end .NET Framework to modern .NET migration across 7 phases, with SDD lifecycle integration | `process` | Read+Write | [spec-kit-fx-to-net](https://github.com/RogerBestMsft/spec-kit-FxToNet) |
 | Onboard | Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step | `process` | Read+Write | [spec-kit-onboard](https://github.com/dmux/spec-kit-onboard) |
@@ -99,7 +98,6 @@ The following community-contributed extensions are available in [`catalog.commun
 | Project Health Check | Diagnose a Spec Kit project and report health issues across structure, agents, features, scripts, extensions, and git | `visibility` | Read-only | [spec-kit-doctor](https://github.com/KhawarHabibKhan/spec-kit-doctor) |
 | Project Status | Show current SDD workflow progress — active feature, artifact status, task completion, workflow phase, and extensions summary | `visibility` | Read-only | [spec-kit-status](https://github.com/KhawarHabibKhan/spec-kit-status) |
 | QA Testing Extension | Systematic QA testing with browser-driven or CLI-based validation of acceptance criteria from spec | `code` | Read-only | [spec-kit-qa](https://github.com/arunt14/spec-kit-qa) |
-| Quality Gates (Enforcement Layer) | Deterministic quality enforcement for Spec Kit projects at three boundaries — agent hooks, git pre-commit, CI — with one policy file and provable enforcement (attestations, canaries, verified parity). | `process` | Read+Write | [spec-gates](https://github.com/schwichtgit/spec-gates) |
 | RAG Azure Builder | Spec Kit extension for onboarding and operating an Azure RAG stack with guided workflows. | `process` | Read+Write | [spec-kit-extension-rag-azure-builder](https://github.com/Sertxito/spec-kit-extension-rag-azure-builder) |
 | Ralph Loop | Autonomous implementation loop using AI agent CLI | `code` | Read+Write | [spec-kit-ralph](https://github.com/Rubiss-Projects/spec-kit-ralph) |
 | Reconcile Extension | Reconcile implementation drift by surgically updating feature artifacts. | `docs` | Read+Write | [spec-kit-reconcile](https://github.com/stn1slv/spec-kit-reconcile) |
@@ -121,7 +119,6 @@ The following community-contributed extensions are available in [`catalog.commun
 | Spec Diagram | Auto-generate Mermaid diagrams of SDD workflow state, feature progress, and task dependencies | `visibility` | Read-only | [spec-kit-diagram-](https://github.com/Quratulain-bilal/spec-kit-diagram-) |
 | Spec Kit Discovery Extension | Run technical discovery commands for feasibility, technology selection, scenario-specific technical decisions, legacy codebase assessment, implementation understanding, and proof-of-concept validation | `process` | Read+Write | [spec-kit-discovery](https://github.com/bigsmartben/spec-kit-discovery) |
 | Spec Kit Figma | Agent-agnostic SpecKit extension that grounds spec, plan & task generation in Figma design context — REST + optional MCP, single/mono/multi-repo, macOS/Linux/Windows. | `integration` | Read+Write | [spec-kit-figma](https://github.com/Fyloss/spec-kit-figma) |
-| Spec Kit Memory | Recalls prior specs and decisions from configurable memory tools (e.g. memsearch) before SDLC stages, so planning and specification start from what the project already knows | `docs` | Read+Write | [spec-kit-memory](https://github.com/zaytsevand/spec-kit-memory) |
 | Spec Kit Preview | Generate evidence-backed low, mid, or high fidelity previews from Spec Kit artifacts as Markdown or self-contained HTML | `docs` | Read+Write | [spec-kit-preview](https://github.com/bigsmartben/spec-kit-preview) |
 | Spec Kit Schedule | Optimal multi-agent task scheduling via CP-SAT — DAG precedence, hallucination-aware caps, file-conflict avoidance, stochastic durations, replanning, and interactive HTML output | `process` | Read+Write | [spec-kit-schedule](https://github.com/jfranc38/spec-kit-schedule) |
 | Spec Kit TLDR | Render a feature's spec.md / plan.md into a review-oriented TLDR (self-contained HTML dashboard + PR-native Markdown) that surfaces risks for faster PR review. | `visibility` | Read+Write | [speckit-tldr](https://github.com/qurore/speckit-tldr) |
@@ -11,7 +11,6 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | Agent Parity Governance | Adds shared-guidance parity, audit-ready Spec-Kit run evidence, and agent-neutral model-routing guidance across a project's declared AI-agent instruction surfaces so agent guidance does not drift. | 6 templates, 3 commands | — | [spec-kit-preset-agent-parity-governance](https://github.com/hindermath/spec-kit-preset-agent-parity-governance) |
 | AIDE In-Place Migration | Adapts the AIDE extension workflow for in-place technology migrations (X → Y pattern) — adds migration objectives, verification gates, knowledge documents, and behavioral equivalence criteria | 2 templates, 8 commands | AIDE extension | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
 | Architecture Governance | Adds secure software architecture, STRIDE+CAPEC threat modeling, arc42 security cross-cutting concepts, S-ADRs, Zero Trust applicability, OWASP SAMM governance, BSI C3A cloud autonomy, BSI C5 cloud compliance assurance, and audit-ready Spec Kit run evidence | 13 templates, 3 commands | — | [spec-kit-preset-architecture-governance](https://github.com/hindermath/spec-kit-preset-architecture-governance) |
-| Autonomous Run Governance | Adds permission-bounded, evidence-first governance for autonomous Spec Kit delivery, convergence, resume, closeout, and retrospective learning. | 12 templates, 2 commands, 2 scripts | — | [spec-kit-preset-autonomous-run-governance](https://github.com/hindermath/spec-kit-preset-autonomous-run-governance) |
 | Canon Core | Adapts original Spec Kit workflow to work together with Canon extension | 2 templates, 8 commands | — | [spec-kit-canon](https://github.com/maximiliamus/spec-kit-canon) |
 | Claude AskUserQuestion | Upgrades `/speckit.clarify` and `/speckit.checklist` on Claude Code from Markdown-table prompts to the native AskUserQuestion picker, with a recommended option and reasoning on every question | 2 commands | — | [spec-kit-preset-claude-ask-questions](https://github.com/0xrafasec/spec-kit-preset-claude-ask-questions) |
 | Command Density | Compacts the nine core Spec Kit command prompts while preserving scripts, handoffs, placeholders, hook output blocks, and rule structure | 9 commands | — | [spec-kit-preset-command-density](https://github.com/Xopoko/spec-kit-preset-command-density) |
@@ -29,7 +28,6 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | SicarioSpec Core | Baseline secure-by-default Spec Kit governance profile. | 5 templates | — | [sicario-spec](https://github.com/dfirs1car1o/sicario-spec) |
 | Spec2Cloud | Spec-driven workflow tuned for shipping to Azure: spec → plan → tasks → implement → deploy | 5 templates, 8 commands | — | [spec2cloud](https://github.com/Azure-Samples/Spec2Cloud) |
 | Table of Contents Navigation | Adds a navigable Table of Contents to generated spec.md, plan.md, and tasks.md documents | 3 templates, 3 commands | — | [spec-kit-preset-toc-navigation](https://github.com/Quratulain-bilal/spec-kit-preset-toc-navigation) |
-| Test-First Governance | Governs TDD with coverage-complete BDD/ATDD Gherkin scenarios, explicit suite ownership, professional test reports, traceability, and risk-based quality gates. | 10 templates, 8 commands | — | [spec-kit-preset-test-first-governance](https://github.com/ka-zo/spec-kit-preset-test-first-governance) |
 | VS Code Ask Questions | Enhances the clarify command to use `vscode/askQuestions` for batched interactive questioning. | 1 command | — | [spec-kit-presets](https://github.com/fdcastel/spec-kit-presets) |
 | Workflow Preset | Behavior-first specification, design artifacts, and agent-native handoff orchestration — adds requirement-phase behavior drafts, formal BDD/UIF/behavior contracts, optional design artifacts, and scoped implementation handoffs with Core Agent, Vertical Planner Agent, and Worker Agent modes | 22 templates, 8 commands | — | [spec-kit-workflow-preset](https://github.com/bigsmartben/spec-kit-workflow-preset) |

@@ -86,30 +86,8 @@ Lists workflows installed in the current project.
 specify workflow add <source>
 ```

-| Option          | Description                                            |
-| --------------- | ------------------------------------------------------ |
-| `--dev`         | Install from a local workflow YAML file or directory   |
-| `--from <url>`  | Install from a custom URL (`<source>` names the expected workflow ID) |
-
 Installs a workflow from the catalog, a URL (HTTPS required), or a local file path.

-## Update Workflows
-
-```bash
-specify workflow update [workflow_id]
-```
-
-Updates one installed catalog workflow — or all of them when no ID is given — to the latest catalog version. Prompts for confirmation and keeps the installed copy if a download or validation fails.
-
-## Enable or Disable a Workflow
-
-```bash
-specify workflow enable <workflow_id>
-specify workflow disable <workflow_id>
-```
-
-Disabled workflows stay installed and listed (marked `[disabled]`) but refuse to run until re-enabled.
-
 ## Remove a Workflow

 ```bash
@@ -124,10 +102,9 @@ Removes an installed workflow from the project.
 specify workflow search [query]
 ```

-| Option     | Description       |
-| ---------- | ----------------- |
-| `--tag`    | Filter by tag     |
-| `--author` | Filter by author  |
+| Option  | Description     |
+| ------- | --------------- |
+| `--tag` | Filter by tag   |

 Searches all active catalogs for workflows matching the query.

