@softspark/ai-toolkit 4.16.0 → 4.16.1

package/CHANGELOG.md

@@ -7,6 +7,15 @@ Versioning follows [Semantic Versioning](https://semver.org/).
 
 ---
 
+## v4.16.1 — Copilot skill remnant recovery (2026-07-24)
+
+### Fixed
+
+- **Legacy Copilot skill remnants no longer abort local updates** — `.github/skills/ai-toolkit-*` directories left behind by pre-manifest cleanups (assets without `SKILL.md`) are rebuilt in place instead of raising `Refusing user-owned Copilot skill collision`, which aborted the entire `install --local` / `update` run on affected projects. User files inside a remnant that do not collide with generated output are preserved; any directory that still contains a `SKILL.md` stays protected and is never reclaimed.
+- **Readable installer errors** — `scripts/install.py` reports fail-closed `RuntimeError` conditions as a single `ERROR:` line instead of a raw traceback.
+
+Test count: 1477 → 1479.
+
 ## v4.16.0 — Native tool-output filtering (2026-07-24)
 
 Minor release. Adds a dependency-free, opt-in native tool-output filter for Claude Code and hardens the enterprise configuration, session-isolation, and editor-adapter surfaces around it. The filter ships disabled; `observe` and `safe` are per-project opt-ins. No source catalog count change (44 agents, 108 skills).

package/README.md

@@ -6,17 +6,18 @@
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
 [![Skills](https://img.shields.io/badge/skills-108-brightgreen)](app/skills/)
 [![Agents](https://img.shields.io/badge/agents-44-blue)](app/agents/)
-[![Tests](https://img.shields.io/badge/tests-1477%20passing-success)](tests/)
+[![Tests](https://img.shields.io/badge/tests-1479%20passing-success)](tests/)
 
-## What's New in v4.16.0
+## What's New in v4.16.1
 
-v4.16.0 adds a dependency-free, opt-in native tool-output filter for Claude Code and hardens the enterprise configuration surface around it.
+v4.16.1 ships the native tool-output filter introduced in v4.16.0 and fixes local updates crashing on legacy Copilot skill remnants.
 
 - **Native tool-output filter**: opt-in `PostToolUse` filter with `off`, `observe`, and `safe` modes; ships disabled, handles only allowlisted successful Bash test/validation output.
 - **Exact ephemeral recovery**: every safe replacement keeps a private, bounded, session-scoped copy of the original response, recoverable via `ai-toolkit output-filter recover`.
 - **Output-filter CLI**: `ai-toolkit output-filter status|inspect|recover|clean` plus a deterministic benchmark for the built-in profiles.
 - **Stricter config validation**: unknown top-level config keys are rejected, plugin manifests must declare `requires`, and lock files go stale on toolkit version bumps.
 - **GitHub Copilot compatibility reference**: new `kb/reference/copilot-compatibility.md` documenting the Copilot integration surface.
+- **Copilot remnant recovery**: asset-only `.github/skills/ai-toolkit-*` leftovers from older cleanups are rebuilt in place instead of aborting `install --local` / `update`.
 
 See [CHANGELOG.md](CHANGELOG.md) for full history.
 
