@aperant/framework 0.6.7 → 0.7.0

package/CHANGELOG.md

@@ -5,6 +5,66 @@ All notable changes to `@aperant/framework` are documented here. See
 
 ## [Unreleased]
 
+## 0.7.0 — 2026-05-17 — install/discovery/ship pipeline hardening (8-bug bundle)
+
+This release ships the 7.0 bug bundle: 8 framework defects discovered during the 0.6.6→0.6.7 self-upgrade pipeline (FRAMEWORK-BUG-017 through -024). Each fix was independently verified by Codex/GPT-5 review before implementation. -021 and -022 bundled atomically per Codex recommendation.
+
+### Highlights
+
+- **`/apt:update` reliability** (-017): in-band drift detection in `apt-tools route` synthesizes the `update_check` chip when the workspace source is ahead of `.aperant/deps/`; new `requireMinVersion` helper for cmd preflight as a future-guard for new flags; `apt:update --from-source` skill flag for monorepo self-host case.
+- **`/apt:ship` honesty** (-018): CI watcher banner now distinguishes state-recording from wake-registration. New four-way branch in §7.2 reads `scheduler_handle`; when null, emits explicit next-action instruction (`Register a wake-up: CronCreate every ~3min running '/apt:watch-ci --tick --pr {N}'`). Applied to both primary and ask-deferred paths.
+- **`/apt:watch-ci` worktree safety** (-019): auto-merge unconditionally forbids `gh pr merge --delete-branch` from the worktree-rooted watcher (the flag tries to `git switch <base>` in the cwd, which fails when base is checked out in the primary worktree). Local branch + worktree cleanup remains `/apt:close-task`'s job via existing `computeWorktreeCleanup` (best-effort with named failure modes).
+- **`task close-merged --narrate-only`** (-020): the flag was documented as SKILL-level but `parseFlags` parsed it generically and the cmd silently dropped it. Now wired as a CLI flag — read-only enumeration of `pending_narration[]` returning one entry per row in `closed[]` with `narration_pending: true`. SKILL.md §4 calls this before iterating per-row drain via the existing `narration-drain` primitive. At-least-once retry safe (verified narrator idempotence in `apt-team-docs-narrator`).
+- **Install/discovery surface** (-021 + -022, bundled): `init` now detects + removes the legacy `.agents/skills/` codex tree per file against a shared `LEGACY_INSTALL_PATHS` constant (user-added skills preserved). Opt-out via `--keep-legacy`. New `legacy_cleanup` envelope field. **Health-check unified with check-version**: `readSkillInstallState` is now manifest-aware (`apt-file-manifest.json` precedence over `.apt-version` legacy fallback). Malformed manifests surface as stale (not silently healthy). `host` field stays `'claude-code'` for backward compat; new `runtime` field exposes descriptor id.
+- **CLAUDE.md catalog generator** (-023): the hardcoded `APT_SECTION` constant in `copy.mjs` is gone. The section is built from `discoverSkills` (filesystem source of truth — same helper the router uses). Hand-curated sub-sections (Fast Path Guarantee, Discoverability, Feature Registry, Config) live in `templates/aperant-claude-md-appendix.md`. Foreign-row defensive check with `--force-overwrite-catalog` escape hatch (exit-2 on foreign rows). **Breaking for unattended upgrades:** unattended `init` flows on projects with custom CLAUDE.md rows must pass `--force-overwrite-catalog`.