@@ -1,6 +1,6 @@
 {
  "schema_version": "1.0",
-  "updated_at": "2026-07-13T00:00:00Z",
+  "updated_at": "2026-07-10T00:00:00Z",
  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
  "extensions": {
    "aide": {
@@ -1106,10 +1106,10 @@
    "docguard": {
      "name": "DocGuard — CDD Enforcement",
      "id": "docguard",
-      "description": "Doc-integrity engine with MCP server, SARIF output, and zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, spec-kit hooks. Pure Node.js.",
+      "description": "The only doc-integrity engine with an MCP server, SARIF output, and a deterministic zero-LLM core. Validates, scores, and traces documentation against code — 24 validators, stable finding codes, GitHub Action with PR annotations, spec-kit hooks. Pure Node.js, one pinned dep.",
      "author": "raccioly",
-      "version": "0.32.0",
-      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.32.0/spec-kit-docguard-v0.32.0.zip",
+      "version": "0.30.0",
+      "download_url": "https://github.com/raccioly/docguard/releases/download/v0.30.0/spec-kit-docguard-v0.30.0.zip",
      "repository": "https://github.com/raccioly/docguard",
      "homepage": "https://www.npmjs.com/package/docguard-cli",
      "documentation": "https://github.com/raccioly/docguard/blob/main/extensions/spec-kit-docguard/README.md",
@@ -1124,14 +1124,6 @@
            "name": "node",
            "version": ">=18.0.0",
            "required": true
-          },
-          {
-            "name": "npx",
-            "required": true
-          },
-          {
-            "name": "specify",
-            "required": false
          }
        ]
      },
@@ -1153,7 +1145,7 @@
      "downloads": 0,
      "stars": 0,
      "created_at": "2026-03-13T00:00:00Z",
-      "updated_at": "2026-07-13T00:00:00Z"
+      "updated_at": "2026-07-06T00:00:00Z"
    },
    "doctor": {
      "name": "Project Health Check",
@@ -1435,57 +1427,6 @@
      "created_at": "2026-05-06T00:00:00Z",
      "updated_at": "2026-05-06T00:00:00Z"
    },
-    "gates": {
-      "name": "Quality Gates (Enforcement Layer)",
-      "id": "gates",
-      "description": "Deterministic quality enforcement for Spec Kit projects at three boundaries — agent hooks, git pre-commit, CI — with one policy file and provable enforcement (attestations, canaries, verified parity).",
-      "author": "schwichtgit",
-      "version": "0.1.0",
-      "download_url": "https://github.com/schwichtgit/spec-gates/releases/download/v0.1.0/gates-0.1.0.zip",
-      "repository": "https://github.com/schwichtgit/spec-gates",
-      "homepage": "https://github.com/schwichtgit/spec-gates",
-      "documentation": "https://github.com/schwichtgit/spec-gates/blob/main/docs/how-it-works.md",
-      "license": "MIT",
-      "category": "process",
-      "effect": "read-write",
-      "requires": {
-        "speckit_version": ">=0.12.0",
-        "tools": [
-          {
-            "name": "jq",
-            "required": true
-          },
-          {
-            "name": "git",
-            "required": true
-          },
-          {
-            "name": "node",
-            "required": false
-          },
-          {
-            "name": "shellcheck",
-            "required": false
-          }
-        ]
-      },
-      "provides": {
-        "commands": 5,
-        "hooks": 1
-      },
-      "tags": [
-        "quality",
-        "enforcement",
-        "hooks",
-        "ci",
-        "governance"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-07-09T00:00:00Z",
-      "updated_at": "2026-07-13T00:00:00Z"
-    },
    "github-issues": {
      "name": "GitHub Issues Integration 1",
      "id": "github-issues",
@@ -2276,42 +2217,6 @@
      "created_at": "2026-05-08T00:00:00Z",
      "updated_at": "2026-05-08T00:00:00Z"
    },
-    "memory": {
-      "name": "Spec Kit Memory",
-      "id": "memory",
-      "description": "Recalls prior specs and decisions from configurable memory tools (e.g. memsearch) before SDLC stages, so planning and specification start from what the project already knows.",
-      "author": "Andrey Zaytsev",
-      "version": "0.3.0",
-      "download_url": "https://github.com/zaytsevand/spec-kit-memory/archive/refs/tags/v0.3.0.zip",
-      "repository": "https://github.com/zaytsevand/spec-kit-memory",
-      "homepage": "https://github.com/zaytsevand/spec-kit-memory",
-      "documentation": "https://github.com/zaytsevand/spec-kit-memory/blob/main/README.md",
-      "changelog": "",
-      "license": "MIT",
-      "category": "docs",
-      "effect": "read-write",
-      "requires": {
-        "speckit_version": ">=0.2.0",
-        "tools": [
-          { "name": "memsearch", "required": false }
-        ]
-      },
-      "provides": {
-        "commands": 2,
-        "hooks": 3
-      },
-      "tags": [
-        "memory",
-        "recall",
-        "research",
-        "memsearch"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-07-10T00:00:00Z",
-      "updated_at": "2026-07-10T00:00:00Z"
-    },
    "memory-loader": {
      "name": "Memory Loader",
      "id": "memory-loader",
@@ -2466,48 +2371,6 @@
      "created_at": "2026-05-04T02:51:52Z",
      "updated_at": "2026-06-18T00:00:00Z"
    },
-    "multi-repo-sync": {
-      "name": "Multi-Repo Branch Sync",
-      "id": "multi-repo-sync",
-      "description": "Creates the feature branch in affected sub-repositories and git submodules via plan/tasks hooks",
-      "author": "Fyloss",
-      "version": "1.0.0",
-      "download_url": "https://github.com/fyloss/spec-kit-multi-repo-sync/releases/download/v1.0.0/spec-kit-multi-repo-sync.zip",
-      "sha256": "12a5c7392145b4424b20715aaa3d8b6a8218c143dea596873e344146c1a76ba0",
-      "repository": "https://github.com/fyloss/spec-kit-multi-repo-sync",
-      "homepage": "https://github.com/fyloss/spec-kit-multi-repo-sync",
-      "documentation": "https://github.com/fyloss/spec-kit-multi-repo-sync/blob/main/README.md",
-      "changelog": "https://github.com/fyloss/spec-kit-multi-repo-sync/blob/main/CHANGELOG.md",
-      "license": "MIT",
-      "category": "process",
-      "effect": "read-write",
-      "requires": {
-        "speckit_version": ">=0.2.0",
-        "tools": [
-          {
-            "name": "git",
-            "version": ">=2.31",
-            "required": true
-          }
-        ]
-      },
-      "provides": {
-        "commands": 3,
-        "hooks": 2
-      },
-      "tags": [
-        "git",
-        "branching",
-        "multi-repo",
-        "submodules",
-        "workflow"
-      ],
-      "verified": false,
-      "downloads": 0,
-      "stars": 0,
-      "created_at": "2026-07-13T00:00:00Z",
-      "updated_at": "2026-07-13T00:00:00Z"
-    },
    "multi-sites": {
      "name": "Multi-Sites Spec Kit",
      "id": "multi-sites",
@@ -1,6 +1,6 @@
 {
  "schema_version": "1.0",
-  "updated_at": "2026-07-14T00:00:00Z",
+  "updated_at": "2026-06-30T00:00:00Z",
  "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/presets/catalog.community.json",
  "presets": {
    "a11y-governance": {
@@ -131,35 +131,6 @@
      "created_at": "2026-04-27T00:00:00Z",
      "updated_at": "2026-06-14T00:00:00Z"
    },
-    "autonomous-run-governance": {
-      "name": "Autonomous Run Governance",
-      "id": "autonomous-run-governance",
-      "version": "0.1.4",
-      "description": "Adds permission-bounded, evidence-first governance for autonomous Spec Kit delivery, convergence, resume, closeout, and retrospective learning.",
-      "author": "Thorsten Hindermann",
-      "repository": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance",
-      "download_url": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance/archive/refs/tags/v0.1.4.zip",
-      "homepage": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance",
-      "documentation": "https://github.com/hindermath/spec-kit-preset-autonomous-run-governance/blob/v0.1.4/README.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.8.3"
-      },
-      "provides": {
-        "templates": 12,
-        "commands": 2,
-        "scripts": 2
-      },
-      "tags": [
-        "autonomous",
-        "governance",
-        "evidence",
-        "permissions",
-        "retrospective"
-      ],
-      "created_at": "2026-07-13T00:00:00Z",
-      "updated_at": "2026-07-14T00:00:00Z"
-    },
    "canon-core": {
      "name": "Canon Core",
      "id": "canon-core",
@@ -647,34 +618,6 @@
      "created_at": "2026-04-30T00:00:00Z",
      "updated_at": "2026-04-30T00:00:00Z"
    },
-    "test-first-governance": {
-      "name": "Test-First Governance",
-      "id": "test-first-governance",
-      "version": "1.3.0",
-      "description": "Governs TDD with coverage-complete BDD/ATDD Gherkin scenarios, explicit suite ownership, professional test reports, traceability, and risk-based quality gates.",
-      "author": "Zoltán Katona, PhD",
-      "repository": "https://github.com/ka-zo/spec-kit-preset-test-first-governance",
-      "download_url": "https://github.com/ka-zo/spec-kit-preset-test-first-governance/archive/refs/tags/1.3.0.zip",
-      "homepage": "https://github.com/ka-zo/spec-kit-preset-test-first-governance",
-      "documentation": "https://github.com/ka-zo/spec-kit-preset-test-first-governance/blob/main/README.md",
-      "license": "MIT",
-      "requires": {
-        "speckit_version": ">=0.12.11"
-      },
-      "provides": {
-        "templates": 10,
-        "commands": 8
-      },
-      "tags": [
-        "tdd",
-        "bdd",
-        "atdd",
-        "quality-gates",
-        "traceability"
-      ],
-      "created_at": "2026-07-13T00:00:00Z",
-      "updated_at": "2026-07-13T00:00:00Z"
-    },
    "toc-navigation": {
      "name": "Table of Contents Navigation",
      "id": "toc-navigation",
@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.12.15"
+version = "0.12.13"
 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"
@@ -24,7 +24,6 @@ GITHUB_HOSTS = frozenset({
    "api.github.com",
    "codeload.github.com",
 })
-_MAX_RELEASE_METADATA_BYTES = 5 * 1024 * 1024


 def build_github_request(url: str) -> urllib.request.Request:
@@ -69,8 +68,6 @@ def resolve_github_release_asset_api_url(
    open_url_fn: Callable,
    timeout: int = 60,
    github_hosts: tuple[str, ...] = (),
-    redirect_validator: Callable[[str, str], None] | None = None,
-    max_metadata_bytes: int = _MAX_RELEASE_METADATA_BYTES,
 ) -> Optional[str]:
    """Resolve a GitHub release browser-download URL to its REST API asset URL.

@@ -94,8 +91,6 @@ def resolve_github_release_asset_api_url(
            authenticated release-metadata lookup.
        timeout: Per-request timeout in seconds.
        github_hosts: Host patterns to treat as GitHub Enterprise Server.
-        redirect_validator: Optional policy applied to metadata redirects.
-        max_metadata_bytes: Maximum release-metadata response size.
    """
    import json
    import urllib.error
@@ -154,33 +149,13 @@ def resolve_github_release_asset_api_url(
    release_url = f"{api_base}/repos/{owner}/{repo}/releases/tags/{encoded_tag}"

    try:
-        open_kwargs = {"timeout": timeout}
-        if redirect_validator is not None:
-            open_kwargs["redirect_validator"] = redirect_validator
-        with open_url_fn(release_url, **open_kwargs) as response:
-            raw_release_data = response.read(max_metadata_bytes + 1)
-            if len(raw_release_data) > max_metadata_bytes:
-                raise ValueError("GitHub release metadata exceeds size limit")
-            release_data = json.loads(raw_release_data)
-    except (
-        urllib.error.URLError,
-        json.JSONDecodeError,
-        TypeError,
-        ValueError,
-    ):
+        with open_url_fn(release_url, timeout=timeout) as response:
+            release_data = json.loads(response.read())
+    except (urllib.error.URLError, json.JSONDecodeError):
        return None

-    if not isinstance(release_data, dict):
-        return None
-    assets = release_data.get("assets", [])
-    if not isinstance(assets, list):
-        return None
-    for asset in assets:
-        if (
-            isinstance(asset, dict)
-            and asset.get("name") == asset_name
-            and asset.get("url")
-        ):
+    for asset in release_data.get("assets", []):
+        if asset.get("name") == asset_name and asset.get("url"):
            return str(asset["url"])

    return None
@@ -14,7 +14,7 @@ def save_init_options(project_path: Path, options: dict[str, Any]) -> None:
    dest = project_path / INIT_OPTIONS_FILE
    dest.parent.mkdir(parents=True, exist_ok=True)
    dest.write_text(
-        json.dumps(options, indent=2, sort_keys=True, ensure_ascii=False) + "\n",
+        json.dumps(options, indent=2, sort_keys=True, ensure_ascii=False),
        encoding="utf-8",
    )

@@ -10,8 +10,6 @@ from __future__ import annotations
 import json
 import os
 import re
-import stat
-import tempfile
 from pathlib import Path, PurePosixPath
 from typing import Any

@@ -89,63 +87,17 @@ def loads_json(text: str, *, origin: str = "<string>") -> Any:


 def dump_json(path: Path, data: Any, *, within: Path | None = None) -> Path:
-    """Atomically write pretty JSON to *path* (optionally confined to *within*)."""
+    """Write *data* as pretty JSON to *path* (optionally confined to *within*)."""
    path = Path(path)
    if within is not None:
        path = ensure_within(within, path)
-    fd = -1
-    temp_path: Path | None = None
    try:
        path.parent.mkdir(parents=True, exist_ok=True)
-        fd, temp_name = tempfile.mkstemp(
-            dir=path.parent,
-            prefix=f".{path.name}.",
-            suffix=".tmp",
-        )
-        temp_path = Path(temp_name)
-        with os.fdopen(os.dup(fd), "w", encoding="utf-8") as handle:
+        with path.open("w", encoding="utf-8") as handle:
            json.dump(data, handle, indent=2, sort_keys=False)
            handle.write("\n")
-
-        try:
-            if path.exists():
-                existing = path.stat(follow_symlinks=False)
-                if stat.S_ISREG(existing.st_mode) and hasattr(os, "fchmod"):
-                    os.fchmod(fd, stat.S_IMODE(existing.st_mode))
-                if stat.S_ISREG(existing.st_mode) and hasattr(os, "fchown"):
-                    try:
-                        os.fchown(fd, existing.st_uid, existing.st_gid)
-                    except PermissionError:
-                        pass
-        except OSError:
-            pass
-
-        staged = os.stat(temp_path, follow_symlinks=False)
-        opened = os.fstat(fd)
-        if (
-            not stat.S_ISREG(staged.st_mode)
-            or staged.st_dev != opened.st_dev
-            or staged.st_ino != opened.st_ino
-        ):
-            raise OSError("staged JSON file changed before commit")
-
-        os.close(fd)
-        fd = -1
-        os.replace(temp_path, path)
-        temp_path = None
    except OSError as exc:
        raise BundlerError(f"Could not write {path}: {exc}") from exc
-    finally:
-        if fd >= 0:
-            try:
-                os.close(fd)
-            except OSError:
-                pass
-        if temp_path is not None:
-            try:
-                temp_path.unlink(missing_ok=True)
-            except OSError:
-                pass
    return path


@@ -187,41 +187,19 @@ def remove_bundle(

    still_needed = components_still_needed(records, exclude_bundle_id=bundle_id)
    result = InstallResult(bundle_id=bundle_id)
-    remove_attempted = False

-    try:
-        for component in target.contributed_components:
-            key = (component.kind, component.id)
-            if key in still_needed:
-                result.skipped.append(component)
-                continue
-            if installer.is_installed(project_root, component):
-                remove_attempted = True
-                installer.remove(project_root, component)
-                result.uninstalled.append(component)
-        save_records(project_root, remove_record(records, bundle_id))
-    except Exception as exc:  # noqa: BLE001
-        if result.uninstalled:
-            detail = (
-                f"{len(result.uninstalled)} component(s) were already removed "
-                "before this failure; the bundle record was left unchanged, "
-                "so the project may be partially uninstalled."
-            )
-        elif remove_attempted:
-            detail = (
-                "No components were removed, but the failing component may "
-                "have made partial changes before raising, so the project "
-                "may be partially uninstalled."