@@ -126,7 +127,7 @@ See [CLI Reference](kb/reference/cli-reference.md) for all commands and options.
 | Gemini CLI | `~/.gemini/GEMINI.md` | ✅ | global |
 | GitHub Copilot | Project: `AGENTS.md` + `.github/copilot-instructions.md` + `.github/{instructions,prompts,agents,skills,hooks}/` + `.github/mcp.json`; user: `$COPILOT_HOME/copilot-instructions.md` + `$COPILOT_HOME/{instructions,agents,skills,hooks}/` + `$COPILOT_HOME/mcp-config.json` | ✅ | project + user |
 | Cline | `~/Documents/Cline/Rules/*.md` + `~/.cline/skills/*` + `.clinerules/*.md` | — | global + project |
-| Roo Code | `~/.roo/rules/*.md` + `.roomodes` + `.roo/rules/*.md` | — | global rules + project |
+| Roo Code / [Zoo Code](https://zoocode.dev/) | `~/.roo/rules/*.md` + `.roomodes` + `.roo/rules/*.md` | — | global rules + project |
 | Aider | `~/.aider.conf.yml` + `.aider.conf.yml` + `CONVENTIONS.md` | — | global + project |
 | Augment | `~/.augment/rules/*.md` + `.augment/rules/ai-toolkit-*.md` | ✅ | global + project |
 | Google Antigravity | `.agents/rules/*.md` + `.agents/workflows/*.md` + skill pointer in `.agent/skills/*` (IDE) and `.agents/skills/*` (CLI) | — | project |
@@ -169,7 +170,7 @@ ai-toolkit/
 │   └── ARCHITECTURE.md  # Full system design
 ├── kb/                  # Reference docs, procedures, plans
 ├── scripts/             # Validation, install, evaluation scripts
-├── tests/               # Bats and Python test suite (1477 tests)
+├── tests/               # Bats and Python test suite (1479 tests)
 └── CHANGELOG.md
 ```
 

package/app/.claude-plugin/plugin.json

@@ -3,7 +3,7 @@
   "name": "ai-toolkit",
   "displayName": "AI Toolkit",
   "description": "Professional-grade engineering skills, agents, rules, and lifecycle guardrails for Claude Code, Claude Chat, and Cowork.",
-  "version": "4.16.0",
+  "version": "4.16.1",
   "author": {
     "name": "SoftSpark",
     "url": "https://github.com/softspark"

package/manifest.json

@@ -1,5 +1,5 @@
 {
-  "version": "4.16.0",
+  "version": "4.16.1",
   "components": {
     "agents": {
       "description": "44 specialized agents (orchestrator, backend, frontend, security, devops, etc.)",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@softspark/ai-toolkit",
-  "version": "4.16.0",
+  "version": "4.16.1",
   "description": "AI coding toolkit: 108 skills, 44 agents, 12 developer-tool integrations, recoverable native tool-output filtering, Claude Chat/Cowork export, safety constitution, SARIF audit, and signed npm provenance.",
   "keywords": [
     "claude",

package/scripts/generate_copilot.py

@@ -974,6 +974,23 @@ def _is_managed_skill_dir(path: Path) -> bool:
     return path.is_dir() and not path.is_symlink() and _is_managed(skill_file)
 
 
+def _is_skill_remnant(path: Path) -> bool:
+    """Asset-only leftover of a legacy managed skill.
+
+    Pre-manifest toolkit versions tracked only SKILL.md as managed, so their
+    cleanup removed SKILL.md and left reference/ and scripts/ assets behind.
+    Without SKILL.md the directory is not a functional Copilot skill, so it is
+    safe to rebuild in place; a directory that still has any SKILL.md (managed
+    or not) is never classified as a remnant.
+    """
+    return (
+        path.is_dir()
+        and not path.is_symlink()
+        and not (path / "SKILL.md").exists()
+        and not (path / "SKILL.md").is_symlink()
+    )
+
+
 def _managed_skill_paths(path: Path) -> set[Path]:
     manifest = path / SKILL_MANIFEST
     if not manifest.is_file() or manifest.is_symlink():
@@ -999,7 +1016,8 @@ def _has_user_skill_extras(path: Path) -> bool:
 
 
 def _copy_user_skill_extras(existing: Path, staging: Path,
-                            generated_paths: set[Path]) -> None:
+                            generated_paths: set[Path],
+                            *, skip_stale_assets: bool = False) -> None:
     """Preserve files a user added inside a previously managed skill."""
     old_managed = _managed_skill_paths(existing)
     for source in sorted(existing.rglob("*")):
@@ -1011,6 +1029,8 @@ def _copy_user_skill_extras(existing: Path, staging: Path,
         if not source.is_file():
             continue
         if relative in generated_paths:
+            if skip_stale_assets:
+                continue
             raise RuntimeError(
                 f"Copilot skill update would overwrite a user asset: {source}"
             )
@@ -1046,7 +1066,10 @@ def _stage_skill(skills_root: Path, source_dir: Path,
             encoding="utf-8",
         )
         if existing is not None:
-            _copy_user_skill_extras(existing, staging, generated_paths)
+            _copy_user_skill_extras(
+                existing, staging, generated_paths,
+                skip_stale_assets=_is_skill_remnant(existing),
+            )
         return staging, name
     except Exception:
         shutil.rmtree(staging, ignore_errors=True)
@@ -1058,7 +1081,10 @@ def _replace_skill_dir(staging: Path, destination: Path) -> None:
     backup: Path | None = None
     try:
         if destination.exists():
-            if destination.is_symlink() or not _is_managed_skill_dir(destination):
+            if destination.is_symlink() or not (
+                _is_managed_skill_dir(destination)
+                or _is_skill_remnant(destination)
+            ):
                 raise RuntimeError(
                     f"Refusing user-owned Copilot skill collision: {destination}"
                 )
@@ -1125,7 +1151,12 @@ def _sync_copilot_skills(customization_root: Path, *, label: str) -> None:
         expected_dirs.add(destination_name)
         existing = destination if destination.exists() else None
         if existing is not None and not _is_managed_skill_dir(existing):
-            raise RuntimeError(f"Refusing user-owned Copilot skill collision: {destination}")
+            if not _is_skill_remnant(existing):
+                raise RuntimeError(f"Refusing user-owned Copilot skill collision: {destination}")
+            print(
+                f"Note: rebuilding asset-only Copilot skill remnant '{destination}'",
+                file=sys.stderr,
+            )
         staging, rendered_name = _stage_skill(skill_root, source_dir, existing)
         if rendered_name != logical_name:
             shutil.rmtree(staging, ignore_errors=True)

package/scripts/install.py

@@ -841,4 +841,8 @@ def _infer_modules_from_legacy(profile: str, only: str) -> list[str]:
 
 
 if __name__ == "__main__":
-    main()
+    try:
+        main()
+    except RuntimeError as error:
+        print(f"ERROR: {error}", file=sys.stderr)
+        sys.exit(1)