chore: bump version to 0.7.4

* fix(copilot): use --yolo to grant all permissions in non-interactive mode

The Copilot CLI's --allow-all-tools flag only covers tool execution
permissions but does not grant path or URL access. When the Copilot
agent autonomously runs shell commands (e.g. npm run build) during
workflow execution, the CLI blocks path access and cannot prompt for
approval in non-interactive mode, producing:

  Permission denied and could not request permission from user

Replace --allow-all-tools with --yolo (equivalent to --allow-all-tools
--allow-all-paths --allow-all-urls) to grant all three permission types.

Rename the opt-out env var from SPECKIT_ALLOW_ALL_TOOLS to
SPECKIT_COPILOT_ALLOW_ALL to match the formal --allow-all alias and
scope it to the Copilot integration.

Fixes #2294

* review: deprecate SPECKIT_ALLOW_ALL_TOOLS, rename to SPECKIT_COPILOT_ALLOW_ALL_TOOLS

Address Copilot review feedback:

- Honour the old SPECKIT_ALLOW_ALL_TOOLS env var as a fallback with a
  DeprecationWarning so existing opt-outs are not silently ignored.
- Rename the new canonical env var to SPECKIT_COPILOT_ALLOW_ALL_TOOLS.
- New var takes precedence when both are set.
- Use monkeypatch in tests to avoid flakiness from ambient env vars.
- Add tests for deprecation warning, precedence, and opt-out paths.

* review: use UserWarning instead of DeprecationWarning

DeprecationWarning is suppressed by default in Python, so users relying
on the old SPECKIT_ALLOW_ALL_TOOLS env var would never see the
deprecation notice during normal CLI runs. Switch to UserWarning which
is always shown. Update test to also assert the warning category.

.zenodo.json

@@ -0,0 +1,29 @@
+{
+  "title": "Spec Kit",
+  "description": "Spec Kit is an open source toolkit for Spec-Driven Development (SDD) — a methodology that helps software teams build high-quality software faster by focusing on product scenarios and predictable outcomes. It provides the Specify CLI, slash-command templates, extensions, presets, workflows, and integrations for popular AI coding agents.",
+  "creators": [
+    {
+      "name": "Delimarsky, Den"
+    },
+    {
+      "name": "Riem, Manfred"
+    }
+  ],
+  "license": "MIT",
+  "upload_type": "software",
+  "keywords": [
+    "spec-driven development",
+    "ai coding agents",
+    "software engineering",
+    "cli",
+    "copilot",
+    "specification"
+  ],
+  "related_identifiers": [
+    {
+      "identifier": "https://github.com/github/spec-kit",
+      "relation": "isSupplementTo",
+      "scheme": "url"
+    }
+  ]
+}

CHANGELOG.md

@@ -2,6 +2,22 @@
 
 <!-- insert new changelog below this comment -->
 
+## [0.7.4] - 2026-04-21
+
+### Changed
+
+- fix(copilot): use --yolo to grant all permissions in non-interactive mode (#2298)
+- feat: add CITATION.cff and .zenodo.json for academic citation support (#2291)
+- Add spec-validate to community catalog (#2274)
+- feat: register Ripple in community catalog (#2272)
+- Add version-guard to community catalog (#2286)
+- Add spec-reference-loader to community catalog (#2285)
+- Add memory-loader to community catalog (#2284)
+- fix(integrations): strip UTF-8 BOM when reading agent context files (#2283)
+- Preset fiction book writing1.6 (#2270)
+- fix(integrations): migrate Antigravity (agy) layout to .agents/ and deprecate --skills (#2276)
+- chore: release 0.7.3, begin 0.7.4.dev0 development (#2263)
+
 ## [0.7.3] - 2026-04-17
 
 ### Changed

CITATION.cff

@@ -0,0 +1,31 @@
+cff-version: 1.2.0
+message: >-
+  If you use Spec Kit in your research or reference it in a paper,
+  please cite it using the metadata below.
+type: software
+title: "Spec Kit"
+abstract: >-
+  Spec Kit is an open source toolkit for Spec-Driven Development (SDD) —
+  a methodology that helps software teams build high-quality software faster
+  by focusing on product scenarios and predictable outcomes. It provides the
+  Specify CLI, slash-command templates, extensions, presets, workflows, and
+  integrations for popular AI coding agents.
+authors:
+  - given-names: Den
+    family-names: Delimarsky
+    alias: localden
+  - given-names: Manfred
+    family-names: Riem
+    alias: mnriem
+repository-code: "https://github.com/github/spec-kit"
+url: "https://github.github.io/spec-kit/"
+license: MIT
+version: "0.7.3"
+date-released: "2026-04-17"
+keywords:
+  - spec-driven development
+  - ai coding agents
+  - software engineering
+  - cli
+  - copilot
+  - specification