-            )
+    for component in target.contributed_components:
+        key = (component.kind, component.id)
+        if key in still_needed:
+            result.skipped.append(component)
+            continue
+        if installer.is_installed(project_root, component):
+            installer.remove(project_root, component)
+            result.uninstalled.append(component)
        else:
-            detail = (
-                "No components were removed and no removal was attempted; "
-                "the bundle record was left unchanged."
-            )
-        raise BundlerError(
-            f"Failed to remove bundle '{bundle_id}': {exc}. {detail}"
-        ) from exc
+            result.skipped.append(component)

+    save_records(project_root, remove_record(records, bundle_id))
    return result


@@ -220,45 +220,16 @@ def register(app: typer.Typer) -> None:
                console.print(
                    f"[yellow]Warning:[/yellow] Current directory is not empty ({len(existing_items)} items)"
                )
+                console.print(
+                    "[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]"
+                )
                if force:
-                    # Proceeding: the merge/overwrite warning is accurate here.
-                    console.print(
-                        "[yellow]Template files will be merged with existing content and may overwrite existing files[/yellow]"
-                    )
                    console.print(
                        "[cyan]--force supplied: skipping confirmation and proceeding with merge[/cyan]"
                    )
                else:
-                    # Fold the merge risk into the confirmation prompt rather than
-                    # printing it unconditionally first: on the EOF/no-input path
-                    # below the command exits without changing anything, so a
-                    # standalone "will be merged" line would mislead. Interactive
-                    # users still see the risk as part of the question.
-                    #
-                    # Call typer.confirm normally so piped y/n is honored — e.g.
-                    # `echo y | specify init --here` keeps reaching the
-                    # non-destructive preserve-merge path.
-                    try:
-                        proceed = typer.confirm(
-                            "Template files will be merged with existing content "
-                            "and may overwrite existing files. Do you want to continue?"
-                        )
-                    except (typer.Abort, EOFError):
-                        # typer.confirm raises Abort for BOTH an interactive Ctrl+C
-                        # and an EOF on closed/empty stdin. Distinguish them: a real
-                        # TTY cancellation is a normal exit (0, "cancelled"), while a
-                        # missing-input EOF (non-interactive) becomes an actionable
-                        # error pointing at --force.
-                        if _stdin_is_interactive():
-                            console.print("[yellow]Operation cancelled[/yellow]")
-                            raise typer.Exit(0) from None
-                        console.print(
-                            "[red]Error:[/red] Current directory is not empty and no "
-                            "confirmation input is available. Re-run with "
-                            "[bold]--force[/bold] to merge into it."
-                        )
-                        raise typer.Exit(1) from None
-                    if not proceed:
+                    response = typer.confirm("Do you want to continue?")
+                    if not response:
                        console.print("[yellow]Operation cancelled[/yellow]")
                        raise typer.Exit(0)
        else:
@@ -2737,36 +2737,6 @@ class ConfigManager:
        config_file = self.extension_dir / "local-config.yml"
        return self._load_yaml_config(config_file)

-    def _sibling_extension_ids(self) -> list[str]:
-        """Return IDs of other extensions installed alongside this one.
-
-        Sourced from ``ExtensionRegistry`` (``.specify/extensions/.registry``)
-        rather than a directory scan: ``ExtensionManager.remove(...,
-        keep_config=True)`` deliberately preserves the extension directory
-        while dropping the registry entry, so a directory scan would treat
-        that config-only leftover as an installed sibling and keep silently
-        absorbing its ``SPECKIT_<sibling>_*`` env vars into no one. The
-        registry is the source of truth for "installed".
-
-        Returns an empty list if the registry is missing or corrupted
-        (fresh project, ad-hoc test harness) so ``_get_env_config`` degrades
-        to its pre-fix behaviour rather than crashing. ``UnicodeError`` is
-        caught alongside ``OSError`` because ``ExtensionRegistry._load()``
-        opens the file in text mode and only handles ``JSONDecodeError`` /
-        ``FileNotFoundError``, so a registry file with non-UTF-8 bytes would
-        otherwise surface a ``UnicodeDecodeError`` here and break *every*
-        config read instead of degrading gracefully.
-
-        Used by ``_get_env_config`` to detect env vars whose remainder claims
-        a longer, sibling-owned prefix (e.g. ``SPECKIT_GIT_HOOKS_URL`` is
-        owned by ``git-hooks`` when it is co-installed with ``git``).
-        """
-        extensions_dir = self.project_root / ".specify" / "extensions"
-        try:
-            return list(ExtensionRegistry(extensions_dir).keys())
-        except (OSError, UnicodeError):
-            return []
-
    def _get_env_config(self) -> Dict[str, Any]:
        """Get configuration from environment variables.

@@ -2786,49 +2756,15 @@ class ConfigManager:
        ext_id_upper = self.extension_id.replace("-", "_").upper()
        prefix = f"SPECKIT_{ext_id_upper}_"

-        # Cross-extension prefix collision: because ``_`` doubles as both the
-        # separator between the extension ID and the config path *and* the
-        # substitute for ``-`` inside an extension ID, an env var like
-        # ``SPECKIT_GIT_HOOKS_URL`` begins with *both* the ``SPECKIT_GIT_``
-        # prefix of the ``git`` extension and the ``SPECKIT_GIT_HOOKS_`` prefix
-        # of a co-installed ``git-hooks`` extension. It logically belongs to
-        # the extension whose normalized ID is the longer, more specific match
-        # — otherwise config intended for one extension silently surfaces
-        # inside another and can drive hooks that only inspect
-        # ``config.<field> is set``. Build the list of sibling-owned
-        # remainder-prefixes here so a later env var can be skipped if it
-        # matches one.
-        sibling_prefixes: list[str] = []
-        for sibling_id in self._sibling_extension_ids():
-            if sibling_id == self.extension_id:
-                continue
-            sib_upper = sibling_id.replace("-", "_").upper()
-            # A sibling collides only when its normalized ID *extends* our own
-            # (i.e. starts with ``<US>_``). ``git`` vs ``not-git`` is not a
-            # collision; ``git`` vs ``git-hooks`` is.
-            if sib_upper.startswith(ext_id_upper + "_"):
-                # The portion of the env-var *remainder* the sibling claims,
-                # including the trailing ``_`` so a shorter ID that shares a
-                # non-boundary prefix cannot false-positive (e.g. sibling
-                # ``hook`` would not eat env vars under key ``hooks``).
-                sibling_prefixes.append(sib_upper[len(ext_id_upper) + 1 :] + "_")
-
        for key, value in os.environ.items():
            if not key.startswith(prefix):
                continue

-            remainder = key[len(prefix) :]
-            # Skip when a longer sibling ID claims this var — see the block
-            # above. Keeps ``SPECKIT_GIT_HOOKS_URL`` out of the ``git``
-            # extension's config when ``git-hooks`` is co-installed.
-            if any(remainder.startswith(sp) for sp in sibling_prefixes):
-                continue
-
            # Remove prefix and split into parts. Drop empty components from a
            # malformed name (e.g. ``SPECKIT_<EXT>_`` with no key, or
            # consecutive underscores ``SPECKIT_X__Y``) so we never create an
            # entry under an empty key.
-            config_path = [p for p in remainder.lower().split("_") if p]
+            config_path = [p for p in key[len(prefix) :].lower().split("_") if p]
            if not config_path:
                continue

@@ -190,15 +190,7 @@ def _parse_integration_options(integration: Any, raw_options: str) -> dict[str,
    """
    import shlex
    parsed: dict[str, Any] = {}
-    try:
-        tokens = shlex.split(raw_options)
-    except ValueError as exc:
-        # An unbalanced quote (e.g. --integration-options='--commands-dir "foo')
-        # makes shlex raise "No closing quotation". Translate it into the same
-        # clean exit-1 UX as every other bad-input path below rather than
-        # letting a raw traceback escape.
-        console.print(f"[red]Error:[/red] Could not parse integration options: {exc}.")
-        raise typer.Exit(1)
+    tokens = shlex.split(raw_options)
    declared_options = list(integration.options())
    declared = {opt.name.lstrip("-"): opt for opt in declared_options}
    allowed = ", ".join(sorted(opt.name for opt in declared_options))
@@ -1122,17 +1122,6 @@ class TomlIntegration(IntegrationBase):
 # YamlIntegration — YAML-format agents (Goose)
 # ---------------------------------------------------------------------------

-# Characters a YAML literal block scalar cannot carry: C0 controls other
-# than tab/LF (a bare CR acts as a line break inside the scalar), DEL, the
-# C1 range, lone UTF-16 surrogates, and the non-characters U+FFFE/U+FFFF.
-# NEL (U+0085) is YAML-printable but, like LS/PS (U+2028/U+2029), YAML 1.1
-# treats it as a line break, which corrupts the block scalar's structure
-# just the same, so all three are included.
-_YAML_BLOCK_SCALAR_UNSAFE = re.compile(
-    r"[\x00-\x08\x0b-\x1f\x7f-\x9f\u2028\u2029\ud800-\udfff\ufffe\uffff]"
-)
-
-
 class YamlIntegration(IntegrationBase):
    """Concrete base for integrations that use YAML recipe format.

@@ -1238,9 +1227,9 @@ class YamlIntegration(IntegrationBase):
    def _render_yaml(cls, title: str, description: str, body: str, source_id: str) -> str:
        """Render a YAML recipe file from title, description, and body.

-        Produces a Goose-compatible recipe with a literal block scalar for
-        normal prompt content, or an escaped quoted scalar when control
-        characters require it. Uses ``yaml.safe_dump()`` for the header fields.
+        Produces a Goose-compatible recipe with a literal block scalar
+        for the prompt content.  Uses ``yaml.safe_dump()`` for the
+        header fields to ensure proper escaping.
        """
        header = cls._build_yaml_header(title, description)

@@ -1251,23 +1240,6 @@ class YamlIntegration(IntegrationBase):
            default_flow_style=False,
        ).strip()

-        # YAML forbids C0 control characters (except tab and newline) and
-        # DEL in every scalar form, and a bare CR acts as a line break
-        # inside a block scalar. A literal block scalar emits such bytes
-        # verbatim, producing a recipe the YAML parser rejects, so fall
-        # back to an escaped double-quoted scalar for those bodies.
-        if _YAML_BLOCK_SCALAR_UNSAFE.search(body):
-            prompt_yaml = yaml.safe_dump(
-                {"prompt": body}, allow_unicode=True, default_style='"', width=sys.maxsize
-            ).strip()
-            lines = [
-                header_yaml,
-                prompt_yaml,
-                "",
-                f"# Source: {source_id}",
-            ]
-            return "\n".join(lines) + "\n"
-
        # 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
@@ -27,10 +27,3 @@ class KiroCliIntegration(MarkdownIntegration):
        "args": _KIRO_ARG_FALLBACK,
        "extension": ".md",
    }
-
-    # Kiro CLI keeps everything under a static, isolated agent root
-    # (``.kiro/`` with commands in ``.kiro/prompts``) that no other
-    # integration writes to, so it is safe to install alongside others
-    # (issue #3471). The registry's multi-install-safe contract tests
-    # enforce that isolation for every integration setting this flag.
-    multi_install_safe = True
@@ -2588,39 +2588,6 @@ class PresetResolver:
                self._manifest_cache[key] = None
        return self._manifest_cache[key]

-    def _manifest_declared_template(
-        self, pack_dir: Path, template_name: str, template_type: str
-    ) -> tuple[dict | None, Path | None]:
-        """Resolve a preset's manifest-declared template entry and usable file.
-
-        Returns ``(entry, candidate)``:
-        - ``entry`` is the matching ``provides.templates`` mapping, or ``None`` if
-          the manifest is absent or does not list this ``(name, type)``.
-        - ``candidate`` is the declared ``file:`` resolved under ``pack_dir`` IFF
-          it is a regular file (``is_file()``); ``None`` otherwise — a missing,
-          empty, or non-file (e.g. directory) declaration yields ``(entry, None)``.
-
-        The manifest is authoritative: when it declares a template (``entry`` is
-        not ``None``) but the file is unusable (``candidate`` is ``None``),
-        callers must NOT fall back to the convention lookup — that would mask a
-        typo or pick up an undeclared file. Shared by ``resolve()`` and
-        ``collect_all_layers()`` so their manifest-first resolution cannot
-        silently diverge again (the divergence this fix addressed).
-        """
-        manifest = self._get_manifest(pack_dir)
-        if not manifest:
-            return None, None
-        for tmpl in manifest.templates:
-            if tmpl.get("name") == template_name and tmpl.get("type") == template_type:
-                file_path = tmpl.get("file")
-                if file_path:
-                    manifest_candidate = pack_dir / file_path
-                    return tmpl, (
-                        manifest_candidate if manifest_candidate.is_file() else None
-                    )
-                return tmpl, None
-        return None, None
-
    def _get_all_extensions_by_priority(self) -> list[tuple[int, str, dict | None]]:
        """Build unified list of registered and unregistered extensions sorted by priority.

