@aperant/framework 0.8.1 → 0.8.6

package/dist/cli/install/legacy-paths.d.mts

@@ -11,28 +11,50 @@
  *     pre-manifest install still surfaces as "installed" rather than
  *     "missing-skills".
  *
- * Derivation: the codex `framework_files` list was extracted from
- * `git show 1a8dd8a8 --stat` (the original "make Codex a first-class
- * skill install surface" commit) — every `.agents/skills/…` path the
- * installer once wrote, including the `.apt-version` stamp and the
- * apt-pr-review / apt-discuss / apt-verify-proof sub-files. When the
- * codex installer was retargeted to `.codex/`, that entire tree became
- * orphaned on upgrading projects.
+ * Codex evolution: v0.7/v0.8 retargeted the codex transform to write
+ * markdown skills under `.codex/agents/` + `.codex/commands/` (with the
+ * apt-file-manifest.json next to them). Codex CLI 0.132.0 does not
+ * discover skills at either path — its documented surface is
+ * `.agents/skills/<folder>/SKILL.md` (per
+ * https://developers.openai.com/codex/skills). The v0.8.2 fix inverts
+ * this registry: the dead `.codex/` markdown tree becomes the legacy
+ * target so `runLegacyCleanup` GCs it on the next `apt-tools init`.
  *
  * Schema:
  *   { [runtimeId]: {
  *       install_root:     relative path the runtime once wrote into,
- *       version_file:     relative path of the legacy `.apt-version` stamp,
+ *       version_file:     relative path of the legacy `.apt-version` stamp
+ *                         (or a path known to never exist, when no version
+ *                         stamp was ever written for the legacy topology),
+ *       honor_manifest:   when true (default), a present apt-file-manifest.json
+ *                         at install_root signals a managed install and the
+ *                         cleanup no-ops (`reason: 'managed'`). When false,
+ *                         the legacy root is known-dead so the manifest is
+ *                         removed alongside framework files (used for surfaces
+ *                         like the v0.7/v0.8 codex misdirect that will never
+ *                         again be a managed install root).
  *       framework_files:  array of relative paths the installer once owned
  *                         (under install_root).
  *   } }
  *
  * Frozen via Object.freeze so callers cannot mutate the shared registry.
  */
-/** @type {Record<string, { install_root: string, version_file: string, framework_files: ReadonlyArray<string> }>} */
-export const LEGACY_INSTALL_PATHS: Record<string, {
+/**
+ * @typedef {Object} LegacyInstallPath
+ * @property {string} install_root
+ * @property {string} version_file
+ * @property {boolean} [honor_manifest]  default true; false for known-dead surfaces
+ * @property {ReadonlyArray<string>} framework_files
+ */
+/** @type {Record<string, LegacyInstallPath>} */
+export const LEGACY_INSTALL_PATHS: Record<string, LegacyInstallPath>;
+export type LegacyInstallPath = {
     install_root: string;
     version_file: string;
+    /**
+     * default true; false for known-dead surfaces
+     */
+    honor_manifest?: boolean | undefined;
     framework_files: ReadonlyArray<string>;
-}>;
+};
 //# sourceMappingURL=legacy-paths.d.mts.map

package/dist/cli/install/legacy-paths.d.mts.map

@@ -1 +1 @@
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+{"version":3,"file":"legacy-paths.d.mts","sourceRoot":"","sources":["../../../src/cli/install/legacy-paths.mjs"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAwCG;AAEH;;;;;;GAMG;AAEH,gDAAgD;AAChD,mCADW,MAAM,CAAC,MAAM,EAAE,iBAAiB,CAAC,CA+I1C;;kBArJY,MAAM;kBACN,MAAM;;;;;qBAEN,aAAa,CAAC,MAAM,CAAC"}