+- **`/apt:spar` partner transport ladder** (-024): replaced single-transport gate (`codex-companion.mjs` only) with 3-rung ladder: MCP tool → plugin shim → raw CLI. MCP-first per user preference with 60s timeout + automatic fallthrough to next rung on hang. Symmetric for codex/claude/gemini. `host-detect` extended additively with `host.partner_transports`. Raw codex invocation is `codex exec` (precedent from `apt-pr-review`).
+
+### Spec-gaps cross-reference
+
+All 8 entries at `docs/frameworks/spec-gaps.md#framework-bug-017-installed-deps-drift` through `#framework-bug-024-spar-partner-transport-too-narrow`. Each entry includes the Codex review verdict that drove the implementation choices.
+
+### Commits
+
+- `cac1db9c` BUG-017 — deps drift detection
+- `3d9b1a2f` BUG-019 — forbid `gh pr merge --delete-branch`
+- `cdd24c79` BUG-024 — apt:spar 3-rung partner transport ladder
+- `a21c7d32` BUG-023 — CLAUDE.md APT_SECTION generator + appendix
+- `bf51f438` BUG-023 — typecheck fix
+- `42251bd2` BUG-021+022 — codex legacy cleanup + health-check manifest-aware
+- `256edc11` BUG-018 — apt:ship CI watcher banner honesty
+- `8a74b0f9` BUG-020 — task close-merged --narrate-only
+
+### FRAMEWORK-BUG-023 — CLAUDE.md catalog generator (no more stale `APT_SECTION`)
+
+`apt-tools init` previously regenerated the `## Aperant Framework` block
+in `CLAUDE.md` / `AGENTS.md` from a hardcoded 19-row constant in
+`src/cli/util/copy.mjs`, silently dropping the 18 skills added after the
+constant was last hand-edited. The constant is gone; the section is now
+built from `discoverSkills` (filesystem source of truth — same helper
+the router uses at runtime), and the hand-curated sub-sections (Fast
+Path Guarantee, Discoverability, Feature Registry, Config) live in a
+template file at `templates/aperant-claude-md-appendix.md`.
+
+- **NEW** `src/cli/util/aperant-section.mjs` — `buildAptSection({...})`
+  emits the wrapped section. Skills are filtered to `user_invocable &&
+  !internal`, sorted with the bare `apt` router first then ASCII by
+  name, and pipe characters in descriptions are escaped (`apt:triage`
+  is a live case).
+- **NEW** `templates/aperant-claude-md-appendix.md` — hand-curated
+  sub-sections, read verbatim by the generator. Editing this file is a
+  normal docs PR with no `.mjs` rebuild.
+- **NEW** `--force-overwrite-catalog` flag on `apt-tools init`.
+  **Breaking for unattended upgrades:** if the on-disk CLAUDE.md /
+  AGENTS.md contains row IDs the generator does NOT produce ("foreign
+  rows"), init now exits 2 with the structured envelope
+  `{ code: 'instruction-file.foreign-rows', foreignRowIds: [...] }`
+  instead of silently clobbering. Re-run with
+  `--force-overwrite-catalog` to regenerate anyway, or remove the
+  foreign rows manually. Greenfield installs and brownfield installs
+  with NO foreign rows are unaffected.
+
+
+
 ### persona-aware release-notes system (task persona-aware-changelog-and-release-note_16-05-26)
 