README.md

@@ -223,6 +223,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | MAQA Jira Integration | Jira integration for MAQA — syncs Stories and Subtasks as features progress through the board | `integration` | Read+Write | [spec-kit-maqa-jira](https://github.com/GenieRobot/spec-kit-maqa-jira) |
 | MAQA Linear Integration | Linear integration for MAQA — syncs issues and sub-issues across workflow states as features progress | `integration` | Read+Write | [spec-kit-maqa-linear](https://github.com/GenieRobot/spec-kit-maqa-linear) |
 | MAQA Trello Integration | Trello board integration for MAQA — populates board from specs, moves cards, real-time checklist ticking | `integration` | Read+Write | [spec-kit-maqa-trello](https://github.com/GenieRobot/spec-kit-maqa-trello) |
+| Memory Loader | Loads .specify/memory/ files before lifecycle commands so LLM agents have project governance context | `docs` | Read-only | [spec-kit-memory-loader](https://github.com/KevinBrown5280/spec-kit-memory-loader) |
 | MemoryLint | Agent memory governance tool: Automatically audits and fixes boundary conflicts between AGENTS.md and the constitution. | `process` | Read+Write | [memorylint](https://github.com/RbBtSn0w/spec-kit-extensions/tree/main/memorylint) |
 | Onboard | Contextual onboarding and progressive growth for developers new to spec-kit projects. Explains specs, maps dependencies, validates understanding, and guides the next step | `process` | Read+Write | [spec-kit-onboard](https://github.com/dmux/spec-kit-onboard) |
 | Optimize | Audit and optimize AI governance for context efficiency — token budgets, rule health, interpretability, compression, coherence, and echo detection | `process` | Read+Write | [spec-kit-optimize](https://github.com/sakitA/spec-kit-optimize) |
@@ -239,15 +240,18 @@ The following community-contributed extensions are available in [`catalog.commun
 | Retro Extension | Sprint retrospective analysis with metrics, spec accuracy assessment, and improvement suggestions | `process` | Read+Write | [spec-kit-retro](https://github.com/arunt14/spec-kit-retro) |
 | Retrospective Extension | Post-implementation retrospective with spec adherence scoring, drift analysis, and human-gated spec updates | `docs` | Read+Write | [spec-kit-retrospective](https://github.com/emi-dm/spec-kit-retrospective) |
 | Review Extension | Post-implementation comprehensive code review with specialized agents for code quality, comments, tests, error handling, type design, and simplification | `code` | Read-only | [spec-kit-review](https://github.com/ismaelJimenez/spec-kit-review) |
+| Ripple | Detect side effects that tests can't catch after implementation — delta-anchored analysis across 9 domain-agnostic categories | `code` | Read+Write | [spec-kit-ripple](https://github.com/chordpli/spec-kit-ripple) |
 | SDD Utilities | Resume interrupted workflows, validate project health, and verify spec-to-task traceability | `process` | Read+Write | [speckit-utils](https://github.com/mvanhorn/speckit-utils) |
 | Security Review | Comprehensive security audit of codebases using AI-powered DevSecOps analysis | `code` | Read-only | [spec-kit-security-review](https://github.com/DyanGalih/spec-kit-security-review) |
 | SFSpeckit | Enterprise Salesforce SDLC with 18 commands for the full SDD lifecycle. | `process` | Read+Write | [spec-kit-sf](https://github.com/ysumanth06/spec-kit-sf) |
 | Ship Release Extension | Automates release pipeline: pre-flight checks, branch sync, changelog generation, CI verification, and PR creation | `process` | Read+Write | [spec-kit-ship](https://github.com/arunt14/spec-kit-ship) |
+| Spec Reference Loader | Reads the ## References section from the feature spec and loads only the listed docs into context | `docs` | Read-only | [spec-kit-spec-reference-loader](https://github.com/KevinBrown5280/spec-kit-spec-reference-loader) |
 | Spec Critique Extension | Dual-lens critical review of spec and plan from product strategy and engineering risk perspectives | `docs` | Read-only | [spec-kit-critique](https://github.com/arunt14/spec-kit-critique) |
 | Spec Diagram | Auto-generate Mermaid diagrams of SDD workflow state, feature progress, and task dependencies | `visibility` | Read-only | [spec-kit-diagram-](https://github.com/Quratulain-bilal/spec-kit-diagram-) |
 | Spec Refine | Update specs in-place, propagate changes to plan and tasks, and diff impact across artifacts | `process` | Read+Write | [spec-kit-refine](https://github.com/Quratulain-bilal/spec-kit-refine) |
 | Spec Scope | Effort estimation and scope tracking — estimate work, detect creep, and budget time per phase | `process` | Read-only | [spec-kit-scope-](https://github.com/Quratulain-bilal/spec-kit-scope-) |
 | Spec Sync | Detect and resolve drift between specs and implementation. AI-assisted resolution with human approval | `docs` | Read+Write | [spec-kit-sync](https://github.com/bgervin/spec-kit-sync) |