package/dist/cli/install/legacy-paths.mjs

@@ -11,58 +11,182 @@
  *     pre-manifest install still surfaces as "installed" rather than
  *     "missing-skills".
  *
- * Derivation: the codex `framework_files` list was extracted from
- * `git show 1a8dd8a8 --stat` (the original "make Codex a first-class
- * skill install surface" commit) — every `.agents/skills/…` path the
- * installer once wrote, including the `.apt-version` stamp and the
- * apt-pr-review / apt-discuss / apt-verify-proof sub-files. When the
- * codex installer was retargeted to `.codex/`, that entire tree became
- * orphaned on upgrading projects.
+ * Codex evolution: v0.7/v0.8 retargeted the codex transform to write
+ * markdown skills under `.codex/agents/` + `.codex/commands/` (with the
+ * apt-file-manifest.json next to them). Codex CLI 0.132.0 does not
+ * discover skills at either path — its documented surface is
+ * `.agents/skills/<folder>/SKILL.md` (per
+ * https://developers.openai.com/codex/skills). The v0.8.2 fix inverts
+ * this registry: the dead `.codex/` markdown tree becomes the legacy
+ * target so `runLegacyCleanup` GCs it on the next `apt-tools init`.
  *
  * Schema:
  *   { [runtimeId]: {
  *       install_root:     relative path the runtime once wrote into,
- *       version_file:     relative path of the legacy `.apt-version` stamp,
+ *       version_file:     relative path of the legacy `.apt-version` stamp
+ *                         (or a path known to never exist, when no version
+ *                         stamp was ever written for the legacy topology),
+ *       honor_manifest:   when true (default), a present apt-file-manifest.json
+ *                         at install_root signals a managed install and the
+ *                         cleanup no-ops (`reason: 'managed'`). When false,
+ *                         the legacy root is known-dead so the manifest is
+ *                         removed alongside framework files (used for surfaces
+ *                         like the v0.7/v0.8 codex misdirect that will never
+ *                         again be a managed install root).
  *       framework_files:  array of relative paths the installer once owned
  *                         (under install_root).
  *   } }
  *
  * Frozen via Object.freeze so callers cannot mutate the shared registry.
  */
-/** @type {Record<string, { install_root: string, version_file: string, framework_files: ReadonlyArray<string> }>} */
+/**
+ * @typedef {Object} LegacyInstallPath
+ * @property {string} install_root
+ * @property {string} version_file
+ * @property {boolean} [honor_manifest]  default true; false for known-dead surfaces
+ * @property {ReadonlyArray<string>} framework_files
+ */
+/** @type {Record<string, LegacyInstallPath>} */
 export const LEGACY_INSTALL_PATHS = Object.freeze({
     codex: Object.freeze({
-        install_root: '.agents/skills',
-        version_file: '.agents/skills/.apt-version',
+        // The v0.7/v0.8 misdirect lived under `.codex/agents/` + `.codex/commands/`
+        // (with the orphan apt-file-manifest.json at `.codex/apt-file-manifest.json`).
+        // Codex CLI 0.132.0 does not consume any of those paths — see header.
+        install_root: '.codex',
+        // No `.apt-version` was ever written under `.codex/`; point at a path
+        // that doesn't exist so `existsSync` returns false in
+        // skill-installs.mjs:67-68 (legacy version_file fallback). The bare
+        // apt-file-manifest.json (handled by framework_files) is enough to
+        // signal the legacy install.
+        version_file: '.codex/.apt-version',
+        // Known-dead surface: this `.codex/` topology will never again be
+        // a managed Aperant install root, so a manifest sitting here is
+        // always stale. Skip the no-op-on-manifest safety and remove the
+        // manifest alongside framework_files. Default-true elsewhere
+        // preserves the safety for legacy roots that could legitimately
+        // re-host a managed install.
+        honor_manifest: false,
+        // Enumerated from BOTH canonical sources (drift-checked at test time
+        // by legacy-cleanup-codex.test.ts):
+        //   - For each `packages/framework/skills/apt-*/` directory: the v0.7/v0.8
+        //     transform emitted BOTH `agents/<dir>.md` AND `commands/<dir>.md`.
+        //   - For each top-level `packages/framework/skills/apt-*.md` file
+        //     (fileType=agent in the pipeline): the transform emitted
+        //     `agents/<basename>.md`.
+        //   - For each `packages/framework/agents/apt-*.md` file: the transform
+        //     emitted `agents/<basename>.md` (last-write-wins de-dupe applied
+        //     by the pipeline for overlapping outputs).
+        //   - Plus the orphan apt-file-manifest.json the install pipeline
+        //     stamps at install_root.
+        // TODO: follow-up — derive this programmatically per spec ID-06 so
+        // new apt-* skills auto-extend the legacy set without an edit here.
         framework_files: Object.freeze([
-            '.apt-version',
-            'apt/SKILL.md',
-            'apt-debug/SKILL.md',
-            'apt-discuss/SKILL.md',
-            'apt-discuss/examples/rationalization-example.md',
-            'apt-docs/SKILL.md',
-            'apt-execute/SKILL.md',