 Two-skill split: `/apt:docs changelog` keeps the dev-flavored

package/dist/cli/commands/ci-watch.d.mts.map

@@ -1 +1 @@
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+{"version":3,"file":"ci-watch.d.mts","sourceRoot":"","sources":["../../../src/cli/commands/ci-watch.mjs"],"names":[],"mappings":"AAyFA;;;;GAIG;AACH,uCAJW,MAAM,cACN,MAAM,aACN,MAAM,EAAE,8CAyBlB"}

package/dist/cli/commands/ci-watch.mjs

@@ -25,12 +25,33 @@
  */
 import { randomBytes } from 'node:crypto';
 import { existsSync, readFileSync } from 'node:fs';
-import { resolve } from 'node:path';
+import { dirname, resolve } from 'node:path';
+import { fileURLToPath } from 'node:url';
 import { acquireLock, releaseLock } from '../ci-watch/lock.mjs';
 import { deleteState, listWatches, readState, writeState } from '../ci-watch/state.mjs';
 import { classify, isFailing } from '../ci-watch/stop-matrix.mjs';
 import { parseFlags } from '../util/args.mjs';
 import { err, exitWith, ok } from '../util/result.mjs';
+import { requireMinVersion } from '../util/version-preflight.mjs';
+/**
+ * Installed kernel version — read once at module scope, same pattern as
+ * commands/check-version.mjs:108-109. Used by the version-preflight in
+ * `doTick` to fail loud (instead of infra-backoff-loop) when a future
+ * framework fix introduces a new tick flag and the user is on a stale
+ * install. See FRAMEWORK-BUG-017 rung 2 + the helper docstring for the
+ * "future-guard" framing.
+ */
+const INSTALLED_KERNEL_VERSION = (() => {
+    try {
+        const here = dirname(fileURLToPath(import.meta.url));
+        const pkgPath = resolve(here, '..', '..', '..', 'package.json');
+        const pkg = JSON.parse(readFileSync(pkgPath, 'utf-8'));
+        return typeof pkg?.version === 'string' ? pkg.version : null;
+    }
+    catch {
+        return null;
+    }
+})();
 const DEFAULT_TICK_INTERVAL_MS = 300_000; // 5 minutes
 const MAX_TICK_INTERVAL_MS = 30 * 60 * 1000; // 30 min
 const WALL_BUDGET_MS = 4 * 60 * 60 * 1000; // 4 hours
@@ -110,12 +131,14 @@ function doStart(root, flags) {
             command: 'ci-watch-start',
             pr: Number(pr),
             reason: 'already-armed',
+            scheduler_handle: existingState.scheduler_handle ?? null,
             existing: {
                 task_id: existingState.task_id,
                 host: existingState.host,
                 attempts: existingState.attempts,
                 started_at: existingState.started_at,
                 deadline: existingState.deadline,
+                scheduler_handle: existingState.scheduler_handle ?? null,
             },
         }, 2);
     }
@@ -238,6 +261,21 @@ function summarize(s) {
 // tick
 // ---------------------------------------------------------------------------
 function doTick(root, flags) {
+    // FRAMEWORK-BUG-017 rung 2 (future-guard): emit a structured
+    // version_drift envelope when a future framework fix requires a
+    // new tick flag and the installed kernel predates it. The current
+    // pin to 0.6.7 (the version that introduced --payload-file) is a
+    // no-op on every 0.6.7+ install — but the scaffolding is in place
+    // for the NEXT new-flag fix to bump `introducedIn` without
+    // re-discovering the silent-infra-backoff failure mode.
+    const versionGate = requireMinVersion({
+        feature: 'payload-file',
+        introducedIn: '0.6.7',
+        installedVersion: INSTALLED_KERNEL_VERSION,
+        missingFlag: '--payload-file',
+    });
+    if (versionGate)
+        return exitWith(versionGate, 1);
     const prCheck = validatePr(flags.get('pr'));
     if (typeof prCheck !== 'string')
         return prCheck;

package/dist/cli/commands/ci-watch.mjs.map

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package/dist/cli/commands/health-check.mjs

@@ -135,7 +135,7 @@ export function cmdHealthCheck(projectDir) {
             issues.push({
                 type: 'missing-skills',
                 severity: 'warning',
-                detail: 'No installed skill version stamps found under .claude/skills or .agents/skills',
+                detail: 'No apt install manifests or version stamps found for any supported runtime',
                 install_surfaces: installs,
             });
         }

package/dist/cli/commands/health-check.mjs.map

@@ -1 +1 @@
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package/dist/cli/commands/init.d.mts