@@ -2723,27 +2690,6 @@ class PresetResolver:
            registry = PresetRegistry(self.presets_dir)
            for pack_id, _metadata in registry.list_by_priority():
                pack_dir = self.presets_dir / pack_id
-                # The preset manifest is authoritative: if it declares this
-                # template with an explicit ``file:``, resolve to that path —
-                # and do NOT fall back to convention when it's missing, to
-                # avoid masking typos or picking up an undeclared file. Only
-                # when the manifest is absent or doesn't list this template do
-                # we use the convention-based subdir lookup. Mirrors
-                # collect_all_layers()/resolve_content() so resolve() and
-                # resolve_with_source() agree with them instead of returning
-                # the core template (or a stray convention file).
-                entry, manifest_candidate = self._manifest_declared_template(
-                    pack_dir, template_name, template_type
-                )
-                if manifest_candidate is not None:
-                    return manifest_candidate
-                if entry is not None:
-                    # Manifest declares this template but the file is missing,
-                    # non-file (e.g. a directory), or an empty/falsey ``file``
-                    # value. The manifest is authoritative, so skip this pack's
-                    # convention fallback rather than mask a typo — mirrors
-                    # collect_all_layers().
-                    continue
                for subdir in subdirs:
                    if subdir:
                        candidate = pack_dir / subdir / f"{template_name}{ext}"
@@ -3011,22 +2957,31 @@ class PresetResolver:
                pack_dir = self.presets_dir / pack_id
                # Read strategy and manifest file path from preset manifest
                strategy = "replace"
+                manifest_file_path = None
                manifest_has_strategy = False
-                entry, manifest_candidate = self._manifest_declared_template(
-                    pack_dir, template_name, template_type
-                )
-                if entry is not None:
-                    strategy = entry.get("strategy", "replace")
-                    manifest_has_strategy = "strategy" in entry
-                # Use the manifest's declared file when it's a usable regular file;
-                # only fall back to convention-based lookup when the manifest
-                # doesn't list this template at all, so preset.yml stays
-                # authoritative (a declared-but-unusable file skips convention —
-                # parity with resolve()).
+                manifest_found_entry = False
+                manifest = self._get_manifest(pack_dir)
+                if manifest:
+                    for tmpl in manifest.templates:
+                        if (tmpl.get("name") == template_name
+                                and tmpl.get("type") == template_type):
+                            strategy = tmpl.get("strategy", "replace")
+                            manifest_has_strategy = "strategy" in tmpl
+                            manifest_file_path = tmpl.get("file")
+                            manifest_found_entry = True
+                            break
+                # Use manifest file path if specified, otherwise convention-based
+                # lookup — but only when the manifest doesn't exist or doesn't
+                # list this template, so preset.yml stays authoritative.
                candidate = None
-                if manifest_candidate is not None:
-                    candidate = manifest_candidate
-                elif entry is None:
+                if manifest_file_path:
+                    manifest_candidate = pack_dir / manifest_file_path
+                    if manifest_candidate.exists():
+                        candidate = manifest_candidate
+                    # Explicit file path that doesn't exist: skip convention
+                    # fallback to avoid masking typos or picking up unintended files.
+                elif not manifest_found_entry:
+                    # Manifest doesn't list this template — check convention paths
                    candidate = _find_in_subdirs(pack_dir)
                if candidate:
                    # Legacy fallback: if manifest doesn't explicitly declare a
@@ -13,8 +13,6 @@ from __future__ import annotations
 import hashlib
 import json
 import os
-import stat
-import tempfile
 import time
 from dataclasses import dataclass
 from pathlib import Path
@@ -73,180 +71,48 @@ class WorkflowRegistry:
        self.registry_path = self.workflows_dir / self.REGISTRY_FILE
        self.data = self._load()

-    def _has_symlinked_parent(self) -> bool:
-        """Return True if any directory under .specify/workflows is a symlink."""
-        current = self.project_root
-        for part in (".specify", "workflows"):
-            current = current / part
-            if current.is_symlink():
-                return True
-        return False
-
    def _load(self) -> dict[str, Any]:
        """Load registry from disk or create default."""
-        default_registry: dict[str, Any] = {
-            "schema_version": self.SCHEMA_VERSION,
-            "workflows": {},
-        }
-        # Defense-in-depth: refuse to read through symlinked parents or a
-        # symlinked registry file. Unlike StepRegistry (read-only best-effort
-        # elsewhere), a fabricated empty registry here is not safe: read-only
-        # callers (notably the bundler's remove path) query is_installed()
-        # before ever writing, and would otherwise conclude an installed
-        # workflow is absent, skip removing it, then delete the bundle
-        # record -- leaving the workflow untracked but still on disk. Fail
-        # closed here just like the unreadable-file case below.
-        if self._has_symlinked_parent() or self.registry_path.is_symlink():
-            raise OSError(
-                f"Refusing to read workflow registry at {self.registry_path}: "
-                "a parent directory or the registry file itself is a symlink"
-            )
        if self.registry_path.exists():
            try:
                with open(self.registry_path, encoding="utf-8") as f:
                    data = json.load(f)
-            except OSError as exc:
-                # The real data may still be intact on disk. Fail closed at
-                # construction rather than fabricating an empty registry that
-                # a read-only caller could mistake for "nothing installed."
-                raise OSError(
-                    f"Failed to read workflow registry at {self.registry_path}: {exc}"
-                ) from exc
-            except (
-                json.JSONDecodeError,
-                ValueError,
-                UnicodeError,
-            ) as exc:
-                raise OSError(
-                    f"Workflow registry at {self.registry_path} is corrupted: "
-                    f"{exc}"
-                ) from exc
-            # Validate shape: must be a dict with a dict "workflows" field.
-            if not isinstance(data, dict):
-                raise OSError(
-                    f"Workflow registry at {self.registry_path} is corrupted: "
-                    "top-level value must be an object"
-                )
-            if not isinstance(data.get("workflows"), dict):
-                raise OSError(
-                    f"Workflow registry at {self.registry_path} is corrupted: "
-                    "'workflows' must be an object"
-                )
-            return data
-        return default_registry
+                # Validate shape: must be a dict with a dict "workflows" field,
+                # otherwise every method that indexes data["workflows"] crashes.
+                # Mirrors StepRegistry._load.
+                if not isinstance(data, dict):
+                    return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}
+                if not isinstance(data.get("workflows"), dict):
+                    data["workflows"] = {}
+                return data
+            except (json.JSONDecodeError, ValueError, OSError, UnicodeError):
+                # Corrupted registry file — reset to default
+                return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}
+        return {"schema_version": self.SCHEMA_VERSION, "workflows": {}}

    def save(self) -> None:
-        """Persist registry to disk atomically."""
-        # Refuse to write through symlinked parents (mirrors StepRegistry.save
-        # and the CLI-level _reject_unsafe_dir guard).
-        if self._has_symlinked_parent() or self.registry_path.is_symlink():
-            raise OSError(
-                "Refusing to write workflow registry through a symlinked path."
-            )
+        """Persist registry to disk."""
        self.workflows_dir.mkdir(parents=True, exist_ok=True)
-        # Unique, exclusive temp then replace: a failed dump cannot truncate
-        # the registry, a pre-created symlink cannot redirect the write, and
-        # concurrent CLI processes cannot collide on the same temp path.
-        fd, tmp = tempfile.mkstemp(
-            dir=str(self.registry_path.parent),
-            prefix=f".{self.registry_path.name}.",
-            suffix=".tmp",
-        )
-        try:
-            # Write through a duplicate so the exclusive mkstemp descriptor
-            # stays open for fd-based metadata updates and inode verification.
-            with os.fdopen(os.dup(fd), "w", encoding="utf-8") as f:
-                json.dump(self.data, f, indent=2)
-            # mkstemp creates the temp file at 0600. A pre-existing registry
-            # may be shared more permissively (e.g. 0640/0644); preserve its
-            # mode across the replace so a save doesn't silently lock other
-            # project users out. A brand-new registry has no prior mode to
-            # preserve, so mkstemp's secure 0600 default stands. Mirrors
-            # _utils.py's atomic_write_json (best-effort; data safety over
-            # metadata preservation).
-            try:
-                if self.registry_path.exists():
-                    existing_stat = self.registry_path.stat(
-                        follow_symlinks=False
-                    )
-                    if stat.S_ISREG(existing_stat.st_mode) and hasattr(
-                        os, "fchmod"
-                    ):
-                        os.fchmod(fd, stat.S_IMODE(existing_stat.st_mode))
-                    if stat.S_ISREG(existing_stat.st_mode) and hasattr(
-                        os, "fchown"
-                    ):
-                        try:
-                            os.fchown(
-                                fd, existing_stat.st_uid, existing_stat.st_gid
-                            )
-                        except PermissionError:
-                            pass
-            except OSError:
-                pass
-            staged_stat = os.stat(tmp, follow_symlinks=False)
-            open_stat = os.fstat(fd)
-            if (
-                not stat.S_ISREG(staged_stat.st_mode)
-                or staged_stat.st_dev != open_stat.st_dev
-                or staged_stat.st_ino != open_stat.st_ino
-            ):
-                raise OSError(
-                    "Refusing to replace workflow registry: "
-                    "staged file changed before commit"
-                )
-            os.close(fd)
-            fd = -1
-            os.replace(tmp, self.registry_path)
-        except BaseException:
-            if fd >= 0:
-                try:
-                    os.close(fd)
-                except OSError:
-                    pass
-            try:
-                os.unlink(tmp)
-            except OSError:
-                pass
-            raise
+        with open(self.registry_path, "w", encoding="utf-8") as f:
+            json.dump(self.data, f, indent=2)

    def add(self, workflow_id: str, metadata: dict[str, Any]) -> None:
        """Add or update an installed workflow entry."""
        from datetime import datetime, timezone

-        raw_existing = self.data["workflows"].get(workflow_id)
-        had_entry = workflow_id in self.data["workflows"]
-        # Corrupted-but-parseable registries may hold non-dict entries.
-        existing = raw_existing if isinstance(raw_existing, dict) else {}
+        existing = self.data["workflows"].get(workflow_id, {})
        metadata["installed_at"] = existing.get(
            "installed_at", datetime.now(timezone.utc).isoformat()
        )
        metadata["updated_at"] = datetime.now(timezone.utc).isoformat()
        self.data["workflows"][workflow_id] = metadata
-        try:
-            self.save()
-        except (OSError, TypeError, ValueError):
-            # Roll back the in-memory mutation so a later successful save
-            # cannot persist metadata for a write that failed.
-            if had_entry:
-                self.data["workflows"][workflow_id] = raw_existing
-            else:
-                del self.data["workflows"][workflow_id]
-            raise
+        self.save()

    def remove(self, workflow_id: str) -> bool:
        """Remove an installed workflow entry. Returns True if found."""
        if workflow_id in self.data["workflows"]:
-            removed_entry = self.data["workflows"][workflow_id]
            del self.data["workflows"][workflow_id]
-            try:
-                self.save()
-            except (OSError, TypeError, ValueError):
-                # Roll back the in-memory deletion so a save failure can't
-                # desync this instance from the untouched file on disk,
-                # mirroring add()'s rollback-on-save-failure.
-                self.data["workflows"][workflow_id] = removed_entry
-                raise
+            self.save()
            return True
        return False

@@ -299,20 +165,8 @@ class WorkflowCatalog:
        """Validate that a catalog URL uses HTTPS (localhost HTTP allowed)."""
        from urllib.parse import urlparse

-        # A malformed authority (e.g. an unterminated IPv6 bracket
-        # "https://[::1") makes urlparse / hostname access raise ValueError.
-        # This validator's contract is to raise WorkflowValidationError for a
-        # bad URL, so surface that rather than leaking a raw ValueError past the
-        # command handler (which only catches WorkflowValidationError). Mirrors
-        # specify_cli.catalogs (#3435).
-        try:
-            parsed = urlparse(url)
-            hostname = parsed.hostname
-        except ValueError:
-            raise WorkflowValidationError(
-                f"Catalog URL is malformed: {url}"
-            ) from None
-        is_localhost = hostname in ("localhost", "127.0.0.1", "::1")
+        parsed = urlparse(url)
+        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
        if parsed.scheme != "https" and not (
            parsed.scheme == "http" and is_localhost
        ):
@@ -320,7 +174,7 @@ class WorkflowCatalog:
                f"Catalog URL must use HTTPS (got {parsed.scheme}://). "
                "HTTP is only allowed for localhost."
            )
-        if not hostname:
+        if not parsed.hostname:
            raise WorkflowValidationError(
                "Catalog URL must be a valid URL with a host."
            )
@@ -486,26 +340,15 @@ class WorkflowCatalog:
        from specify_cli.authentication.http import open_url as _open_url

        def _validate_catalog_url(url: str) -> None:
-            # A malformed authority (e.g. "https://[::1") makes urlparse /
-            # hostname access raise ValueError; treat it as a refused fetch
-            # rather than leaking a raw ValueError (this also validates the
-            # post-redirect resp.geturl(), so a hostile redirect target cannot
-            # crash the fetch either).