-            'apt-pause/SKILL.md',
-            'apt-plan/SKILL.md',
-            'apt-pr-review/SCHEMA.md',
-            'apt-pr-review/SKILL.md',
-            'apt-pr-review/prompts/fp-gate-codex.md',
-            'apt-pr-review/templates/external-comment.md',
-            'apt-quick/SKILL.md',
-            'apt-resume/SKILL.md',
-            'apt-review/SKILL.md',
-            'apt-roadmap/SKILL.md',
-            'apt-roundtable/SKILL.md',
-            'apt-run/SKILL.md',
-            'apt-scan/SKILL.md',
-            'apt-setup/SKILL.md',
-            'apt-ship/SKILL.md',
-            'apt-stress-test/SKILL.md',
-            'apt-verify/SKILL.md',
-            'apt-verify-proof/SKILL.md',
-            'apt-verify-proof/references/multi-model-setup.md',
-            'apt-verify-proof/references/multi-model-verification.md',
-            'apt-verify-proof/references/proof-capture.md',
+            'apt-file-manifest.json',
+            // agents/<dir>.md — one per skill directory (39 dirs)
+            'agents/apt.md',
+            'agents/apt-author-skill.md',
+            'agents/apt-bootstrap.md',
+            'agents/apt-caveman.md',
+            'agents/apt-classify.md',
+            'agents/apt-close-task.md',
+            'agents/apt-create-docs.md',
+            'agents/apt-debug.md',
+            'agents/apt-design.md',
+            'agents/apt-diagram.md',
+            'agents/apt-discuss.md',
+            'agents/apt-docs.md',
+            'agents/apt-execute.md',
+            'agents/apt-fan-out.md',
+            'agents/apt-handoff.md',
+            'agents/apt-improve.md',
+            'agents/apt-mockup.md',
+            'agents/apt-pause.md',
+            'agents/apt-personas.md',
+            'agents/apt-plan.md',
+            'agents/apt-pr-review.md',
+            'agents/apt-prototype.md',
+            'agents/apt-quick.md',
+            'agents/apt-release-notes.md',
+            'agents/apt-research.md',
+            'agents/apt-resume.md',
+            'agents/apt-review.md',
+            'agents/apt-roadmap.md',
+            'agents/apt-roundtable.md',
+            'agents/apt-run.md',
+            'agents/apt-scan.md',
+            'agents/apt-setup.md',
+            'agents/apt-ship.md',
+            'agents/apt-spar.md',
+            'agents/apt-stress-test.md',
+            'agents/apt-terminal.md',
+            'agents/apt-triage.md',
+            'agents/apt-update.md',
+            'agents/apt-verify.md',
+            'agents/apt-verify-proof.md',
+            'agents/apt-watch-ci.md',
+            'agents/apt-zoom-out.md',
+            // commands/<dir>.md — one per skill directory (mirrors agents/)
+            'commands/apt.md',
+            'commands/apt-author-skill.md',
+            'commands/apt-bootstrap.md',
+            'commands/apt-caveman.md',
+            'commands/apt-classify.md',
+            'commands/apt-close-task.md',
+            'commands/apt-create-docs.md',
+            'commands/apt-debug.md',
+            'commands/apt-design.md',
+            'commands/apt-diagram.md',
+            'commands/apt-discuss.md',
+            'commands/apt-docs.md',
+            'commands/apt-execute.md',
+            'commands/apt-fan-out.md',
+            'commands/apt-handoff.md',
+            'commands/apt-improve.md',
+            'commands/apt-mockup.md',
+            'commands/apt-pause.md',
+            'commands/apt-personas.md',
+            'commands/apt-plan.md',
+            'commands/apt-pr-review.md',
+            'commands/apt-prototype.md',
+            'commands/apt-quick.md',
+            'commands/apt-release-notes.md',
+            'commands/apt-research.md',
+            'commands/apt-resume.md',
+            'commands/apt-review.md',
+            'commands/apt-roadmap.md',
+            'commands/apt-roundtable.md',
+            'commands/apt-run.md',
+            'commands/apt-scan.md',
+            'commands/apt-setup.md',
+            'commands/apt-ship.md',
+            'commands/apt-spar.md',
+            'commands/apt-stress-test.md',
+            'commands/apt-terminal.md',
+            'commands/apt-triage.md',
+            'commands/apt-update.md',
+            'commands/apt-verify.md',
+            'commands/apt-verify-proof.md',
+            'commands/apt-watch-ci.md',
+            'commands/apt-zoom-out.md',
+            // agents/<basename>.md — packages/framework/agents/apt-*.md (17 files)
+            // (overlap with skills/apt-*.md top-level — same outputPath, de-dupe)
+            'agents/apt-docs-author.md',
+            'agents/apt-executor.md',
+            'agents/apt-improver.md',
+            'agents/apt-planner.md',
+            'agents/apt-pr-review-codebase-fit.md',
+            'agents/apt-pr-review-fixer.md',
+            'agents/apt-pr-review-logic.md',
+            'agents/apt-pr-review-performance.md',
+            'agents/apt-pr-review-quality.md',
+            'agents/apt-pr-review-security.md',
+            'agents/apt-pr-review-self-reviewer.md',
+            'agents/apt-pr-review-test-integrity.md',
+            'agents/apt-pr-review-validator.md',
+            'agents/apt-researcher.md',
+            'agents/apt-reviewer.md',
+            'agents/apt-team-docs-narrator.md',
+            'agents/apt-verifier.md',
         ]),
     }),
 });