@@ -21,8 +21,15 @@
  * additive: callers without the flag still get the no-op short-circuit
  * (preserves `init-upgrade-drift.test.ts` case (a)).
  *
+ * 0.7.0 — `--force-overwrite-catalog` (FRAMEWORK-BUG-023) bypasses the
+ * foreign-row defensive check in `injectInstructionFile`. Power-user
+ * flag only — no interview prompt. Without it, an instruction file
+ * carrying rows the generator didn't produce causes init to exit 2 with
+ * `code: 'instruction-file.foreign-rows'` so unattended upgrade flows
+ * surface the would-be data loss instead of silently clobbering it.
+ *
  * @param {string[]} args
- * @returns {{ runtimes: string[], runtimes_explicit: boolean, target: string|null, interactive: boolean, skipBootstrap: boolean, visibility?: 'solo'|'team', autonomy?: 0|1|2|3, accept_new_defaults: boolean, yes: boolean, forceRuntimes: boolean }}
+ * @returns {{ runtimes: string[], runtimes_explicit: boolean, target: string|null, interactive: boolean, skipBootstrap: boolean, visibility?: 'solo'|'team', autonomy?: 0|1|2|3, accept_new_defaults: boolean, yes: boolean, forceRuntimes: boolean, forceOverwriteCatalog: boolean, keepLegacy: boolean }}
  */
 export function parseInstallFlags(args: string[]): {
     runtimes: string[];
@@ -35,6 +42,8 @@ export function parseInstallFlags(args: string[]): {
     accept_new_defaults: boolean;
     yes: boolean;
     forceRuntimes: boolean;
+    forceOverwriteCatalog: boolean;
+    keepLegacy: boolean;
 };
 /**
  * Main entry — invoked from bin/apt-tools.mjs.

package/dist/cli/commands/init.d.mts.map

@@ -1 +1 @@
-{"version":3,"file":"init.d.mts","sourceRoot":"","sources":["../../../src/cli/commands/init.mjs"],"names":[],"mappings":"AAmEA;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AACH,wCAHW,MAAM,EAAE,GACN;IAAE,QAAQ,EAAE,MAAM,EAAE,CAAC;IAAC,iBAAiB,EAAE,OAAO,CAAC;IAAC,MAAM,EAAE,MAAM,GAAC,IAAI,CAAC;IAAC,WAAW,EAAE,OAAO,CAAC;IAAC,aAAa,EAAE,OAAO,CAAC;IAAC,UAAU,CAAC,EAAE,MAAM,GAAC,MAAM,CAAC;IAAC,QAAQ,CAAC,EAAE,CAAC,GAAC,CAAC,GAAC,CAAC,GAAC,CAAC,CAAC;IAAC,mBAAmB,EAAE,OAAO,CAAC;IAAC,GAAG,EAAE,OAAO,CAAC;IAAC,aAAa,EAAE,OAAO,CAAA;CAAE,CAoDrP;AA23BD;;;;;;GAMG;AACH,oCAJW,MAAM,cACN,MAAM,EAAE,GACN,OAAO,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,CAoK3D;;;;;cAhiCa,MAAM,EAAE;;;;qBACR,CAAC,GAAC,CAAC,GAAC,CAAC,GAAC,CAAC;;;;gBACP,MAAM,GAAC,MAAM;;;;4BACb,MAAM,EAAE;;;;aACR,OAAO;;;;mBACP,OAAO;eACP,OAAO,0BAA0B,EAAE,eAAe;;;;;;;;;aAErC,MAAM;eAAS,OAAO;cAAQ,MAAM;iBAAW,MAAM;;;;;;aAErD,MAAM;eAAS,OAAO;gBAAU,MAAM;;;;;;kBAEvC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC;0BAAoB,OAAO,EAAE;2BAAqB,OAAO,EAAE;oBAAc,OAAO,EAAE"}
+{"version":3,"file":"init.d.mts","sourceRoot":"","sources":["../../../src/cli/commands/init.mjs"],"names":[],"mappings":"AAqEA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgCG;AACH,wCAHW,MAAM,EAAE,GACN;IAAE,QAAQ,EAAE,MAAM,EAAE,CAAC;IAAC,iBAAiB,EAAE,OAAO,CAAC;IAAC,MAAM,EAAE,MAAM,GAAC,IAAI,CAAC;IAAC,WAAW,EAAE,OAAO,CAAC;IAAC,aAAa,EAAE,OAAO,CAAC;IAAC,UAAU,CAAC,EAAE,MAAM,GAAC,MAAM,CAAC;IAAC,QAAQ,CAAC,EAAE,CAAC,GAAC,CAAC,GAAC,CAAC,GAAC,CAAC,CAAC;IAAC,mBAAmB,EAAE,OAAO,CAAC;IAAC,GAAG,EAAE,OAAO,CAAC;IAAC,aAAa,EAAE,OAAO,CAAC;IAAC,qBAAqB,EAAE,OAAO,CAAC;IAAC,UAAU,EAAE,OAAO,CAAA;CAAE,CA8D1S;AA23BD;;;;;;GAMG;AACH,oCAJW,MAAM,cACN,MAAM,EAAE,GACN,OAAO,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,CAgM3D;;;;;cA5jCa,MAAM,EAAE;;;;qBACR,CAAC,GAAC,CAAC,GAAC,CAAC,GAAC,CAAC;;;;gBACP,MAAM,GAAC,MAAM;;;;4BACb,MAAM,EAAE;;;;aACR,OAAO;;;;mBACP,OAAO;eACP,OAAO,0BAA0B,EAAE,eAAe;;;;;;;;;aAErC,MAAM;eAAS,OAAO;cAAQ,MAAM;iBAAW,MAAM;;;;;;aAErD,MAAM;eAAS,OAAO;gBAAU,MAAM;;;;;;kBAEvC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC;0BAAoB,OAAO,EAAE;2BAAqB,OAAO,EAAE;oBAAc,OAAO,EAAE"}