+| Spec Validate | Comprehension validation, review gating, and approval state for spec-kit artifacts — staged quizzes, peer review SLA, and a hard gate before /speckit.implement | `process` | Read+Write | [spec-kit-spec-validate](https://github.com/aeltayeb/spec-kit-spec-validate) |
 | SpecTest | Auto-generate test scaffolds from spec criteria, map coverage, and find untested requirements | `code` | Read+Write | [spec-kit-spectest](https://github.com/Quratulain-bilal/spec-kit-spectest) |
 | Staff Review Extension | Staff-engineer-level code review that validates implementation against spec, checks security, performance, and test coverage | `code` | Read-only | [spec-kit-staff-review](https://github.com/arunt14/spec-kit-staff-review) |
 | Status Report | Project status, feature progress, and next-action recommendations for spec-driven workflows | `visibility` | Read-only | [Open-Agent-Tools/spec-kit-status](https://github.com/Open-Agent-Tools/spec-kit-status) |
@@ -256,6 +260,7 @@ The following community-contributed extensions are available in [`catalog.commun
 | V-Model Extension Pack | Enforces V-Model paired generation of development specs and test specs with full traceability | `docs` | Read+Write | [spec-kit-v-model](https://github.com/leocamello/spec-kit-v-model) |
 | Verify Extension | Post-implementation quality gate that validates implemented code against specification artifacts | `code` | Read-only | [spec-kit-verify](https://github.com/ismaelJimenez/spec-kit-verify) |
 | Verify Tasks Extension | Detect phantom completions: tasks marked [X] in tasks.md with no real implementation | `code` | Read-only | [spec-kit-verify-tasks](https://github.com/datastone-inc/spec-kit-verify-tasks) |
+| Version Guard | Verify tech stack versions against live npm registries before planning and implementation | `process` | Read-only | [spec-kit-version-guard](https://github.com/KevinBrown5280/spec-kit-version-guard) |
 | What-if Analysis | Preview the downstream impact (complexity, effort, tasks, risks) of requirement changes before committing to them | `visibility` | Read-only | [spec-kit-whatif](https://github.com/DevAbdullah90/spec-kit-whatif) |
 | Worktree Isolation | Spawn isolated git worktrees for parallel feature development without checkout switching | `process` | Read+Write | [spec-kit-worktree](https://github.com/Quratulain-bilal/spec-kit-worktree) |
 | Worktrees | Default-on worktree isolation for parallel agents — sibling or nested layout | `process` | Read+Write | [spec-kit-worktree-parallel](https://github.com/dango85/spec-kit-worktree-parallel) |
@@ -274,7 +279,7 @@ The following community-contributed presets customize how Spec Kit behaves — o
 | 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) |
 | 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) |
 | Explicit Task Dependencies | Adds explicit `(depends on T###)` dependency declarations and an Execution Wave DAG to tasks.md for parallel scheduling | 1 template, 1 command | — | [spec-kit-preset-explicit-task-dependencies](https://github.com/Quratulain-bilal/spec-kit-preset-explicit-task-dependencies) |
-| Fiction Book Writing | It adapts the Spec-Driven Development workflow for storytelling to create books or audiobooks (with annotations): features become story elements, specs become story briefs, plans become story structures, and tasks become scene-by-scene writing tasks. Supports single and multi-POV, all major plot structure frameworks, and two style modes: an author voice sample or humanized AI prose with 5 prose profiles. Supports interactive elements like brainstorming, interview, roleplay. | 21 templates, 26 commands | — | [spec-kit-preset-fiction-book-writing](https://github.com/adaumann/speckit-preset-fiction-book-writing) |
+| Fiction Book Writing | It adapts the Spec-Driven Development workflow for storytelling to create books or audiobooks (with annotations) in 12 languages: features become story elements, specs become story briefs, plans become story structures, and tasks become scene-by-scene writing tasks. Supports single and multi-POV, all major plot structure frameworks, and two style modes: an author voice sample or humanized AI prose. Supports interactive elements like brainstorming, interview, roleplay and extras like statistics, cover builder and bio command. Export with templates for KDP, D2D etc. | 22 templates, 27 commands | — | [spec-kit-preset-fiction-book-writing](https://github.com/adaumann/speckit-preset-fiction-book-writing) |
 | Multi-Repo Branching | Coordinates feature branch creation across multiple git repositories (independent repos and submodules) during plan and tasks phases | 2 commands | — | [spec-kit-preset-multi-repo-branching](https://github.com/sakitA/spec-kit-preset-multi-repo-branching) |
 | Pirate Speak (Full) | Transforms all Spec Kit output into pirate speak — specs become "Voyage Manifests", plans become "Battle Plans", tasks become "Crew Assignments" | 6 templates, 9 commands | — | [spec-kit-presets](https://github.com/mnriem/spec-kit-presets) |
 | 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) |