package/dist/cli/install/legacy-paths.mjs.map

@@ -1 +1 @@
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package/dist/cli/install/runtime-detect.mjs

@@ -47,7 +47,7 @@ export const RUNTIMES = Object.freeze([
     {
         id: 'codex',
         flag: '--codex',
-        installRoot: '.codex',
+        installRoot: '.agents',
         markers: ['.codex/config.toml'],
         cliId: 'codex',
     },

package/dist/cli/install/runtime-detect.mjs.map

@@ -1 +1 @@
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+{"version":3,"file":"runtime-detect.mjs","sourceRoot":"","sources":["../../../src/cli/install/runtime-detect.mjs"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAA;AAC9C,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAA;AAChC,OAAO,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAA;AAElD;;;;;;;;;;;;;;;;;;GAkBG;AAEH,kCAAkC;AAClC,MAAM,CAAC,MAAM,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC;IACrC;QACC,EAAE,EAAE,QAAQ;QACZ,IAAI,EAAE,UAAU;QAChB,WAAW,EAAE,SAAS;QACtB,OAAO,EAAE,CAAC,uBAAuB,EAAE,6BAA6B,CAAC;QACjE,KAAK,EAAE,aAAa;KACpB;IACD;QACC,EAAE,EAAE,OAAO;QACX,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,SAAS;QACtB,OAAO,EAAE,CAAC,oBAAoB,CAAC;QAC/B,KAAK,EAAE,OAAO;KACd;IACD;QACC,EAAE,EAAE,QAAQ;QACZ,IAAI,EAAE,UAAU;QAChB,WAAW,EAAE,SAAS;QACtB,OAAO,EAAE,CAAC,uBAAuB,CAAC;QAClC,KAAK,EAAE,QAAQ;KACf;IACD;QACC,EAAE,EAAE,QAAQ;QACZ,IAAI,EAAE,UAAU;QAChB,WAAW,EAAE,SAAS;QACtB,OAAO,EAAE,CAAC,uBAAuB,CAAC;QAClC,KAAK,EAAE,YAAY;KACnB;IACD;QACC,EAAE,EAAE,UAAU;QACd,IAAI,EAAE,YAAY;QAClB,WAAW,EAAE,WAAW;QACxB,OAAO,EAAE,CAAC,uBAAuB,CAAC;QAClC,KAAK,EAAE,UAAU;KACjB;IACD;QACC,EAAE,EAAE,IAAI;QACR,IAAI,EAAE,MAAM;QACZ,WAAW,EAAE,KAAK;QAClB,OAAO,EAAE,CAAC,mBAAmB,EAAE,YAAY,EAAE,aAAa,CAAC;QAC3D,KAAK,EAAE,IAAI;KACX;IACD;QACC,EAAE,EAAE,MAAM;QACV,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,OAAO;QACpB,OAAO,EAAE,CAAC,mBAAmB,CAAC;QAC9B,KAAK,EAAE,MAAM;QACb,kEAAkE;QAClE,gEAAgE;QAChE,6DAA6D;QAC7D,YAAY,EAAE,WAAW;KACzB;IACD;QACC,EAAE,EAAE,SAAS;QACb,IAAI,EAAE,WAAW;QACjB,WAAW,EAAE,iBAAiB;QAC9B,OAAO,EAAE,CAAC,iCAAiC,CAAC;QAC5C,KAAK,EAAE,SAAS;KAChB;IACD;QACC,EAAE,EAAE,aAAa;QACjB,IAAI,EAAE,eAAe;QACrB,WAAW,EAAE,cAAc;QAC3B,OAAO,EAAE,CAAC,0BAA0B,CAAC;QACrC,KAAK,EAAE,aAAa;KACpB;IACD;QACC,EAAE,EAAE,UAAU;QACd,IAAI,EAAE,YAAY;QAClB,WAAW,EAAE,WAAW;QACxB,OAAO,EAAE,CAAC,gBAAgB,CAAC;QAC3B,KAAK,EAAE,UAAU;KACjB;IACD;QACC,EAAE,EAAE,SAAS;QACb,IAAI,EAAE,WAAW;QACjB,WAAW,EAAE,UAAU;QACvB,OAAO,EAAE,CAAC,sBAAsB,CAAC;QACjC,KAAK,EAAE,SAAS;KAChB;IACD;QACC,EAAE,EAAE,MAAM;QACV,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,OAAO;QACpB,OAAO,EAAE,CAAC,mBAAmB,CAAC;QAC9B,KAAK,EAAE,MAAM;KACb;IACD;QACC,EAAE,EAAE,MAAM;QACV,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,OAAO;QACpB,OAAO,EAAE,CAAC,mBAAmB,CAAC;QAC9B,KAAK,EAAE,MAAM;KACb;IACD;QACC,EAAE,EAAE,OAAO;QACX,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,QAAQ;QACrB,OAAO,EAAE,CAAC,oBAAoB,CAAC;QAC/B,KAAK,EAAE,OAAO;KACd;IACD;QACC,EAAE,EAAE,WAAW;QACf,IAAI,EAAE,aAAa;QACnB,WAAW,EAAE,YAAY;QACzB,OAAO,EAAE,CAAC,wBAAwB,CAAC;QACnC,KAAK,EAAE,WAAW;KAClB;CACD,CAAC,CAAA;AAEF,0BAA0B;AAC1B,MAAM,CAAC,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAE7D;;;;;GAKG;AACH,MAAM,UAAU,UAAU,CAAC,EAAE;IAC5B,OAAO,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,IAAI,IAAI,CAAA;AACjD,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,eAAe,CAAC,SAAS;IACxC,MAAM,GAAG,GAAG,EAAE,CAAA;IACd,KAAK,MAAM,CAAC,IAAI,QAAQ,EAAE,CAAC;QAC1B,IAAI,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,EAAE,CAAC;YAChD,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;YACd,SAAQ;QACT,CAAC;QACD,IAAI,CAAC,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YAC3D,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;QACf,CAAC;IACF,CAAC;IACD,OAAO,GAAG,CAAA;AACX,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,uBAAuB,CAAC,SAAS;IAChD,MAAM,GAAG,GAAG,EAAE,CAAA;IACd,KAAK,MAAM,CAAC,IAAI,QAAQ,EAAE,CAAC;QAC1B,MAAM,YAAY,GAAG,IAAI,CAAC,SAAS,EAAE,CAAC,CAAC,WAAW,EAAE,iBAAiB,CAAC,CAAA;QACtE,IAAI,CAAC,UAAU,CAAC,YAAY,CAAC;YAAE,SAAQ;QACvC,IAAI,CAAC;YACJ,IAAI,QAAQ,CAAC,YAAY,CAAC,CAAC,MAAM,EAAE;gBAAE,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACjD,CAAC;QAAC,MAAM,CAAC;YACR,0DAA0D;QAC3D,CAAC;IACF,CAAC;IACD,OAAO,GAAG,CAAA;AACX,CAAC"}