package/dist/cli/commands/init.mjs

@@ -29,8 +29,10 @@ import { detectArchetype } from '../install/archetype.mjs';
 import { installKernel } from '../install/install-kernel.mjs';
 import { discoverCanonicalFiles, runInstall, writeLastInstallSummary, } from '../install/pipeline.mjs';
 import { RUNTIMES, suggestRuntimes } from '../install/runtime-detect.mjs';
+import { runLegacyCleanup } from '../install/runtime-migrate.mjs';
 import { CLASS_A_SETTINGS, CLASS_B_SETTINGS, findClassDescriptor, parseClassFlags, } from '../install/setting-class.mjs';
 import { detectAgentRuntime } from '../util/agent-runtime.mjs';
+import { buildAptSection } from '../util/aperant-section.mjs';
 import { atomicWriteJson } from '../util/atomic-write.mjs';
 import { aperantBanner } from '../util/banner.mjs';
 import { copyDirRecursive, injectInstructionFile } from '../util/copy.mjs';
@@ -66,8 +68,15 @@ const TRANSFORM_LOADERS = new Map(RUNTIMES.map((r) => [r.id, () => import(`../in
  * additive: callers without the flag still get the no-op short-circuit
  * (preserves `init-upgrade-drift.test.ts` case (a)).
  *
+ * 0.7.0 — `--force-overwrite-catalog` (FRAMEWORK-BUG-023) bypasses the
+ * foreign-row defensive check in `injectInstructionFile`. Power-user
+ * flag only — no interview prompt. Without it, an instruction file
+ * carrying rows the generator didn't produce causes init to exit 2 with
+ * `code: 'instruction-file.foreign-rows'` so unattended upgrade flows
+ * surface the would-be data loss instead of silently clobbering it.
+ *
  * @param {string[]} args
- * @returns {{ runtimes: string[], runtimes_explicit: boolean, target: string|null, interactive: boolean, skipBootstrap: boolean, visibility?: 'solo'|'team', autonomy?: 0|1|2|3, accept_new_defaults: boolean, yes: boolean, forceRuntimes: boolean }}
+ * @returns {{ runtimes: string[], runtimes_explicit: boolean, target: string|null, interactive: boolean, skipBootstrap: boolean, visibility?: 'solo'|'team', autonomy?: 0|1|2|3, accept_new_defaults: boolean, yes: boolean, forceRuntimes: boolean, forceOverwriteCatalog: boolean, keepLegacy: boolean }}
  */
 export function parseInstallFlags(args) {
     const flagSet = new Set(args.filter((a) => a.startsWith('--')));
@@ -83,11 +92,21 @@ export function parseInstallFlags(args) {
     // 0.6.7 (Bug 2 fix) — opt-in bypass of the upgrade_noop short-circuit
     // so /apt:update can re-stamp runtime files on a no-drift upgrade.
     const forceRuntimes = flagSet.has('--force-runtimes');
+    // 0.7.0 (FRAMEWORK-BUG-023) — opt-in bypass of the foreign-row check
+    // in injectInstructionFile. Power-user flag only.
+    const forceOverwriteCatalog = flagSet.has('--force-overwrite-catalog');
+    // 0.7.0 (FRAMEWORK-BUG-021) — opt out of the codex legacy-tree cleanup
+    // that fires when `codex` is in the runtime set. Defaults to false so
+    // the cleanup runs by default; pass `--keep-legacy` to preserve the
+    // orphaned `.agents/skills/` tree on upgrades.
+    const keepLegacy = flagSet.has('--keep-legacy');
     const classFlags = parseClassFlags(args);
     const base = {
         target,
         skipBootstrap,
         forceRuntimes,
+        forceOverwriteCatalog,
+        keepLegacy,
         visibility: classFlags.visibility,
         autonomy: classFlags.autonomy,
         accept_new_defaults: classFlags.accept_new_defaults,
@@ -1066,12 +1085,36 @@ export async function cmdInit(projectDir, extraArgs = []) {