extensions/catalog.community.json

@@ -1,6 +1,6 @@
 {
   "schema_version": "1.0",
-  "updated_at": "2026-04-17T02:00:00Z",
+  "updated_at": "2026-04-21T00:00:00Z",
   "catalog_url": "https://raw.githubusercontent.com/github/spec-kit/main/extensions/catalog.community.json",
   "extensions": {
     "aide": {
@@ -1167,6 +1167,37 @@
       "created_at": "2026-03-26T00:00:00Z",
       "updated_at": "2026-03-26T00:00:00Z"
     },
+    "memory-loader": {
+      "name": "Memory Loader",
+      "id": "memory-loader",
+      "description": "Loads .specify/memory/ files before spec-kit lifecycle commands so LLM agents have project governance context",
+      "author": "KevinBrown5280",
+      "version": "1.0.0",
+      "download_url": "https://github.com/KevinBrown5280/spec-kit-memory-loader/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/KevinBrown5280/spec-kit-memory-loader",
+      "homepage": "https://github.com/KevinBrown5280/spec-kit-memory-loader",
+      "documentation": "https://github.com/KevinBrown5280/spec-kit-memory-loader/blob/main/README.md",
+      "changelog": "https://github.com/KevinBrown5280/spec-kit-memory-loader/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.6.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 7
+      },
+      "tags": [
+        "context",
+        "memory",
+        "governance",
+        "hooks"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-04-20T00:00:00Z",
+      "updated_at": "2026-04-20T00:00:00Z"
+    },
     "memorylint": {
       "name": "MemoryLint",
       "id": "memorylint",
@@ -1657,6 +1688,38 @@
       "created_at": "2026-03-06T00:00:00Z",
       "updated_at": "2026-04-09T00:00:00Z"
     },
+    "ripple": {
+      "name": "Ripple",
+      "id": "ripple",
+      "description": "Detect side effects that tests can't catch after implementation — delta-anchored analysis across 9 domain-agnostic categories with fix-induced side effect detection",
+      "author": "chordpli",
+      "version": "1.0.0",
+      "download_url": "https://github.com/chordpli/spec-kit-ripple/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/chordpli/spec-kit-ripple",
+      "homepage": "https://github.com/chordpli/spec-kit-ripple",
+      "documentation": "https://github.com/chordpli/spec-kit-ripple/blob/main/README.md",
+      "changelog": "https://github.com/chordpli/spec-kit-ripple/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.2.0"
+      },
+      "provides": {
+        "commands": 3,
+        "hooks": 1
+      },
+      "tags": [
+        "side-effects",
+        "post-implementation",
+        "analysis",
+        "quality",
+        "risk-detection"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-04-20T00:00:00Z",
+      "updated_at": "2026-04-20T00:00:00Z"
+    },
     "scope": {
       "name": "Spec Scope",
       "id": "scope",
@@ -1796,6 +1859,69 @@
       "created_at": "2026-04-01T00:00:00Z",
       "updated_at": "2026-04-01T00:00:00Z"
     },
+    "spec-reference-loader": {
+      "name": "Spec Reference Loader",
+      "id": "spec-reference-loader",
+      "description": "Reads the ## References section from the current feature spec and loads the listed files into context",
+      "author": "KevinBrown5280",
+      "version": "1.0.0",
+      "download_url": "https://github.com/KevinBrown5280/spec-kit-spec-reference-loader/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/KevinBrown5280/spec-kit-spec-reference-loader",
+      "homepage": "https://github.com/KevinBrown5280/spec-kit-spec-reference-loader",
+      "documentation": "https://github.com/KevinBrown5280/spec-kit-spec-reference-loader/blob/main/README.md",
+      "changelog": "https://github.com/KevinBrown5280/spec-kit-spec-reference-loader/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.6.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 6
+      },
+      "tags": [
+        "context",
+        "references",
+        "docs",
+        "hooks"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-04-20T00:00:00Z",
+      "updated_at": "2026-04-20T00:00:00Z"
+    },
+    "spec-validate": {
+      "name": "Spec Validate",
+      "id": "spec-validate",
+      "description": "Comprehension validation, review gating, and approval state for spec-kit artifacts — staged-reveal quizzes, peer review SLA, and a hard gate before /speckit.implement.",
+      "author": "Ahmed Eltayeb",
+      "version": "1.0.1",
+      "download_url": "https://github.com/aeltayeb/spec-kit-spec-validate/archive/refs/tags/v1.0.1.zip",
+      "repository": "https://github.com/aeltayeb/spec-kit-spec-validate",
+      "homepage": "https://github.com/aeltayeb/spec-kit-spec-validate",
+      "documentation": "https://github.com/aeltayeb/spec-kit-spec-validate/blob/main/README.md",
+      "changelog": "https://github.com/aeltayeb/spec-kit-spec-validate/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.5.0"
+      },
+      "provides": {
+        "commands": 6,
+        "hooks": 3
+      },
+      "tags": [
+        "validation",
+        "review",
+        "quality",
+        "workflow",
+        "process"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-04-20T00:00:00Z",
+      "updated_at": "2026-04-21T00:00:00Z"
+    },
     "speckit-utils": {
       "name": "SDD Utilities",
       "id": "speckit-utils",
@@ -2155,6 +2281,37 @@
       "created_at": "2026-03-16T00:00:00Z",
       "updated_at": "2026-03-16T00:00:00Z"
     },
+    "version-guard": {
+      "name": "Version Guard",
+      "id": "version-guard",
+      "description": "Verify tech stack versions against live registries before planning and implementation",
+      "author": "KevinBrown5280",
+      "version": "1.0.0",
+      "download_url": "https://github.com/KevinBrown5280/spec-kit-version-guard/archive/refs/tags/v1.0.0.zip",
+      "repository": "https://github.com/KevinBrown5280/spec-kit-version-guard",
+      "homepage": "https://github.com/KevinBrown5280/spec-kit-version-guard",
+      "documentation": "https://github.com/KevinBrown5280/spec-kit-version-guard/blob/main/README.md",
+      "changelog": "https://github.com/KevinBrown5280/spec-kit-version-guard/blob/main/CHANGELOG.md",
+      "license": "MIT",
+      "requires": {
+        "speckit_version": ">=0.2.0"
+      },
+      "provides": {
+        "commands": 1,
+        "hooks": 2
+      },
+      "tags": [
+        "versioning",
+        "npm",
+        "validation",
+        "hooks"
+      ],
+      "verified": false,
+      "downloads": 0,
+      "stars": 0,
+      "created_at": "2026-04-20T00:00:00Z",
+      "updated_at": "2026-04-20T00:00:00Z"
+    },
     "whatif": {
       "name": "What-if Analysis",
       "id": "whatif",