-            try:
-                parsed = urlparse(url)
-                hostname = parsed.hostname
-            except ValueError:
-                raise WorkflowCatalogError(
-                    f"Refusing to fetch catalog from malformed URL: {url}"
-                ) from None
-            is_localhost = hostname in ("localhost", "127.0.0.1", "::1")
+            parsed = urlparse(url)
+            is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
            if parsed.scheme != "https" and not (
                parsed.scheme == "http" and is_localhost
            ):
                raise WorkflowCatalogError(
                    f"Refusing to fetch catalog from non-HTTPS URL: {url}"
                )
-            if not hostname:
+            if not parsed.hostname:
                raise WorkflowCatalogError(
                    f"Refusing to fetch catalog from URL with no hostname: {url}"
                )
@@ -592,7 +435,6 @@ class WorkflowCatalog:
        self,
        query: str | None = None,
        tag: str | None = None,
-        author: str | None = None,
    ) -> list[dict[str, Any]]:
        """Search workflows across all configured catalogs."""
        merged = self._get_merged_workflows()
@@ -617,10 +459,6 @@ class WorkflowCatalog:
                normalized_tags = [t.lower() for t in tags if isinstance(t, str)]
                if tag.lower() not in normalized_tags:
                    continue
-            if author:
-                wf_author = wf_data.get("author", "")
-                if not isinstance(wf_author, str) or wf_author.lower() != author.lower():
-                    continue
            results.append(wf_data)
        return results

@@ -944,20 +782,8 @@ class StepCatalog:
        """Validate that a catalog URL uses HTTPS (localhost HTTP allowed)."""
        from urllib.parse import urlparse

-        # A malformed authority (e.g. an unterminated IPv6 bracket
-        # "https://[::1") makes urlparse / hostname access raise ValueError.
-        # This validator's contract is to raise StepValidationError for a bad
-        # URL, so surface that rather than leaking a raw ValueError past the
-        # command handler (which only catches StepValidationError). Mirrors
-        # specify_cli.catalogs (#3435).
-        try:
-            parsed = urlparse(url)
-            hostname = parsed.hostname
-        except ValueError:
-            raise StepValidationError(
-                f"Catalog URL is malformed: {url}"
-            ) from None
-        is_localhost = hostname in ("localhost", "127.0.0.1", "::1")
+        parsed = urlparse(url)
+        is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
        if parsed.scheme != "https" and not (
            parsed.scheme == "http" and is_localhost
        ):
@@ -965,7 +791,7 @@ class StepCatalog:
                f"Catalog URL must use HTTPS (got {parsed.scheme}://). "
                "HTTP is only allowed for localhost."
            )
-        if not hostname:
+        if not parsed.hostname:
            raise StepValidationError(
                "Catalog URL must be a valid URL with a host."
            )
@@ -1131,26 +957,15 @@ class StepCatalog:
        from specify_cli.authentication.http import open_url as _open_url

        def _validate_url(url: str) -> None:
-            # A malformed authority (e.g. "https://[::1") makes urlparse /
-            # hostname access raise ValueError; treat it as a refused fetch
-            # rather than leaking a raw ValueError (this also validates the
-            # post-redirect resp.geturl(), so a hostile redirect target cannot
-            # crash the fetch either).
-            try:
-                parsed = urlparse(url)
-                hostname = parsed.hostname
-            except ValueError:
-                raise StepCatalogError(
-                    f"Refusing to fetch catalog from malformed URL: {url}"
-                ) from None
-            is_localhost = hostname in ("localhost", "127.0.0.1", "::1")
+            parsed = urlparse(url)
+            is_localhost = parsed.hostname in ("localhost", "127.0.0.1", "::1")
            if parsed.scheme != "https" and not (
                parsed.scheme == "http" and is_localhost
            ):
                raise StepCatalogError(
                    f"Refusing to fetch catalog from non-HTTPS URL: {url}"
                )
-            if not hostname:
+            if not parsed.hostname:
                raise StepCatalogError(
                    f"Refusing to fetch catalog from URL with no hostname: {url}"
                )
@@ -150,7 +150,7 @@ def validate_workflow(definition: WorkflowDefinition) -> list[str]:
            f"'workflow.id' must be a string, got "
            f"{type(definition.id).__name__} ({definition.id!r})."
        )
-    elif not _ID_PATTERN.fullmatch(definition.id):
+    elif not _ID_PATTERN.match(definition.id):
        errors.append(
            f"Workflow ID {definition.id!r} must be lowercase alphanumeric "
            f"with hyphens."
@@ -172,7 +172,7 @@ def validate_workflow(definition: WorkflowDefinition) -> list[str]:
            f"{type(definition.version).__name__} ({definition.version!r}) — "
            f'quote it in YAML (version: "1.0.0").'
        )
-    elif not re.fullmatch(r"\d+\.\d+\.\d+", definition.version):
+    elif not re.match(r"^\d+\.\d+\.\d+$", definition.version):
        errors.append(
            f"Workflow version {definition.version!r} is not valid "
            f"semantic versioning (expected X.Y.Z)."
@@ -416,57 +416,18 @@ class RunState:
        ID into a path so a malicious value cannot probe or read files
        outside ``.specify/workflows/runs/<run_id>/``.
        """
-        if not isinstance(run_id, str) or not cls._RUN_ID_PATTERN.fullmatch(run_id):
+        if not isinstance(run_id, str) or not cls._RUN_ID_PATTERN.match(run_id):
            raise ValueError(
                f"Invalid run_id {run_id!r}: must be alphanumeric with "
                "hyphens/underscores only (and must start with an "
                "alphanumeric character)."
            )

-    @staticmethod
-    def _validate_installed_origin(
-        installed_workflow_id: str | None,
-        installed_registry_root: str | None,
-    ) -> None:
-        """Validate persisted installed-workflow ownership metadata."""
-        if installed_workflow_id is not None:
-            if not isinstance(installed_workflow_id, str):
-                raise ValueError(
-                    "Invalid run state: 'installed_workflow_id' must be a "
-                    f"string or null, got {type(installed_workflow_id).__name__}"
-                )
-            if not _ID_PATTERN.fullmatch(installed_workflow_id):
-                raise ValueError(
-                    "Invalid run state: 'installed_workflow_id' must be a "
-                    "lowercase alphanumeric workflow ID with hyphens"
-                )
-        if installed_registry_root is not None:
-            if not isinstance(installed_registry_root, str):
-                raise ValueError(
-                    "Invalid run state: 'installed_registry_root' must be a "
-                    f"string or null, got {type(installed_registry_root).__name__}"
-                )
-            if not installed_registry_root or not Path(
-                installed_registry_root
-            ).is_absolute():
-                raise ValueError(
-                    "Invalid run state: 'installed_registry_root' must be "
-                    "an absolute path or null"
-                )
-            if installed_workflow_id is None:
-                raise ValueError(
-                    "Invalid run state: 'installed_registry_root' requires "
-                    "'installed_workflow_id'"
-                )
-
    def __init__(
        self,
        run_id: str | None = None,
        workflow_id: str = "",
        project_root: Path | None = None,
-        installed_workflow_id: str | None = None,
-        installed_registry_root: str | None = None,
-        installed_origin_tracked: bool = True,
    ) -> None:
        # ``run_id is None`` (omitted) → auto-generate. An explicit empty
        # string is *not* the same as "omitted" and must be validated like
@@ -478,22 +439,8 @@ class RunState:
        else:
            self.run_id = run_id
        self._validate_run_id(self.run_id)
-        self._validate_installed_origin(
-            installed_workflow_id, installed_registry_root
-        )
        self.workflow_id = workflow_id
        self.project_root = project_root or Path(".")
-        # Identifies the installed workflow (if any) this run was started
-        # from, and the project root that owns its registry — set by
-        # execute() when the source was resolved to an installed ID (see
-        # workflow_run's ownership mapping). None for a direct/non-installed
-        # YAML source. ``installed_origin_tracked`` distinguishes those
-        # explicit None values from legacy state files that predate both
-        # fields, allowing the CLI to conservatively infer same-project
-        # registry ownership before resuming.
-        self.installed_workflow_id = installed_workflow_id
-        self.installed_registry_root = installed_registry_root
-        self.installed_origin_tracked = installed_origin_tracked
        self.status = RunStatus.CREATED
        self.current_step_index = 0
        self.current_step_id: str | None = None
@@ -556,8 +503,6 @@ class RunState:
            state_data = {
                "run_id": self.run_id,
                "workflow_id": self.workflow_id,
-                "installed_workflow_id": self.installed_workflow_id,
-                "installed_registry_root": self.installed_registry_root,
                "status": self.status.value,
                "current_step_index": self.current_step_index,
                "current_step_id": self.current_step_id,
@@ -609,46 +554,11 @@ class RunState:

        with open(state_path, encoding="utf-8") as f:
            state_data = json.load(f)
-        if not isinstance(state_data, dict):
-            raise ValueError("Invalid run state: expected a JSON object")
-        missing_fields = [
-            field
-            for field in ("run_id", "workflow_id", "status")
-            if field not in state_data
-        ]
-        if missing_fields:
-            raise ValueError(
-                "Invalid run state: missing required field(s): "
-                + ", ".join(missing_fields)
-            )
-
-        workflow_id = state_data["workflow_id"]
-        if not isinstance(workflow_id, str) or not _ID_PATTERN.fullmatch(
-            workflow_id
-        ):
-            raise ValueError(
-                "Invalid run state: 'workflow_id' must be a lowercase "
-                "alphanumeric workflow ID with hyphens"
-            )
-
-        has_installed_workflow_id = "installed_workflow_id" in state_data
-        has_installed_registry_root = "installed_registry_root" in state_data
-        if has_installed_workflow_id != has_installed_registry_root:
-            raise ValueError(
-                "Invalid run state: installed workflow origin fields must "
-                "either both be present or both be absent"
-            )
-
-        installed_workflow_id = state_data.get("installed_workflow_id")
-        installed_registry_root = state_data.get("installed_registry_root")

        state = cls(
            run_id=state_data["run_id"],
-            workflow_id=workflow_id,
+            workflow_id=state_data["workflow_id"],
            project_root=project_root,
-            installed_workflow_id=installed_workflow_id,
-            installed_registry_root=installed_registry_root,
-            installed_origin_tracked=has_installed_workflow_id,
        )
        state.status = RunStatus(state_data["status"])
        state.current_step_index = state_data.get("current_step_index", 0)
@@ -661,16 +571,7 @@ class RunState:
        if inputs_path.exists():
            with open(inputs_path, encoding="utf-8") as f:
                inputs_data = json.load(f)
-            if not isinstance(inputs_data, dict):
-                raise ValueError(
-                    "Invalid run inputs: expected a JSON object"
-                )
-            inputs = inputs_data.get("inputs", {})
-            if not isinstance(inputs, dict):
-                raise ValueError(
-                    "Invalid run inputs: 'inputs' must be a JSON object"
-                )
-            state.inputs = inputs
+            state.inputs = inputs_data.get("inputs", {})

        return state

@@ -753,8 +654,6 @@ class WorkflowEngine:
        definition: WorkflowDefinition,
        inputs: dict[str, Any] | None = None,
        run_id: str | None = None,
-        installed_workflow_id: str | None = None,
-        installed_registry_root: Path | None = None,
    ) -> RunState:
        """Execute a workflow definition.

@@ -766,12 +665,6 @@ class WorkflowEngine:
            User-provided input values.
        run_id:
            Optional run ID (uses SPECKIT_WORKFLOW_RUN_ID when set, otherwise auto-generated).
-        installed_workflow_id, installed_registry_root:
-            When the run was started from an installed workflow (as opposed
-            to a direct/non-installed YAML source), identifies it and its
-            owning registry root so a later ``resume`` can re-check the
-            registry's current disabled state before continuing — see
-            ``workflow_resume``.

        Returns
        -------
@@ -789,12 +682,6 @@ class WorkflowEngine:
            run_id=effective_run_id,
            workflow_id=definition.id,
            project_root=self.project_root,
-            installed_workflow_id=installed_workflow_id,
-            installed_registry_root=(
-                str(installed_registry_root)
-                if installed_registry_root is not None
-                else None
-            ),
        )

        # Persist a copy of the workflow definition so resume can
@@ -31,20 +31,6 @@ class CommandStep(StepBase):
    def execute(self, config: dict[str, Any], context: StepContext) -> StepResult:
        command = config.get("command", "")
        input_data = config.get("input", {})
-        # validate() rejects a non-mapping input, but the engine does not
-        # auto-validate before execute(); a workflow that skipped validation can
-        # still reach here. Fail the step with the same contract error rather
-        # than silently coercing to {} and dispatching with empty args — that
-        # would change the command's meaning, hide the config error, and report
-        # COMPLETED, defeating the per-step FAILED / continue_on_error behavior.
-        if not isinstance(input_data, dict):
-            return StepResult(
-                status=StepStatus.FAILED,
-                error=(
-                    f"Command step {config.get('id', '?')!r}: 'input' must be a "
-                    f"mapping, got {type(input_data).__name__}."