                 explicit_inputs: collectExplicitInputs(parsedFlags),
             };
         }
+        // FRAMEWORK-BUG-021 — sweep the legacy `.agents/skills/` codex tree
+        // BEFORE the install pipeline runs so the install can re-stamp
+        // `.codex/` against a clean slate. Only fires when codex is in the
+        // requested runtime set and `--keep-legacy` was not passed; the
+        // helper itself is conservative (no-op on managed installs, no-op
+        // when no legacy framework files are present).
+        let legacyCleanup = null;
+        if (effectiveAnswers.runtimes.includes('codex')) {
+            if (parsedFlags.keepLegacy) {
+                legacyCleanup = { runtime: 'codex', ran: false, reason: '--keep-legacy' };
+            }
+            else {
+                const cleanup = runLegacyCleanup({ targetDir: installTarget });
+                legacyCleanup = { runtime: 'codex', ...cleanup };
+                if (cleanup.ran && cleanup.retained.length > 0) {
+                    process.stderr.write(`[apt-tools] legacy_cleanup retained ${cleanup.retained.length} user-added path(s) under .agents/skills/: ${cleanup.retained.join(', ')}\n`);
+                }
+            }
+        }
         const results = await installRuntimes(effectiveAnswers.runtimes, canonicalRoot, installTarget, version);
         // Provision the project-local kernel BEFORE finishInit runs its JSON
         // output — that way the "structure" summary can reflect the kernel
         // path. We show a spinner in TTY mode because npm install is slow.
         const kernelResult = await runKernelInstall(installTarget, version, interactiveTty);
-        const envelope = finishInit(targetDir, installTarget, canonicalRoot, version, effectiveAnswers.runtimes, results, effectiveAnswers, interactiveTty, kernelResult);
+        const envelope = finishInit(targetDir, installTarget, canonicalRoot, version, effectiveAnswers.runtimes, results, effectiveAnswers, interactiveTty, kernelResult, parsedFlags.forceOverwriteCatalog === true, legacyCleanup);
+        // FRAMEWORK-BUG-023 — finishInit signals the foreign-row defensive
+        // abort by returning an early-exit sentinel envelope.
+        if (envelope?.__earlyExit) {
+            return envelope.__earlyExit;
+        }
         if (interactiveTty) {
             await renderOutro(effectiveAnswers, results, version, kernelResult);
             // TTY mode: envelope was persisted to disk + suppressed from stdout
@@ -1237,8 +1280,21 @@ async function renderOutro(answers, results, version, kernelResult) {
  *                                         deps/` — surfaced in the envelope so
  *                                         downstream tooling can detect a
  *                                         degraded install.
+ * @param {boolean} [forceOverwriteCatalog=false]
+ *                                         FRAMEWORK-BUG-023 — bypass the
+ *                                         foreign-row check in
+ *                                         injectInstructionFile when the user
+ *                                         explicitly opted in via
+ *                                         --force-overwrite-catalog.
+ * @param {object|null} [legacyCleanup=null]
+ *                                         FRAMEWORK-BUG-021 — outcome of the