presets/catalog.community.json

@@ -108,11 +108,11 @@
     "fiction-book-writing": {
       "name": "Fiction Book Writing",
       "id": "fiction-book-writing",
-      "version": "1.5.0",
+      "version": "1.6.0",
-      "description": "Spec-Driven Development for novel and long-form fiction. Replaces software engineering terminology with storytelling craft: specs become story briefs, plans become story structures, and tasks become scene-by-scene writing tasks. Supports 8 POV modes, all major plot structure frameworks, 5 humanized-AI prose profiles, and exports to DOCX/EPUB/LaTeX via pandoc.",
+      "description": "Spec-Driven Development for novel and long-form fiction. 27 AI commands from idea to submission: story bible governance, 9 POV modes, all major plot structure frameworks, scene-by-scene drafting with quality gates, audiobook pipeline (SSML/ElevenLabs), cover design, sensitivity review, pacing and prose statistics, and pandoc-based export to DOCX/EPUB/LaTeX. Two style modes: author voice sample extraction or humanized-AI prose with 5 craft profiles. 12 languages supported.",
       "author": "Andreas Daumann",
       "repository": "https://github.com/adaumann/speckit-preset-fiction-book-writing",
-      "download_url": "https://github.com/adaumann/speckit-preset-fiction-book-writing/archive/refs/tags/v1.5.0.zip",
+      "download_url": "https://github.com/adaumann/speckit-preset-fiction-book-writing/archive/refs/tags/v1.6.0.zip",
       "homepage": "https://github.com/adaumann/speckit-preset-fiction-book-writing",
       "documentation": "https://github.com/adaumann/speckit-preset-fiction-book-writing/blob/main/fiction-book-writing/README.md",
       "license": "MIT",
@@ -120,8 +120,9 @@
         "speckit_version": ">=0.5.0"
       },
       "provides": {
-        "templates": 21,
+        "templates": 22,
-        "commands": 26
+        "commands": 27,
+        "scripts": 1
       },
       "tags": [
         "writing",
@@ -135,10 +136,11 @@
         "book",
         "brainstorming",
         "roleplay",
-        "audiobook"
+        "audiobook",
+        "language-support"
       ],
       "created_at": "2026-04-09T08:00:00Z",
-      "updated_at": "2026-04-16T08:00:00Z"
+      "updated_at": "2026-04-19T08:00:00Z"
     },    
     "multi-repo-branching": {
       "name": "Multi-Repo Branching",

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "specify-cli"
-version = "0.7.3"
+version = "0.7.4"
 description = "Specify CLI, part of GitHub Spec Kit. A tool to bootstrap your projects for Spec-Driven Development (SDD)."
 requires-python = ">=3.11"
 dependencies = [

src/specify_cli/integrations/agy/__init__.py

@@ -1,13 +1,18 @@
 """Antigravity (agy) integration — skills-based agent.
 
-Antigravity uses ``.agent/skills/speckit-<name>/SKILL.md`` layout.
+Antigravity uses ``.agents/skills/speckit-<name>/SKILL.md`` layout (enforced since v1.20.5).
-Explicit command support was deprecated in version 1.20.5;
-``--skills`` defaults to ``True``.
 """
 
 from __future__ import annotations
 
-from ..base import IntegrationOption, SkillsIntegration
+from pathlib import Path
+from typing import TYPE_CHECKING, Any
+
+from ..base import SkillsIntegration
+
+if TYPE_CHECKING:
+    from ..manifest import IntegrationManifest
+
 
 
 class AgyIntegration(SkillsIntegration):
@@ -16,26 +21,32 @@ class AgyIntegration(SkillsIntegration):
     key = "agy"
     config = {
         "name": "Antigravity",
-        "folder": ".agent/",
+        "folder": ".agents/",
         "commands_subdir": "skills",
         "install_url": None,
         "requires_cli": False,
     }
     registrar_config = {
-        "dir": ".agent/skills",
+        "dir": ".agents/skills",
         "format": "markdown",
         "args": "$ARGUMENTS",
         "extension": "/SKILL.md",
     }
     context_file = "AGENTS.md"
 