-                ),
-            )

        # Resolve expressions in input
        resolved_input: dict[str, Any] = {}
@@ -64,18 +50,8 @@ class CommandStep(StepBase):
        # Merge options (workflow defaults ← step overrides)
        options = dict(context.default_options)
        step_options = config.get("options", {})
-        # Same rationale as 'input': a malformed options fails the step rather
-        # than being silently ignored (which would let an invalid step run and
-        # apparently complete).
-        if not isinstance(step_options, dict):
-            return StepResult(
-                status=StepStatus.FAILED,
-                error=(
-                    f"Command step {config.get('id', '?')!r}: 'options' must be a "
-                    f"mapping, got {type(step_options).__name__}."
-                ),
-            )
-        options.update(step_options)
+        if step_options:
+            options.update(step_options)

        # Attempt CLI dispatch
        args_str = str(resolved_input.get("args", ""))
@@ -179,16 +155,4 @@ class CommandStep(StepBase):
            errors.append(
                f"Command step {config.get('id', '?')!r} is missing 'command' field."
            )
-        # execute() iterates input.items() and options.update(step_options); a
-        # non-mapping here would raise at run time. Validate the shape like the
-        # sibling steps (switch 'cases', fan-out 'step') so it is reported, not
-        # crashed on.
-        if "input" in config and not isinstance(config["input"], dict):
-            errors.append(
-                f"Command step {config.get('id', '?')!r}: 'input' must be a mapping."
-            )
-        if "options" in config and not isinstance(config["options"], dict):
-            errors.append(
-                f"Command step {config.get('id', '?')!r}: 'options' must be a mapping."
-            )
        return errors
@@ -24,24 +24,6 @@ class FanInStep(StepBase):
        if not isinstance(output_config, dict):
            output_config = {}

-        # The engine does not auto-validate step config, so an unvalidated run
-        # with a non-list ``wait_for`` reaches here raw. Iterating it then
-        # either crashes the whole run (a scalar like an int or None raises
-        # TypeError) or, worse, silently iterates a string's characters and
-        # yields a bogus join of empty results with a COMPLETED status — the
-        # exact "silent empty result + COMPLETED" wiring bug the engine's
-        # fan-in validation guards against. Fail this step loudly instead,
-        # mirroring the fan-out step's non-list ``items`` handling.
-        if not isinstance(wait_for, list):
-            return StepResult(
-                status=StepStatus.FAILED,
-                error=(
-                    f"Fan-in step {config.get('id', '?')!r}: 'wait_for' must be "
-                    f"a list of step IDs, got {type(wait_for).__name__}."
-                ),
-                output={"results": []},
-            )
-
        # Collect results from referenced steps
        results = []
        for step_id in wait_for:
@@ -6,7 +6,6 @@ contracts/cli-commands.md (offline, discovery-only refusal, not-a-project error)
 """
 from __future__ import annotations

-import io
 import json
 from pathlib import Path
 from unittest.mock import patch
@@ -64,42 +63,6 @@ def test_commands_outside_project_fail_with_guidance(tmp_path: Path, monkeypatch
    assert "Spec Kit project" in result.output


-def test_remove_reports_clean_error_when_primitive_raises_raw_exception(
-    project: Path,
-):
-    """A raw exception from a primitive installer (e.g. an OSError from an
-    unreadable workflow registry surfacing through _WorkflowKindManager's
-    fail-closed construction) must not propagate uncaught through
-    `specify bundle remove` -- the command only catches BundlerError, so
-    without a conversion at the remove_bundle boundary this would exit
-    with an unhandled exception and empty/raw output instead of a clean,
-    actionable message, and no removal side effects should occur either."""
-    from specify_cli.bundler.models.manifest import BundleManifest
-    from specify_cli.bundler.models.records import load_records
-    from specify_cli.bundler.services.adapters import DefaultPrimitiveInstaller
-    from specify_cli.bundler.services.installer import install_bundle
-    from specify_cli.bundler.services.resolver import resolve_install_plan
-    from tests.bundler_helpers import FakeInstaller
-
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    plan = resolve_install_plan(
-        manifest, speckit_version="0.11.2", active_integration="copilot"
-    )
-    install_bundle(project, plan, FakeInstaller(), manifest=manifest)
-
-    def boom(self, project_root, component):
-        raise OSError("workflow registry unreadable")
-
-    with pytest.MonkeyPatch.context() as mp:
-        mp.setattr(DefaultPrimitiveInstaller, "is_installed", boom)
-        result = runner.invoke(app, ["bundle", "remove", "demo-bundle"])
-
-    assert result.exit_code != 0
-    assert result.output.strip() != ""
-    assert result.exception is None or isinstance(result.exception, SystemExit)
-    assert {r.bundle_id for r in load_records(project)} == {"demo-bundle"}
-
-
 def test_fail_writes_error_to_stderr_not_stdout(capsys):
    """_fail must write to stderr, not stdout: every bundle command routes errors
    through it, and under --json the error would otherwise corrupt the JSON payload
@@ -469,16 +432,25 @@ def test_install_integration_override_cannot_bypass_clash_guard(project: Path):
 # ===== Private GitHub release asset URL resolution =====


-class FakeBundleResponse(io.BytesIO):
+class FakeBundleResponse:
    """Minimal context-manager response stub for open_url fakes."""

    def __init__(self, data: bytes, url: str = "https://api.github.com/repos/org/repo/releases/assets/99"):
-        super().__init__(data)
+        self._data = data
        self._url = url

+    def read(self) -> bytes:
+        return self._data
+
    def geturl(self) -> str:
        return self._url

+    def __enter__(self):
+        return self
+
+    def __exit__(self, *_):
+        return False
+

 def _make_catalog_config(catalog_path: Path, project: Path) -> None:
    """Write a bundle-catalogs.yml pointing at *catalog_path* in *project*."""
@@ -11,7 +11,7 @@ import pytest

 from specify_cli.bundler import BundlerError
 from specify_cli.bundler.models.manifest import BundleManifest
-from specify_cli.bundler.models.records import load_records, records_path
+from specify_cli.bundler.models.records import load_records
 from specify_cli.bundler.services.installer import install_bundle, remove_bundle
 from specify_cli.bundler.services.resolver import resolve_install_plan
 from tests.bundler_helpers import FakeInstaller, make_project, valid_manifest_dict
@@ -97,212 +97,6 @@ def test_remove_unknown_bundle_errors(tmp_path: Path):
        remove_bundle(tmp_path, "ghost", FakeInstaller())


-def test_remove_converts_raw_installer_exception_to_bundler_error(tmp_path: Path):
-    """A raw exception from a primitive installer (e.g. an OSError from an
-    unreadable workflow registry surfacing through _WorkflowKindManager's
-    fail-closed construction) must not propagate uncaught out of
-    remove_bundle: install_bundle already converts any non-BundlerError
-    exception into a clean BundlerError, but remove_bundle had no such
-    conversion, so the CLI's `bundle remove` (which only catches
-    BundlerError) would let a raw exception through with no clean message
-    and no removal side effects should occur either."""
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    def boom(project_root, component):
-        raise OSError("workflow registry unreadable")
-
-    with pytest.MonkeyPatch.context() as mp:
-        mp.setattr(installer, "is_installed", boom)
-        with pytest.raises(BundlerError):
-            remove_bundle(tmp_path, "demo-bundle", installer)
-
-    # No removal side effects: the bundle record must still be present.
-    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
-
-
-def test_remove_partial_failure_message_reflects_partial_state(tmp_path: Path):
-    """A failure can occur after earlier components in the same bundle have
-    already been removed from disk. The bundle record is left unchanged
-    (save_records never runs on this path), so it still claims the bundle
-    fully installed -- but the message must not claim "No changes were
-    recorded" when components were, in fact, already removed."""
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    real_remove = installer.remove
-    calls = {"n": 0}
-
-    def remove_then_fail(project_root, component):
-        calls["n"] += 1
-        if calls["n"] == 1:
-            return real_remove(project_root, component)
-        raise OSError("disk full")
-
-    with pytest.MonkeyPatch.context() as mp:
-        mp.setattr(installer, "remove", remove_then_fail)
-        with pytest.raises(BundlerError) as exc_info:
-            remove_bundle(tmp_path, "demo-bundle", installer)
-
-    message = str(exc_info.value)
-    assert "no changes were recorded" not in message.lower()
-    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
-
-
-def test_remove_bundler_error_from_installer_after_partial_removal_reports_partial_state(
-    tmp_path: Path,
-):
-    """If the primitive installer itself raises BundlerError (not a raw/
-    unexpected exception) after an earlier component in the same bundle was
-    already removed, the surfaced message must still carry the same
-    partial-removal detail as the generic-exception path -- a bare
-    ``except BundlerError: raise`` would re-raise the installer's original
-    message verbatim with no mention that the project may now be partially
-    uninstalled."""
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    real_remove = installer.remove
-    calls = {"n": 0}
-
-    def remove_then_raise_bundler_error(project_root, component):
-        calls["n"] += 1
-        if calls["n"] == 1:
-            return real_remove(project_root, component)
-        raise BundlerError("kind manager refused removal")
-
-    with pytest.MonkeyPatch.context() as mp:
-        mp.setattr(installer, "remove", remove_then_raise_bundler_error)
-        with pytest.raises(BundlerError) as exc_info:
-            remove_bundle(tmp_path, "demo-bundle", installer)
-
-    message = str(exc_info.value)
-    assert "no changes were recorded" not in message.lower()
-    assert "kind manager refused removal" in message
-    assert "partially uninstalled" in message.lower()
-    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
-
-
-def test_remove_bundler_error_from_installer_with_zero_removed_reports_no_changes(
-    tmp_path: Path,
-):
-    """When the installer raises BundlerError before anything was actually
-    removed, the message should not misleadingly claim partial state."""
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    def boom(project_root, component):
-        raise BundlerError("kind manager unavailable")
-
-    with pytest.MonkeyPatch.context() as mp:
-        mp.setattr(installer, "is_installed", boom)
-        with pytest.raises(BundlerError) as exc_info:
-            remove_bundle(tmp_path, "demo-bundle", installer)
-
-    message = str(exc_info.value)
-    assert "no components were removed" in message.lower()
-    assert "no removal was attempted" in message.lower()
-    assert "partially uninstalled" not in message.lower()
-    assert "kind manager unavailable" in message
-    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
-
-
-def test_remove_zero_completed_removals_still_cautions_about_partial_changes(
-    tmp_path: Path,
-):
-    """`result.uninstalled` only records a component after its `remove()`
-    call returns successfully. If the very first `remove()` call itself
-    raises after already deleting some files, zero completed removals are
-    recorded even though the project may already be partially uninstalled --
-    the zero-count message must not claim "No components were removed" as
-    an unqualified fact; it must caution that the failing component may
-    have made partial changes before raising."""
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-
-    def boom(project_root, component):
-        # Simulates a remove() that deletes some files before raising --
-        # from the caller's perspective this component was never recorded
-        # as completed, but disk state may already be partially changed.
-        raise OSError("disk full partway through removal")
-
-    with pytest.MonkeyPatch.context() as mp:
-        mp.setattr(installer, "remove", boom)
-        with pytest.raises(BundlerError) as exc_info:
-            remove_bundle(tmp_path, "demo-bundle", installer)
-
-    message = str(exc_info.value)
-    assert "no components were removed" in message.lower()
-    assert "partial" in message.lower()
-    assert "partially uninstalled" in message.lower()
-    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
-
-
-def test_remove_record_save_failure_reports_partial_state(tmp_path: Path):
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-    record_file = records_path(tmp_path)
-    original_record = record_file.read_bytes()
-
-    def fail_dump(_data, handle, *_args, **_kwargs):
-        handle.write('{"partial":')
-        handle.flush()
-        raise OSError("disk full")
-
-    with pytest.MonkeyPatch.context() as mp:
-        mp.setattr(
-            "specify_cli.bundler.lib.yamlio.json.dump",
-            fail_dump,
-        )
-        with pytest.raises(BundlerError) as exc_info:
-            remove_bundle(tmp_path, "demo-bundle", installer)
-
-    message = str(exc_info.value)
-    assert "disk full" in message
-    assert "partially uninstalled" in message.lower()
-    assert installer.installed == set()
-    assert record_file.read_bytes() == original_record
-    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
-
-
-def test_remove_record_save_failure_without_remove_attempt_is_not_partial(
-    tmp_path: Path,
-):
-    make_project(tmp_path)
-    manifest = BundleManifest.from_dict(valid_manifest_dict())
-    installer = FakeInstaller()
-    install_bundle(tmp_path, _plan(manifest), installer, manifest=manifest)
-    installer.installed.clear()
-
-    def fail_save(*_args, **_kwargs):
-        raise OSError("disk full")
-
-    with pytest.MonkeyPatch.context() as mp:
-        mp.setattr(
-            "specify_cli.bundler.services.installer.save_records",
-            fail_save,
-        )
-        with pytest.raises(BundlerError) as exc_info:
-            remove_bundle(tmp_path, "demo-bundle", installer)
-
-    message = str(exc_info.value)
-    assert "no removal was attempted" in message.lower()
-    assert "partially uninstalled" not in message.lower()
-    assert {r.bundle_id for r in load_records(tmp_path)} == {"demo-bundle"}
-
-
 def test_remove_reports_uninstalled_not_installed(tmp_path: Path):
    make_project(tmp_path)
    manifest = BundleManifest.from_dict(valid_manifest_dict())
@@ -334,7 +128,7 @@ def test_remove_counts_only_components_actually_removed(tmp_path: Path):

    assert len(result.uninstalled) == 3
    assert (gone.kind, gone.id) not in installer.remove_calls
-    assert gone not in result.skipped
+    assert gone in result.skipped
    make_project(tmp_path)
    manifest = BundleManifest.from_dict(valid_manifest_dict())
    installer = FakeInstaller()
@@ -115,63 +115,6 @@ class TestInitIntegrationFlag:
        data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
        assert data["integration"] == specify_cli.DEFAULT_INIT_INTEGRATION

-    def test_init_here_nonempty_noninteractive_errors_with_force_guidance(self, tmp_path):
-        """`init --here` on a non-empty directory with no confirmation input (empty
-        stdin) must fail fast with guidance to use --force, instead of the bare
-        'Aborted.' from an EOF on typer.confirm. CliRunner with no `input=` provides
-        empty stdin, so typer.confirm raises Abort, which the command converts to the
-        actionable error."""