package/dist/cli/install/runtime-migrate.d.mts

@@ -1,30 +1,43 @@
 /**
- * Probe the codex legacy install tree at `<targetDir>/.agents/skills/`.
+ * Probe the codex legacy install tree at `<targetDir>/<LEGACY.install_root>`
+ * (currently `.codex/` after the v0.8.2 registry inversion — the v0.7/v0.8
+ * misdirect topology).
  *
  * @param {string} targetDir
  * @returns {LegacyCodexDetection}
  */
 export function detectLegacyCodexTree(targetDir: string): LegacyCodexDetection;
 /**
- * Clean up the legacy `.agents/skills/` tree if it looks orphaned.
+ * Clean up the legacy install tree at `<targetDir>/<LEGACY.install_root>`
+ * if it looks orphaned. Post v0.8.2 the codex legacy root is `.codex/`
+ * with framework files at `agents/<file>.md` + `commands/<file>.md` +
+ * `apt-file-manifest.json`.
  *
  * Branches:
  *   1. `present: false` OR `frameworkFiles.length === 0` → no-op,
  *      `{ ran: false, reason: 'no-legacy' }`.
- *   2. `hasManifest: true` → managed install, no-op,
- *      `{ ran: false, reason: 'managed' }`.
+ *   2. `hasManifest: true` AND `LEGACY.honor_manifest !== false`
+ *      (default true) → managed install, no-op,
+ *      `{ ran: false, reason: 'managed' }`. When `honor_manifest: false`
+ *      (known-dead surface like the v0.7/v0.8 codex misdirect) the
+ *      manifest is treated as orphan and removed alongside framework
+ *      files.
  *   3. Otherwise: per-file `unlinkSync` each framework-owned file;
- *      `rmdirSync` any now-empty `apt-*` subdirectory; sweep
- *      `.agents/skills/` only if it is empty; sweep `.agents/` only if
- *      its `skills/` got removed and `.agents/` is empty.
+ *      `rmdirSync` any subdirectory left empty after the unlinks (e.g.
+ *      `.codex/agents/`, `.codex/commands/`); sweep the install_root
+ *      itself only if it is fully empty after the per-file pass; sweep
+ *      the install_root's parent only if it too became empty (relevant
+ *      for legacy topologies two levels deep, e.g. the pre-0.7
+ *      `.agents/skills/` codex layout).
  *
  * Returns `{ ran: true, removed, retained, rmdirs }` on the cleanup
  * branch:
  *   - `removed`  — relative paths under `install_root` that were unlinked.
  *   - `retained` — relative paths under `install_root` that were NOT
- *     removed (user-added skills / files not in the legacy set).
- *   - `rmdirs`   — absolute paths of directories that were removed
- *     (apt-* subdirs, the install_root itself, .agents/), in removal order.
+ *     removed (user-added skills / files not in the legacy set, e.g.
+ *     `.codex/config.toml`).
+ *   - `rmdirs`   — absolute paths of directories that were removed,
+ *     in removal order.
  *
  * Atomicity: per-file unlink is non-atomic. A partial-failure scenario
  * (process killed mid-loop) is tolerable — the next `init` run will
@@ -50,7 +63,8 @@ export function runLegacyCleanup({ targetDir, dryRun }: {
 };
 export type LegacyCodexDetection = {
     /**
-     * True when `.agents/skills/` exists.
+     * True when the legacy install_root
+     * (currently `.codex/`) exists.
      */
     present: boolean;
     /**
@@ -75,9 +89,15 @@ export type LegacyCodexDetection = {
     /**
      * Whether an
      * `apt-file-manifest.json` is
-     * present at install_root (signals
-     * a managed install — cleanup
-     * should no-op).
+     * present at install_root. When the
+     * legacy entry has
+     * `honor_manifest: true` (default)
+     * this signals a managed install
+     * and cleanup no-ops; when
+     * `honor_manifest: false` the
+     * manifest is treated as orphan
+     * and removed alongside framework
+     * files.
      */
     hasManifest: boolean;
 };

package/dist/cli/install/runtime-migrate.d.mts.map

@@ -1 +1 @@
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+{"version":3,"file":"runtime-migrate.d.mts","sourceRoot":"","sources":["../../../src/cli/install/runtime-migrate.mjs"],"names":[],"mappings":"AAuGA;;;;;;;GAOG;AACH,iDAHW,MAAM,GACJ,oBAAoB,CA0BhC;AAmBD;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyCG;AACH,wDANW;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,MAAM,CAAC,EAAE,OAAO,CAAA;CAAE,GAEjD,GAAC,GAAK;IAAE,GAAG,EAAE,KAAK,CAAC;IAAC,MAAM,EAAE,WAAW,GAAG,SAAS,CAAA;CAAE,GAC/C;IAAE,GAAG,EAAE,IAAI,CAAC;IAAC,OAAO,EAAE,MAAM,EAAE,CAAC;IAAC,QAAQ,EAAE,MAAM,EAAE,CAAC;IAAC,MAAM,EAAE,MAAM,EAAE,CAAA;CAAE,CA2F5E;;;;;;aAvPa,OAAO;;;;;;oBAEP,MAAM,EAAE;;;;;;;;eAGR,MAAM,EAAE;;;;;mBAKR,OAAO;;;;;;;;;;;;;;iBAEP,OAAO"}