-    @classmethod
+    def setup(
-    def options(cls) -> list[IntegrationOption]:
+        self,
-        return [
+        project_root: Path,
-            IntegrationOption(
+        manifest: IntegrationManifest,
-                "--skills",
+        parsed_options: dict[str, Any] | None = None,
-                is_flag=True,
+        **opts: Any,
-                default=True,
+    ) -> list[Path]:
-                help="Install as agent skills (default for Antigravity since v1.20.5)",
+        import click
-            ),
+
-        ]
+        click.secho(
+            "Warning: The .agents/ layout requires Antigravity v1.20.5 or newer. "
+            "Please ensure your agy installation is up to date.",
+            fg="yellow",
+            err=True,
+        )
+        return super().setup(project_root, manifest, parsed_options=parsed_options, **opts)

src/specify_cli/integrations/base.py

@@ -482,7 +482,7 @@ class IntegrationBase(ABC):
         )
 
         if ctx_path.exists():
-            content = ctx_path.read_text(encoding="utf-8")
+            content = ctx_path.read_text(encoding="utf-8-sig")
             start_idx = content.find(self.CONTEXT_MARKER_START)
             end_idx = content.find(
                 self.CONTEXT_MARKER_END,
@@ -547,7 +547,7 @@ class IntegrationBase(ABC):
         if not ctx_path.exists():
             return False
 
-        content = ctx_path.read_text(encoding="utf-8")
+        content = ctx_path.read_text(encoding="utf-8-sig")
         start_idx = content.find(self.CONTEXT_MARKER_START)
         end_idx = content.find(
             self.CONTEXT_MARKER_END,

src/specify_cli/integrations/copilot/__init__.py

@@ -10,7 +10,9 @@ Copilot has several unique behaviors compared to standard markdown agents:
 from __future__ import annotations
 
 import json
+import os
 import shutil
+import warnings
 from pathlib import Path
 from typing import Any
 
@@ -18,6 +20,30 @@ from ..base import IntegrationBase
 from ..manifest import IntegrationManifest
 
 
+def _allow_all() -> bool:
+    """Return True if the Copilot CLI should run with full permissions.
+
+    Checks ``SPECKIT_COPILOT_ALLOW_ALL_TOOLS`` first (new canonical name).
+    Falls back to the deprecated ``SPECKIT_ALLOW_ALL_TOOLS`` if set,
+    emitting a deprecation warning.  Default when neither is set: enabled.
+    """
+    new_var = os.environ.get("SPECKIT_COPILOT_ALLOW_ALL_TOOLS")
+    if new_var is not None:
+        return new_var != "0"
+
+    old_var = os.environ.get("SPECKIT_ALLOW_ALL_TOOLS")
+    if old_var is not None:
+        warnings.warn(
+            "SPECKIT_ALLOW_ALL_TOOLS is deprecated; "
+            "use SPECKIT_COPILOT_ALLOW_ALL_TOOLS instead.",
+            UserWarning,
+            stacklevel=2,
+        )
+        return old_var != "0"
+
+    return True
+
+
 class CopilotIntegration(IntegrationBase):
     """Integration for GitHub Copilot (VS Code IDE + CLI).
 
@@ -50,13 +76,15 @@ class CopilotIntegration(IntegrationBase):
         output_json: bool = True,
     ) -> list[str] | None:
         # GitHub Copilot CLI uses ``copilot -p "prompt"`` for
-        # non-interactive mode.  --allow-all-tools is required for the
+        # non-interactive mode.  --yolo enables all permissions
-        # agent to perform file edits and shell commands.  Controlled
+        # (tools, paths, and URLs) so the agent can perform file
-        # by SPECKIT_ALLOW_ALL_TOOLS env var (default: enabled).
+        # edits and shell commands without interactive prompts.
-        import os
+        # Controlled by SPECKIT_COPILOT_ALLOW_ALL_TOOLS env var
+        # (default: enabled).  The deprecated SPECKIT_ALLOW_ALL_TOOLS
+        # is also honoured as a fallback.
         args = ["copilot", "-p", prompt]
-        if os.environ.get("SPECKIT_ALLOW_ALL_TOOLS", "1") != "0":
+        if _allow_all():
-            args.append("--allow-all-tools")
+            args.append("--yolo")
         if model:
             args.extend(["--model", model])
         if output_json:
@@ -91,13 +119,12 @@ class CopilotIntegration(IntegrationBase):
         agent_name = f"speckit.{stem}"
 
         prompt = args or ""
-        import os
         cli_args = [
             "copilot", "-p", prompt,
             "--agent", agent_name,
         ]
-        if os.environ.get("SPECKIT_ALLOW_ALL_TOOLS", "1") != "0":
+        if _allow_all():
-            cli_args.append("--allow-all-tools")
+            cli_args.append("--yolo")
         if model:
             cli_args.extend(["--model", model])
         if not stream:

tests/integrations/test_integration_agy.py

@@ -5,12 +5,17 @@ from .test_integration_base_skills import SkillsIntegrationTests
 
 class TestAgyIntegration(SkillsIntegrationTests):
     KEY = "agy"
-    FOLDER = ".agent/"
+    FOLDER = ".agents/"
     COMMANDS_SUBDIR = "skills"
-    REGISTRAR_DIR = ".agent/skills"
+    REGISTRAR_DIR = ".agents/skills"
     CONTEXT_FILE = "AGENTS.md"
 
-
+    def test_options_include_skills_flag(self):
+        """Override inherited test: AgyIntegration should not expose a --skills flag because .agents/ is its only layout."""
+        from specify_cli.integrations import get_integration
+        i = get_integration(self.KEY)
+        skills_opts = [o for o in i.options() if o.name == "--skills"]
+        assert len(skills_opts) == 0
 class TestAgyAutoPromote:
     """--ai agy auto-promotes to integration path."""
 