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        project = tmp_path / "nonempty-here"
-        project.mkdir()
-        (project / "existing.txt").write_text("keep me", encoding="utf-8")
-        old_cwd = os.getcwd()
-        try:
-            os.chdir(project)
-            result = CliRunner().invoke(app, [
-                "init", "--here", "--integration", "copilot", "--script", "sh", "--ignore-agent-tools",
-            ], catch_exceptions=False)
-        finally:
-            os.chdir(old_cwd)
-
-        assert result.exit_code == 1, result.output
-        assert "--force" in result.output
-        # Aborted before scaffolding: the pre-existing file is untouched.
-        assert (project / "existing.txt").read_text(encoding="utf-8") == "keep me"
-
-    def test_init_here_interactive_cancel_exits_zero(self, tmp_path, monkeypatch):
-        """An interactive Ctrl+C at the merge confirmation (typer.Abort on a TTY)
-        is a normal cancellation — exit 0, "cancelled" — NOT the missing-input
-        --force error, which is reserved for non-interactive EOF. Guards the
-        regression where Abort was caught unconditionally and every cancel became
-        an exit-1 --force error."""
-        from typer.testing import CliRunner
-        from specify_cli import app
-        import specify_cli.commands.init as init_mod
-
-        # Simulate an interactive terminal so the Abort is treated as a cancel.
-        monkeypatch.setattr(init_mod, "_stdin_is_interactive", lambda: True)
-
-        project = tmp_path / "cancel-here"
-        project.mkdir()
-        (project / "existing.txt").write_text("keep me", encoding="utf-8")
-        old_cwd = os.getcwd()
-        try:
-            os.chdir(project)
-            # No input → typer.confirm raises Abort (stands in for Ctrl+C).
-            result = CliRunner().invoke(app, [
-                "init", "--here", "--integration", "copilot", "--script", "sh", "--ignore-agent-tools",
-            ], catch_exceptions=False)
-        finally:
-            os.chdir(old_cwd)
-
-        assert result.exit_code == 0, result.output
-        assert "cancelled" in result.output.lower()
-        assert "--force" not in result.output  # not the missing-input error
-        assert (project / "existing.txt").read_text(encoding="utf-8") == "keep me"
-
    def test_integration_copilot_auto_promotes(self, tmp_path):
        from typer.testing import CliRunner
        from specify_cli import app
@@ -892,8 +835,7 @@ class TestInitIntegrationFlag:
        assert (scripts_dir / "common.sh").read_text(encoding="utf-8") != custom_content

    def test_init_here_without_force_preserves_shared_infra(self, tmp_path):
-        """E2E: confirming the merge with piped "y" (no --force) preserves
-        existing shared infra files (unlike --force, which overwrites them)."""
+        """E2E: specify init --here (no --force) preserves existing shared infra files."""
        from typer.testing import CliRunner
        from specify_cli import app

@@ -201,36 +201,6 @@ class YamlIntegrationTests:
        parsed = yaml.safe_load("\n".join(yaml_lines))
        assert parsed["prompt"].rstrip("\n") == body

-    def test_yaml_prompt_with_control_characters_stays_valid(self):
-        """A body containing control characters must still produce parseable YAML.
-
-        YAML forbids C0 control characters (except tab and newline), DEL,
-        C1 controls, lone surrogates and U+FFFE/U+FFFF in every scalar form,
-        and YAML 1.1 treats NEL (U+0085), LS (U+2028) and PS (U+2029) as
-        line breaks that corrupt a literal block scalar's structure. The
-        renderer falls back to an escaped double-quoted scalar for such
-        bodies."""
-        for ch in (
-            "\x08", "\x0c", "\x1b", "\x7f",
-            "\x80", "\x84", "\x85", "\x86", "\x9f",
-            "\u2028", "\u2029",
-            "\ud800", "\udfff", "\ufffe", "\uffff",
-        ):
-            body = f"before{ch}after\nsecond line"
-            rendered = YamlIntegration._render_yaml("Title", "Desc", body, "src")
-            parsed = yaml.safe_load(rendered)
-            assert parsed["prompt"].rstrip("\n") == body, f"char {ch!r} round-trip"
-
-    def test_yaml_prompt_with_bare_carriage_return_stays_valid(self):
-        """A bare CR (not part of CRLF) must not break the generated YAML.
-
-        Inside a block scalar a lone \r acts as a line break, corrupting
-        the document structure."""
-        body = "line1\rstill line1\nline2"
-        rendered = YamlIntegration._render_yaml("Title", "Desc", body, "src")
-        parsed = yaml.safe_load(rendered)
-        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.

@@ -2675,27 +2675,6 @@ class TestParseIntegrationOptionsEqualsForm:
        assert result_space["commands_dir"] == "./mydir"
        assert result_equals["commands_dir"] == "./mydir"

-    def test_unbalanced_quote_exits_cleanly(self, capsys):
-        """An unbalanced quote must exit(1) with a message, not a raw ValueError.
-
-        shlex.split() raises ValueError("No closing quotation") on an unbalanced
-        quote; the parser must translate that into the same clean typer.Exit(1)
-        UX as unknown-option / missing-value, rather than letting the traceback
-        escape (issue #3457).
-        """
-        import typer
-
-        from specify_cli.integrations._commands import _parse_integration_options
-        from specify_cli.integrations import get_integration
-
-        integration = get_integration("generic")
-        assert integration is not None
-
-        with pytest.raises(typer.Exit) as excinfo:
-            _parse_integration_options(integration, '--commands-dir "foo')
-        assert excinfo.value.exit_code == 1
-        assert "Error: Could not parse integration options: No closing quotation." in capsys.readouterr().out
-

 class TestUninstallNoManifestClearsInitOptions:
    def test_init_options_cleared_on_no_manifest_uninstall(self, tmp_path):
@@ -272,20 +272,6 @@ class TestMultiInstallSafeContracts:
                f"these files: {sorted(overlap)}"
            )

-    def test_kiro_cli_is_declared_multi_install_safe(self):
-        """kiro-cli confines itself to an isolated ``.kiro/`` root that no
-        other integration touches, so it must be declared multi-install safe
-        (issue #3471).
-
-        Before the fix, co-installing kiro-cli alongside another integration
-        left ``specify integration status`` permanently in ERROR
-        (``unsafe-multi-install``) with no way to acknowledge it. The
-        parametrized isolation/manifest contracts above already exercise
-        kiro-cli once the flag is set; this pins the declaration itself so a
-        future edit cannot silently drop it and reintroduce the error.
-        """
-        assert INTEGRATION_REGISTRY["kiro-cli"].multi_install_safe is True
-

 class TestCatalogParity:
    """The discovery catalog must list every registered integration."""
@@ -7896,135 +7896,3 @@ class TestConfigManagerEnvPrefixCollision:
        cfg = cm._get_env_config()
        assert "" not in cfg
        assert cfg == {"a": {"b": "z"}}
-
-
-class TestConfigManagerCrossExtensionEnvLeak:
-    """Cross-extension env-var leak: a longer, co-installed sibling ID must
-    own its own env vars instead of leaking them into a shorter-prefix sibling.
-
-    Before the fix, ``SPECKIT_GIT_HOOKS_URL`` (intended for a ``git-hooks``
-    extension) also surfaced inside the ``git`` extension's config as
-    ``{'hooks': {'url': ...}}`` because ``SPECKIT_GIT_`` is a strict prefix of
-    ``SPECKIT_GIT_HOOKS_``.
-    """
-
-    def _install(self, project_root, ext_id):
-        extensions_dir = project_root / ".specify" / "extensions"
-        (extensions_dir / ext_id).mkdir(parents=True)
-        # Register in the extension registry — the registry is the source of
-        # truth for "installed" (a bare directory can be a config-only leftover
-        # from ``ExtensionManager.remove(..., keep_config=True)``).
-        ExtensionRegistry(extensions_dir).add(ext_id, {})
-
-    def test_sibling_owns_longer_prefix_env(self, tmp_path, monkeypatch):
-        """SPECKIT_GIT_HOOKS_URL belongs to git-hooks when co-installed with git."""
-        self._install(tmp_path, "git")
-        self._install(tmp_path, "git-hooks")
-        monkeypatch.setenv("SPECKIT_GIT_URL", "for_git")
-        monkeypatch.setenv("SPECKIT_GIT_HOOKS_URL", "for_git_hooks")
-
-        git_cfg = ConfigManager(tmp_path, "git")._get_env_config()
-        gh_cfg = ConfigManager(tmp_path, "git-hooks")._get_env_config()
-
-        # 'git' must NOT see the git-hooks var — no cross-extension leak.
-        assert git_cfg == {"url": "for_git"}
-        # 'git-hooks' still receives its own var (unchanged behaviour).
-        assert gh_cfg == {"url": "for_git_hooks"}
-
-    def test_no_sibling_installed_keeps_legacy_absorption(self, tmp_path, monkeypatch):
-        """Without a longer-prefix sibling installed, the legacy behaviour is
-        preserved: ``SPECKIT_GIT_HOOKS_URL`` is absorbed as a nested key of
-        the ``git`` extension. This keeps the fix strictly to the *collision*
-        case and avoids surprising users who deliberately set a nested key
-        via env with no sibling to disambiguate against.
-        """
-        self._install(tmp_path, "git")
-        monkeypatch.setenv("SPECKIT_GIT_HOOKS_URL", "for_git_hooks")
-
-        cfg = ConfigManager(tmp_path, "git")._get_env_config()
-        assert cfg == {"hooks": {"url": "for_git_hooks"}}
-
-    def test_non_prefix_sibling_ignored(self, tmp_path, monkeypatch):
-        """A sibling whose ID does not extend our own is not a collision.
-
-        e.g. current='git' and sibling='not-git' — 'not-git' normalized to
-        'NOT_GIT' does not start with 'GIT_', so its presence must not
-        influence git's env-var interpretation.
-        """
-        self._install(tmp_path, "git")
-        self._install(tmp_path, "not-git")
-        monkeypatch.setenv("SPECKIT_GIT_HOOKS_URL", "for_git_hooks")
-
-        cfg = ConfigManager(tmp_path, "git")._get_env_config()
-        assert cfg == {"hooks": {"url": "for_git_hooks"}}
-
-    def test_boundary_prevents_false_positive(self, tmp_path, monkeypatch):
-        """Sibling ID 'hook' (not 'hooks') must NOT eat env keys starting
-        with 'hooks'. The trailing-underscore boundary in the sibling prefix
-        prevents this false positive.
-        """
-        self._install(tmp_path, "git")
-        self._install(tmp_path, "git-hook")
-        monkeypatch.setenv("SPECKIT_GIT_HOOKS_URL", "for_git_key_hooks")
-
-        # git-hook's prefix is 'HOOK_', which does not match 'HOOKS_URL',
-        # so 'git' keeps the env var (single-installed semantics).
-        cfg = ConfigManager(tmp_path, "git")._get_env_config()
-        assert cfg == {"hooks": {"url": "for_git_key_hooks"}}
-
-    def test_missing_extensions_dir_does_not_crash(self, tmp_path, monkeypatch):
-        """A ConfigManager built against a project without ``.specify/extensions``
-        (fresh project, ad-hoc test harness) must still evaluate env config
-        rather than raising from the sibling scan.
-        """
-        # Note: no _install call — extensions dir intentionally absent.
-        monkeypatch.setenv("SPECKIT_TESTEXT_URL", "v")
-
-        cfg = ConfigManager(tmp_path, "testext")._get_env_config()
-        assert cfg == {"url": "v"}
-
-    def test_config_only_leftover_not_treated_as_sibling(self, tmp_path, monkeypatch):
-        """A directory left behind by ``remove(..., keep_config=True)`` must
-        NOT be treated as an installed sibling.