package/dist/cli/install/runtime-migrate.mjs

@@ -2,15 +2,14 @@
  * install/runtime-migrate.mjs — at-install cleanup of legacy install
  * trees the framework no longer owns (FRAMEWORK-BUG-021).
  *
- * Codex was originally installed into `.agents/skills/` (commit 1a8dd8a8)
- * and later moved to `.codex/`. Projects that upgraded across that move
- * end up with a stale `.agents/skills/` tree that:
- *
- *   - keeps `.apt-version` on disk → the legacy fallback in
- *     `readSkillInstallState` reports a stale codex install.
- *   - shows up in `health-check` as `stale-skills`.
- *   - leaves dozens of orphaned SKILL.md files the runtime no longer
- *     reads.
+ * Codex shuffled install roots twice:
+ *   - Pre-0.7: installed at `.agents/skills/` (commit 1a8dd8a8).
+ *   - v0.7/v0.8: moved to `.codex/agents/` + `.codex/commands/` — a
+ *     misdirect, since Codex CLI 0.132.0 doesn't discover skills there.
+ *   - v0.8.2 (this fix): moved back to `.agents/skills/<folder>/SKILL.md`
+ *     (Codex's documented surface). The v0.7/v0.8 `.codex/` markdown
+ *     tree is now the legacy target — `LEGACY_INSTALL_PATHS.codex` was
+ *     re-pointed accordingly.
  *
  * `runLegacyCleanup` runs once per `apt-tools init` when codex is in the
  * requested runtime set. It is conservative by default:
@@ -20,8 +19,11 @@
  *     preserved. If anything beyond the known framework set remains,
  *     `retained[]` lists those paths.
  *   - A present-and-current `apt-file-manifest.json` is treated as the
- *     authoritative "this is a managed install, leave it alone" signal:
- *     the function no-ops with `reason: 'managed'`.
+ *     authoritative "this is a managed install, leave it alone" signal
+ *     — but ONLY when the legacy entry has `honor_manifest: true` (the
+ *     default). When `honor_manifest: false` (the current codex entry,
+ *     because `.codex/` is known-dead), the manifest is removed alongside
+ *     framework files.
  *   - The caller can suppress cleanup entirely via `--keep-legacy` at the
  *     init.mjs site; the function itself is dumb about flags.
  */
@@ -31,7 +33,8 @@ import { LEGACY_INSTALL_PATHS } from './legacy-paths.mjs';
 import { MANIFEST_FILENAME } from './manifest.mjs';
 /**
  * @typedef {Object} LegacyCodexDetection
- * @property {boolean} present              True when `.agents/skills/` exists.
+ * @property {boolean} present              True when the legacy install_root
+ *                                          (currently `.codex/`) exists.
  * @property {string[]} frameworkFiles      Subset of `framework_files` that
  *                                          actually exist on disk (relative
  *                                          to install_root).
@@ -44,9 +47,15 @@ import { MANIFEST_FILENAME } from './manifest.mjs';
  *                                          stamp is present.
  * @property {boolean} hasManifest          Whether an
  *                                          `apt-file-manifest.json` is
- *                                          present at install_root (signals
- *                                          a managed install — cleanup
- *                                          should no-op).
+ *                                          present at install_root. When the
+ *                                          legacy entry has
+ *                                          `honor_manifest: true` (default)
+ *                                          this signals a managed install
+ *                                          and cleanup no-ops; when
+ *                                          `honor_manifest: false` the
+ *                                          manifest is treated as orphan
+ *                                          and removed alongside framework
+ *                                          files.
  */
 const LEGACY = LEGACY_INSTALL_PATHS.codex;
 /**
@@ -91,7 +100,9 @@ function walkRelative(dir) {
     return out;
 }
 /**
- * Probe the codex legacy install tree at `<targetDir>/.agents/skills/`.
+ * Probe the codex legacy install tree at `<targetDir>/<LEGACY.install_root>`
+ * (currently `.codex/` after the v0.8.2 registry inversion — the v0.7/v0.8
+ * misdirect topology).
  *
  * @param {string} targetDir
  * @returns {LegacyCodexDetection}
@@ -138,25 +149,36 @@ function rmEmptyDir(dir) {
     }
 }
 /**
- * Clean up the legacy `.agents/skills/` tree if it looks orphaned.