@@ -24,4 +29,17 @@ class TestAgyAutoPromote:
         result = runner.invoke(app, ["init", str(target), "--ai", "agy", "--no-git", "--script", "sh"])
 
         assert result.exit_code == 0, f"init --ai agy failed: {result.output}"
-        assert (target / ".agent" / "skills" / "speckit-plan" / "SKILL.md").exists()
+        assert (target / ".agents" / "skills" / "speckit-plan" / "SKILL.md").exists()
+
+    def test_agy_setup_warning(self, tmp_path):
+        """Agy integration should print a warning about v1.20.5 requirement during setup."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        # Click >= 8.2 separates stdout and stderr natively, mix_stderr is removed
+        runner = CliRunner()
+        target = tmp_path / "test-proj2"
+        result = runner.invoke(app, ["init", str(target), "--ai", "agy", "--no-git", "--script", "sh"])
+
+        assert result.exit_code == 0
+        assert "Warning: The .agents/ layout requires Antigravity v1.20.5 or newer" in result.stderr

tests/integrations/test_integration_claude.py

@@ -1,5 +1,6 @@
 """Tests for ClaudeIntegration."""
 
+import codecs
 import json
 import os
 from unittest.mock import patch
@@ -74,6 +75,46 @@ class TestClaudeIntegration:
         assert "<!-- SPECKIT END -->" in content
         assert "read the current plan" in content
 
+    def test_upsert_context_section_strips_bom(self, tmp_path):
+        """Existing context file with UTF-8 BOM must be cleaned up on upsert."""
+        integration = get_integration("claude")
+        ctx_path = tmp_path / integration.context_file
+
+        # Write a file that starts with a UTF-8 BOM (as the old PowerShell script did)
+        bom = codecs.BOM_UTF8
+        ctx_path.write_bytes(bom + b"# CLAUDE.md\n\nSome existing content.\n")
+
+        integration.upsert_context_section(tmp_path)
+
+        result = ctx_path.read_bytes()
+        assert not result.startswith(bom), "BOM must be stripped after upsert"
+        content = result.decode("utf-8")
+        assert "<!-- SPECKIT START -->" in content
+        assert "Some existing content." in content
+
+    def test_remove_context_section_strips_bom(self, tmp_path):
+        """remove_context_section must clean BOM from context file on Windows-authored files."""
+        integration = get_integration("claude")
+        ctx_path = tmp_path / integration.context_file
+
+        marker_content = (
+            "# CLAUDE.md\n\n"
+            "<!-- SPECKIT START -->\n"
+            "For additional context about technologies to be used, project structure,\n"
+            "shell commands, and other important information, read the current plan\n"
+            "<!-- SPECKIT END -->\n"
+        )
+        ctx_path.write_bytes(codecs.BOM_UTF8 + marker_content.encode("utf-8"))
+
+        result = integration.remove_context_section(tmp_path)
+
+        assert result is True
+        assert ctx_path.exists(), "File should exist (non-empty content remains)"
+        remaining = ctx_path.read_bytes()
+        assert not remaining.startswith(codecs.BOM_UTF8), "BOM must be stripped after remove"
+        assert b"<!-- SPECKIT" not in remaining
+        assert b"# CLAUDE.md" in remaining
+
     def test_ai_flag_auto_promotes_and_enables_skills(self, tmp_path):
         from typer.testing import CliRunner
         from specify_cli import app

tests/test_presets.py

@@ -2447,7 +2447,7 @@ class TestPresetSkills:
     def test_agy_skill_restored_on_preset_remove(self, project_dir, temp_dir):
         """Agy preset removal should restore native skills instead of deleting them."""
         self._write_init_options(project_dir, ai="agy", ai_skills=True)
-        skills_dir = project_dir / ".agent" / "skills"
+        skills_dir = project_dir / ".agents" / "skills"
         self._create_skill(skills_dir, "speckit-specify", body="before override")
 
         core_command = project_dir / ".specify" / "templates" / "commands" / "specify.md"

tests/test_workflows.py

@@ -367,15 +367,49 @@ class TestBuildExecArgs:
         assert args[2] == "do stuff"
         assert "--json" in args
 
-    def test_copilot_exec_args(self):
+    def test_copilot_exec_args(self, monkeypatch):
+        monkeypatch.delenv("SPECKIT_COPILOT_ALLOW_ALL_TOOLS", raising=False)
+        monkeypatch.delenv("SPECKIT_ALLOW_ALL_TOOLS", raising=False)
         from specify_cli.integrations.copilot import CopilotIntegration
         impl = CopilotIntegration()
         args = impl.build_exec_args("do stuff", model="claude-sonnet-4-20250514")
         assert args[0] == "copilot"
         assert "-p" in args
-        assert "--allow-all-tools" in args
+        assert "--yolo" in args
         assert "--model" in args
 