+ *                                         codex `.agents/skills/` cleanup
+ *                                         step. `null` when codex was not in
+ *                                         the runtime set; otherwise the
+ *                                         shape `{ runtime, ran, … }` from
+ *                                         `runLegacyCleanup`.
  */
-function finishInit(targetDir, installTarget, canonicalRoot, version, chosenIds, runtimeResults, answers, suppressStdout = false, kernelResult = null) {
+function finishInit(targetDir, installTarget, canonicalRoot, version, chosenIds, runtimeResults, answers, suppressStdout = false, kernelResult = null, forceOverwriteCatalog = false, legacyCleanup = null) {
     writeLastInstallSummary(targetDir, runtimeResults, version);
     const aperantDir = join(targetDir, '.aperant');
     mkdirSync(join(aperantDir, 'proof'), { recursive: true });
@@ -1353,7 +1409,36 @@ function finishInit(targetDir, installTarget, canonicalRoot, version, chosenIds,
         instructionFile = agentsMdPath;
     else
         instructionFile = claudeMdPath;
-    const injectionResult = injectInstructionFile(instructionFile);
+    // FRAMEWORK-BUG-023 — generate the section from discoverSkills before
+    // handing it to the writer. The writer also runs a foreign-row defensive
+    // check; if rows present in the file aren't in the generated set we
+    // signal exit-2 via the __earlyExit sentinel so cmdInit can route the
+    // envelope through exitWith() without writing a malformed install.
+    const aptSection = buildAptSection({
+        canonicalRoot,
+        targetDir,
+        cli: detectAgentRuntime(),
+    });
+    const injectionOutcome = injectInstructionFile(instructionFile, {
+        aptSection,
+        force: forceOverwriteCatalog,
+    });
+    if (injectionOutcome.status === 'aborted-foreign-rows') {
+        return {
+            __earlyExit: exitWith({
+                ok: false,
+                status: 'error',
+                command: 'init',
+                code: 'instruction-file.foreign-rows',
+                message: `${basename(instructionFile)} contains skill rows not present in the installed framework: ` +
+                    `${injectionOutcome.foreignRowIds.join(', ')}. ` +
+                    'Re-run with --force-overwrite-catalog to regenerate anyway, or remove the foreign rows manually.',
+                foreignRowIds: injectionOutcome.foreignRowIds,
+                instructionFile: basename(instructionFile),
+            }, 2),
+        };
+    }
+    const injectionResult = injectionOutcome.status;
     const installedClaude = chosenIds.includes('claude') || existsSync(join(targetDir, '.claude'));
     const precompactResult = installedClaude
         ? installPrecompactHook(targetDir)
@@ -1456,6 +1541,11 @@ function finishInit(targetDir, installTarget, canonicalRoot, version, chosenIds,
                 ...(kernelResult.reason ? { reason: kernelResult.reason } : {}),
             }
             : null,
+        // FRAMEWORK-BUG-021 — always-present envelope field. `null` when
+        // codex was not in the runtime set; otherwise the cleanup outcome
+        // (uses `{ ran: false, reason }` for every skip case so parsers
+        // see a uniform shape).
+        legacy_cleanup: legacyCleanup,
     };
     if (suppressStdout) {
         // Interactive TTY path — persist the envelope to disk for tooling and