+ * Clean up the legacy install tree at `<targetDir>/<LEGACY.install_root>`
+ * if it looks orphaned. Post v0.8.2 the codex legacy root is `.codex/`
+ * with framework files at `agents/<file>.md` + `commands/<file>.md` +
+ * `apt-file-manifest.json`.
  *
  * Branches:
  *   1. `present: false` OR `frameworkFiles.length === 0` → no-op,
  *      `{ ran: false, reason: 'no-legacy' }`.
- *   2. `hasManifest: true` → managed install, no-op,
- *      `{ ran: false, reason: 'managed' }`.
+ *   2. `hasManifest: true` AND `LEGACY.honor_manifest !== false`
+ *      (default true) → managed install, no-op,
+ *      `{ ran: false, reason: 'managed' }`. When `honor_manifest: false`
+ *      (known-dead surface like the v0.7/v0.8 codex misdirect) the
+ *      manifest is treated as orphan and removed alongside framework
+ *      files.
  *   3. Otherwise: per-file `unlinkSync` each framework-owned file;
- *      `rmdirSync` any now-empty `apt-*` subdirectory; sweep
- *      `.agents/skills/` only if it is empty; sweep `.agents/` only if
- *      its `skills/` got removed and `.agents/` is empty.
+ *      `rmdirSync` any subdirectory left empty after the unlinks (e.g.
+ *      `.codex/agents/`, `.codex/commands/`); sweep the install_root
+ *      itself only if it is fully empty after the per-file pass; sweep
+ *      the install_root's parent only if it too became empty (relevant
+ *      for legacy topologies two levels deep, e.g. the pre-0.7
+ *      `.agents/skills/` codex layout).
  *
  * Returns `{ ran: true, removed, retained, rmdirs }` on the cleanup
  * branch:
  *   - `removed`  — relative paths under `install_root` that were unlinked.
  *   - `retained` — relative paths under `install_root` that were NOT
- *     removed (user-added skills / files not in the legacy set).
- *   - `rmdirs`   — absolute paths of directories that were removed
- *     (apt-* subdirs, the install_root itself, .agents/), in removal order.
+ *     removed (user-added skills / files not in the legacy set, e.g.
+ *     `.codex/config.toml`).
+ *   - `rmdirs`   — absolute paths of directories that were removed,
+ *     in removal order.
  *
  * Atomicity: per-file unlink is non-atomic. A partial-failure scenario
  * (process killed mid-loop) is tolerable — the next `init` run will
@@ -173,7 +195,14 @@ export function runLegacyCleanup({ targetDir, dryRun = false }) {
     if (!detection.present || detection.frameworkFiles.length === 0) {
         return { ran: false, reason: 'no-legacy' };
     }
-    if (detection.hasManifest) {
+    // `honor_manifest: false` means the legacy install_root is a known-dead
+    // surface (the v0.7/v0.8 codex misdirect). A manifest sitting there is
+    // by definition stale — fall through and remove it alongside framework
+    // files. `honor_manifest: true` (default) preserves the managed-install
+    // safety for legacy roots that could legitimately re-host a managed
+    // install.
+    const honorManifest = LEGACY.honor_manifest !== false;
+    if (detection.hasManifest && honorManifest) {
         return { ran: false, reason: 'managed' };
     }
     const installRoot = join(targetDir, LEGACY.install_root);
@@ -225,12 +254,16 @@ export function runLegacyCleanup({ targetDir, dryRun = false }) {
         if (rmEmptyDir(abs))
             rmdirs.push(abs);
     }
-    // Sweep `.agents/skills/` only if fully empty after the per-file
-    // pass — preserves any user-added skill dirs.
+    // Sweep the legacy install_root only if fully empty after the per-file
+    // pass — preserves any user-added content under it (e.g. `.codex/config.toml`
+    // when LEGACY.install_root is `.codex/`).
     if (rmEmptyDir(installRoot)) {
         rmdirs.push(installRoot);
-        // Sweep `.agents/` only if it became empty too (i.e. no other
-        // `.agents/<sibling>` content the user keeps there).
+        // Sweep the install_root's parent only if it became empty too
+        // (relevant for legacy topologies whose install_root sits two
+        // levels deep, e.g. the pre-0.7 `.agents/skills/` codex layout).
+        // No-op when install_root is a top-level dir like `.codex/` —
+        // rmEmptyDir refuses to remove a non-empty project root.
         const agentsRoot = dirname(installRoot);
         if (rmEmptyDir(agentsRoot))
             rmdirs.push(agentsRoot);

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package/dist/cli/install/transforms/codex.d.mts.map

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