+    def test_copilot_new_env_var_disables_yolo(self, monkeypatch):
+        monkeypatch.setenv("SPECKIT_COPILOT_ALLOW_ALL_TOOLS", "0")
+        monkeypatch.delenv("SPECKIT_ALLOW_ALL_TOOLS", raising=False)
+        from specify_cli.integrations.copilot import CopilotIntegration
+        impl = CopilotIntegration()
+        args = impl.build_exec_args("do stuff")
+        assert "--yolo" not in args
+
+    def test_copilot_deprecated_env_var_still_honoured(self, monkeypatch):
+        monkeypatch.delenv("SPECKIT_COPILOT_ALLOW_ALL_TOOLS", raising=False)
+        monkeypatch.setenv("SPECKIT_ALLOW_ALL_TOOLS", "0")
+        import warnings
+        from specify_cli.integrations.copilot import CopilotIntegration
+        impl = CopilotIntegration()
+        with warnings.catch_warnings(record=True) as w:
+            warnings.simplefilter("always")
+            args = impl.build_exec_args("do stuff")
+        assert "--yolo" not in args
+        assert any(
+            "SPECKIT_ALLOW_ALL_TOOLS is deprecated" in str(x.message)
+            and issubclass(x.category, UserWarning)
+            for x in w
+        )
+
+    def test_copilot_new_env_var_takes_precedence(self, monkeypatch):
+        monkeypatch.setenv("SPECKIT_COPILOT_ALLOW_ALL_TOOLS", "1")
+        monkeypatch.setenv("SPECKIT_ALLOW_ALL_TOOLS", "0")
+        from specify_cli.integrations.copilot import CopilotIntegration
+        impl = CopilotIntegration()
+        args = impl.build_exec_args("do stuff")
+        assert "--yolo" in args
+
     def test_ide_only_returns_none(self):
         from specify_cli.integrations.windsurf import WindsurfIntegration
         impl = WindsurfIntegration()
@@ -400,6 +434,7 @@ class TestCommandStep:
     """Test the command step type."""
 
     def test_execute_basic(self):
+        from unittest.mock import patch
         from specify_cli.workflows.steps.command import CommandStep
         from specify_cli.workflows.base import StepContext, StepStatus
 
@@ -413,7 +448,8 @@ class TestCommandStep:
             "command": "speckit.specify",
             "input": {"args": "{{ inputs.name }}"},
         }
-        result = step.execute(config, ctx)
+        with patch("specify_cli.workflows.steps.command.shutil.which", return_value=None):
+            result = step.execute(config, ctx)
         assert result.status == StepStatus.FAILED
         assert result.output["command"] == "speckit.specify"
         assert result.output["integration"] == "claude"
@@ -474,6 +510,7 @@ class TestCommandStep:
 
     def test_dispatch_not_attempted_without_cli(self):
         """When the CLI tool is not installed, step should fail."""
+        from unittest.mock import patch
         from specify_cli.workflows.steps.command import CommandStep
         from specify_cli.workflows.base import StepContext, StepStatus
 
@@ -488,7 +525,8 @@ class TestCommandStep:
             "command": "speckit.specify",
             "input": {"args": "{{ inputs.name }}"},
         }
-        result = step.execute(config, ctx)
+        with patch("specify_cli.workflows.steps.command.shutil.which", return_value=None):
+            result = step.execute(config, ctx)
         assert result.status == StepStatus.FAILED
         assert result.output["dispatched"] is False
         assert result.error is not None
@@ -566,6 +604,7 @@ class TestPromptStep:
     """Test the prompt step type."""
 
     def test_execute_basic(self):
+        from unittest.mock import patch
         from specify_cli.workflows.steps.prompt import PromptStep
         from specify_cli.workflows.base import StepContext, StepStatus
 
@@ -579,7 +618,8 @@ class TestPromptStep:
             "type": "prompt",
             "prompt": "Review {{ inputs.file }} for security issues",
         }
-        result = step.execute(config, ctx)
+        with patch("specify_cli.workflows.steps.prompt.shutil.which", return_value=None):
+            result = step.execute(config, ctx)
         assert result.status == StepStatus.FAILED
         assert result.output["prompt"] == "Review auth.py for security issues"
         assert result.output["integration"] == "claude"
@@ -1311,6 +1351,7 @@ class TestWorkflowEngine:
             engine.load_workflow("nonexistent")
 
     def test_execute_simple_workflow(self, project_dir):
+        from unittest.mock import patch
         from specify_cli.workflows.engine import WorkflowEngine, WorkflowDefinition
         from specify_cli.workflows.base import RunStatus
 
@@ -1333,7 +1374,8 @@ steps:
 """
         definition = WorkflowDefinition.from_string(yaml_str)
         engine = WorkflowEngine(project_dir)
-        state = engine.execute(definition, {"name": "login"})
+        with patch("specify_cli.workflows.steps.command.shutil.which", return_value=None):
+            state = engine.execute(definition, {"name": "login"})
 
         assert state.status == RunStatus.FAILED
         assert "step-one" in state.step_results