-
-        ``ExtensionManager.remove(keep_config=True)`` preserves the extension
-        directory (config files remain, dormant, for a possible reinstall) but
-        removes the registry entry. The sibling scan is sourced from the
-        registry, so a leftover ``git-hooks/`` directory without a registry
-        entry must not silently discard ``SPECKIT_GIT_HOOKS_*`` from ``git``.
-        """
-        self._install(tmp_path, "git")
-        # Simulate ``remove('git-hooks', keep_config=True)``: dir present,
-        # config file preserved, but no registry entry.
-        gh_dir = tmp_path / ".specify" / "extensions" / "git-hooks"
-        gh_dir.mkdir(parents=True)
-        (gh_dir / "git-hooks-config.yml").write_text("url: leftover\n")
-        # Sanity: git-hooks is NOT registered.
-        registry = ExtensionRegistry(tmp_path / ".specify" / "extensions")
-        assert "git-hooks" not in registry.keys()
-
-        monkeypatch.setenv("SPECKIT_GIT_HOOKS_URL", "for_git")
-
-        cfg = ConfigManager(tmp_path, "git")._get_env_config()
-        # git absorbs the var (no registered sibling owns it).
-        assert cfg == {"hooks": {"url": "for_git"}}
-
-    def test_non_utf8_registry_does_not_crash(self, tmp_path, monkeypatch):
-        """A registry file with invalid text encoding must NOT propagate
-        ``UnicodeDecodeError`` out of the sibling scan and abort every
-        config read. ``ExtensionRegistry._load()`` catches ``JSONDecodeError``
-        / ``FileNotFoundError`` only, so ``_sibling_extension_ids`` must
-        additionally swallow ``UnicodeError`` and degrade to the documented
-        pre-fix behaviour.
-        """
-        extensions_dir = tmp_path / ".specify" / "extensions"
-        extensions_dir.mkdir(parents=True)
-        # Write bytes that are not valid UTF-8 to the registry file.
-        (extensions_dir / ExtensionRegistry.REGISTRY_FILE).write_bytes(
-            b"\xff\xfe invalid utf-8 registry \xc3\x28"
-        )
-        monkeypatch.setenv("SPECKIT_TESTEXT_URL", "v")
-
-        # Must not raise; must fall back to the "no siblings" path.
-        cfg = ConfigManager(tmp_path, "testext")._get_env_config()
-        assert cfg == {"url": "v"}
@@ -152,44 +152,6 @@ class TestResolveGitHubReleaseAssetApiUrl:
        )
        assert result is None

-    def test_metadata_lookup_is_bounded_and_redirect_validated(self):
-        """Release metadata reads stay bounded and use the caller's policy."""
-        captured = {}
-
-        class OversizedResponse:
-            def read(self, amount=None):
-                captured["read_amount"] = amount
-                return b"x" * amount
-
-            def __enter__(self):
-                return self
-
-            def __exit__(self, *args):
-                return False
-
-        def redirect_validator(old_url, new_url):
-            return None
-
-        def fake_open(
-            url,
-            timeout=None,
-            extra_headers=None,
-            redirect_validator=None,
-        ):
-            captured["redirect_validator"] = redirect_validator
-            return OversizedResponse()
-
-        result = resolve_github_release_asset_api_url(
-            "https://github.com/org/repo/releases/download/v1/pack.zip",
-            fake_open,
-            redirect_validator=redirect_validator,
-            max_metadata_bytes=8,
-        )
-
-        assert result is None
-        assert captured["read_amount"] == 9
-        assert captured["redirect_validator"] is redirect_validator
-
    def test_tag_with_special_characters_is_url_encoded(self):
        """Tags with reserved characters (e.g. '/') are encoded in the API URL."""
        captured_urls = []
@@ -884,186 +884,6 @@ class TestPresetResolver:
        assert result is not None
        assert "Custom Spec Template" in result.read_text()

-    def _install_pack_with_manifest_file(self, project_dir, *, extra_file=False):
-        """Create a pack whose manifest declares a NON-convention file: path.
-
-        Returns the pack dir under the project. The declared file lives at
-        custom/spec.md (not the convention templates/spec-template.md).
-        """
-        presets_dir = project_dir / ".specify" / "presets"
-        pack_dir = presets_dir / "mypack"
-        (pack_dir / "custom").mkdir(parents=True)
-        (pack_dir / "custom" / "spec.md").write_text(
-            "# Manifest-declared Spec\n", encoding="utf-8"
-        )
-        if extra_file:
-            # An undeclared convention-path file the manifest points away from.
-            (pack_dir / "templates").mkdir()
-            (pack_dir / "templates" / "spec-template.md").write_text(
-                "# Stray Convention Spec\n", encoding="utf-8"
-            )
-        manifest = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "mypack",
-                "name": "My Pack",
-                "version": "1.0.0",
-                "description": "declares a non-convention file path",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "template",
-                        "name": "spec-template",
-                        "file": "custom/spec.md",
-                        "strategy": "replace",
-                    }
-                ]
-            },
-        }
-        with open(pack_dir / "preset.yml", "w") as f:
-            yaml.dump(manifest, f)
-        PresetRegistry(presets_dir).add(
-            "mypack", {"version": "1.0.0", "priority": 10}
-        )
-        return pack_dir
-
-    def test_resolve_uses_manifest_declared_file_path(self, project_dir):
-        """resolve() must honor a manifest-declared non-convention file: path.
-
-        Previously the tier-2 loop was convention-only, so it returned the
-        core template and resolve_with_source() misattributed source='core',
-        diverging from collect_all_layers()/resolve_content().
-        """
-        pack_dir = self._install_pack_with_manifest_file(project_dir)
-        resolver = PresetResolver(project_dir)
-
-        result = resolver.resolve("spec-template")
-        assert result == pack_dir / "custom" / "spec.md"
-        assert "Manifest-declared Spec" in result.read_text()
-
-        sourced = resolver.resolve_with_source("spec-template")
-        assert sourced is not None
-        assert "mypack" in sourced["source"]
-        # resolve() must agree with collect_all_layers()'s top layer.
-        layers = resolver.collect_all_layers("spec-template")
-        assert Path(layers[0]["path"]) == pack_dir / "custom" / "spec.md"
-
-    def test_resolve_manifest_file_wins_over_undeclared_convention_file(
-        self, project_dir
-    ):
-        """A stray convention-path file must not shadow the manifest's file:."""
-        pack_dir = self._install_pack_with_manifest_file(
-            project_dir, extra_file=True
-        )
-        resolver = PresetResolver(project_dir)
-        result = resolver.resolve("spec-template")
-        assert result == pack_dir / "custom" / "spec.md"
-        assert "Manifest-declared Spec" in result.read_text()
-
-    def test_resolve_skips_convention_when_manifest_file_missing(self, project_dir):
-        """When the manifest declares a file: that does not exist, resolve()
-        must NOT fall back to a convention file in the same pack (that would
-        mask a typo) — it skips the pack and resolves core instead."""
-        presets_dir = project_dir / ".specify" / "presets"
-        pack_dir = presets_dir / "mypack"
-        # Manifest declares custom/spec.md (MISSING); a convention file exists
-        # in the pack and must NOT be used.
-        (pack_dir / "templates").mkdir(parents=True)
-        (pack_dir / "templates" / "spec-template.md").write_text(
-            "# Stray Convention Spec\n", encoding="utf-8"
-        )
-        manifest = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "mypack",
-                "name": "My Pack",
-                "version": "1.0.0",
-                "description": "declares a missing file path",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "template",
-                        "name": "spec-template",
-                        "file": "custom/spec.md",
-                        "strategy": "replace",
-                    }
-                ]
-            },
-        }
-        with open(pack_dir / "preset.yml", "w") as f:
-            yaml.dump(manifest, f)
-        PresetRegistry(presets_dir).add(
-            "mypack", {"version": "1.0.0", "priority": 10}
-        )
-
-        resolver = PresetResolver(project_dir)
-        result = resolver.resolve("spec-template")
-        assert result is not None
-        content = result.read_text()
-        assert "Stray Convention Spec" not in content  # pack convention skipped
-        assert "Core Spec Template" in content  # fell through to core
-
-    def test_resolve_skips_convention_when_manifest_file_is_directory(
-        self, project_dir
-    ):
-        """When the manifest's file: path resolves to a DIRECTORY (not a regular
-        file), resolve()/collect_all_layers() must treat it as missing — exists()
-        would accept it and downstream read_text() on a directory would crash.
-        The pack is skipped (no convention fallback), so core wins."""
-        presets_dir = project_dir / ".specify" / "presets"
-        pack_dir = presets_dir / "mypack"
-        # Declared file: custom/spec.md is created as a DIRECTORY.
-        (pack_dir / "custom" / "spec.md").mkdir(parents=True)
-        # A convention file also exists and must NOT be used.
-        (pack_dir / "templates").mkdir(parents=True)
-        (pack_dir / "templates" / "spec-template.md").write_text(
-            "# Stray Convention Spec\n", encoding="utf-8"
-        )
-        manifest = {
-            "schema_version": "1.0",
-            "preset": {
-                "id": "mypack",
-                "name": "My Pack",
-                "version": "1.0.0",
-                "description": "declares a file: that is actually a directory",
-            },
-            "requires": {"speckit_version": ">=0.1.0"},
-            "provides": {
-                "templates": [
-                    {
-                        "type": "template",
-                        "name": "spec-template",
-                        "file": "custom/spec.md",
-                        "strategy": "replace",
-                    }
-                ]
-            },
-        }
-        with open(pack_dir / "preset.yml", "w") as f:
-            yaml.dump(manifest, f)
-        PresetRegistry(presets_dir).add(
-            "mypack", {"version": "1.0.0", "priority": 10}
-        )
-
-        resolver = PresetResolver(project_dir)
-        result = resolver.resolve("spec-template")
-        assert result is not None
-        assert result.is_file()  # never a directory
-        content = result.read_text()
-        assert "Stray Convention Spec" not in content  # pack convention skipped
-        assert "Core Spec Template" in content  # fell through to core
-        # collect_all_layers() must agree: the directory is not a layer.
-        layers = resolver.collect_all_layers("spec-template")
-        assert all(Path(layer["path"]).is_file() for layer in layers)
-        assert all(
-            Path(layer["path"]) != pack_dir / "custom" / "spec.md"
-            for layer in layers
-        )
-
    def test_resolve_override_takes_priority_over_pack(self, project_dir, pack_dir):
        """Test that overrides take priority over installed packs."""
        # Install the pack
@@ -5016,13 +4836,26 @@ class TestPresetAddFromUrlResolution:

        captured_urls = []

+        class FakeResponse:
+            def __init__(self, data):
+                self._data = data
+
+            def read(self):
+                return self._data
+
+            def __enter__(self):
+                return self
+
+            def __exit__(self, *a):
+                return False
+
        def fake_open_url(url, timeout=None, extra_headers=None, redirect_validator=None):
            captured_urls.append((url, extra_headers))
            if "releases/tags/" in url:
-                return io.BytesIO(json.dumps({
+                return FakeResponse(json.dumps({
                    "assets": [{"name": "preset.zip", "url": "https://api.github.com/repos/org/repo/releases/assets/42"}]
                }).encode())
-            return io.BytesIO(zip_bytes)
+            return FakeResponse(zip_bytes)

        runner = CliRunner()
        with patch.object(Path, "cwd", return_value=project_dir), \
@@ -5061,9 +4894,22 @@ class TestPresetAddFromUrlResolution:

        captured_urls = []

+        class FakeResponse:
+            def __init__(self, data):
+                self._data = data
+
+            def read(self):
+                return self._data
+
+            def __enter__(self):
+                return self
+
+            def __exit__(self, *a):
+                return False
+
        def fake_open_url(url, timeout=None, extra_headers=None, redirect_validator=None):
            captured_urls.append((url, extra_headers))
-            return io.BytesIO(zip_bytes)
+            return FakeResponse(zip_bytes)

        runner = CliRunner()
        with patch.object(Path, "cwd", return_value=project_dir), \
@@ -5105,13 +4951,26 @@ class TestPresetAddFromUrlResolution:

        captured_urls = []

+        class FakeResponse:
+            def __init__(self, data):
+                self._data = data
+
+            def read(self):
+                return self._data
+
+            def __enter__(self):
+                return self
+
+            def __exit__(self, *a):
+                return False
+
        def fake_open_url(url, timeout=None, extra_headers=None, redirect_validator=None):
            captured_urls.append((url, extra_headers))
            if "releases/tags/" in url:
-                return io.BytesIO(json.dumps({
+                return FakeResponse(json.dumps({
                    "assets": [{"name": "preset.zip", "url": "https://ghes.example/api/v3/repos/org/repo/releases/assets/42"}]
                }).encode())
-            return io.BytesIO(zip_bytes)
+            return FakeResponse(zip_bytes)

        runner = CliRunner()
        with patch.object(Path, "cwd", return_value=project_dir), \