@aperant/framework 0.6.6 → 0.7.0

package/src/cli/commands/check-version.mjs

@@ -16,7 +16,26 @@
  *       stale_files: [{ path, reason }],
  *       update_available: false
  *     }],
- *     legacy_install: false   // true when only the old .apt-version exists
+ *     legacy_install: false,  // true when only the old .apt-version exists
+ *     // === 0.6.7 cache-merge fields (Bug 1 fix) ===
+ *     // Merged from the SessionStart worker's cache at
+ *     // ~/.cache/aperant/apt-update-check.json when fresh (< 1 h,
+ *     // schema_version=1). When stale, missing, or malformed, the same
+ *     // field names are present with null/false/0 sentinel values so
+ *     // the skill's parser stays single-shape.
+ *     //
+ *     // Note: framework.installed_version is intentionally absent.
+ *     // The live kernel version is always in the top-level
+ *     // `framework_version` field (read from package.json, never from
+ *     // the cache).
+ *     framework: {
+ *       latest_version: '0.6.7' | null
+ *     },
+ *     update_available: false,
+ *     dev_install_ahead: false,
+ *     not_published: false,
+ *     stale_files_total: 0,
+ *     lookup_error: null
  *   }
  *
  * Per-file `reason` values:
@@ -31,6 +50,7 @@ import { dirname, join, resolve } from 'node:path'
 import { fileURLToPath } from 'node:url'
 import { readManifest } from '../install/manifest.mjs'
 import { detectInstalledRuntimes } from '../install/runtime-detect.mjs'
+import { readFreshUpdateCache } from '../install/update-chips.mjs'
 import { inspectManifestFiles } from '../install/version-header.mjs'
 import { err, ok } from '../util/result.mjs'
 
@@ -56,6 +76,10 @@ function inspectRuntime(targetDir, descriptor) {
 			runtime: descriptor.id,
 			installed_version: null,
 			stale_files: [],
+			// 0.6.7 — per-runtime `update_available` is retained as `false` for
+			// backward shape compatibility with pre-0.6.7 callers. The real
+			// npm-bump signal now lives on the TOP-LEVEL `update_available`
+			// field (merged from the SessionStart worker's cache below).
 			update_available: false,
 		}
 	}
@@ -67,10 +91,14 @@ function inspectRuntime(targetDir, descriptor) {
 		runtime: descriptor.id,
 		installed_version: manifest.framework_version,
 		stale_files: stale,
+		// See note above — top-level `update_available` carries the real signal.
 		update_available: false,
 	}
 }
 
+/** Cache freshness window — 1 hour, matches the worker's CACHE_TTL_MS. */
+const CACHE_TTL_MS = 60 * 60 * 1_000
+
 /**
  * @param {string} projectDir
  */
@@ -106,6 +134,39 @@ export function cmdCheckVersion(projectDir) {
 		messageParts.push(`Skills are up to date for ${runtimes.length} runtime(s).`)
 	}
 
+	// 0.6.7 (Bug 1 fix) — merge the SessionStart worker's cache fields when
+	// the cache file is fresh (< 1 h, schema_version=1). On a stale / missing
+	// / malformed cache the same field names are emitted with null/false/0
+	// sentinel values so the skill's parser stays single-shape (ID-03).
+	//
+	// LOG-001: stale_files_total is always derived from the live per-runtime
+	// walk (totalStale). The cache value is intentionally NOT merged — it is
+	// up to 1 h old and would hide drift that occurred since the last worker
+	// run.
+	//
+	// LOG-002: installed_version always comes from the kernel's own
+	// package.json (frameworkVersion). The cache's installed_version is
+	// stale by definition and is NOT merged into the envelope. Consumers
+	// that need the live kernel version use the top-level `framework_version`
+	// field, which is identical.
+	const cacheResult = readFreshUpdateCache(CACHE_TTL_MS)
+	let latestVersion = null
+	let updateAvailable = false
+	let devInstallAhead = false
+	let notPublished = false
+	let lookupError = null
+	if (cacheResult.fresh) {
+		const c = cacheResult.cache
+		const fw = c.framework && typeof c.framework === 'object' ? c.framework : {}
+		// latest_version is semver-validated inside readFreshUpdateCache (SEC-001).
+		if (typeof fw.latest_version === 'string') latestVersion = fw.latest_version
+		if (typeof c.update_available === 'boolean') updateAvailable = c.update_available
+		if (typeof c.dev_install_ahead === 'boolean') devInstallAhead = c.dev_install_ahead
+		if (typeof c.not_published === 'boolean') notPublished = c.not_published
+		// stale_files_total intentionally NOT taken from cache (LOG-001).
+		if (typeof c.lookup_error === 'string') lookupError = c.lookup_error
+	}
+
 	return ok({
 		status,
 		command: 'check-version',
@@ -113,5 +174,16 @@ export function cmdCheckVersion(projectDir) {
 		runtimes,
 		legacy_install: legacyInstall,
 		message: messageParts.join(' '),
+		// Cache-merge fields (additive, nullable). Documented in the
+		// file-header schema comment.
+		framework: {
+			latest_version: latestVersion,
+		},
+		update_available: updateAvailable,
+		dev_install_ahead: devInstallAhead,
+		not_published: notPublished,
+		// stale_files_total: always the live sum from per-runtime walks (LOG-001).
+		stale_files_total: totalStale,
+		lookup_error: lookupError,
 	})
 }

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

@@ -16,16 +16,43 @@
  * reads the gh payload from that file instead of shelling out. The stub
  * shape is `{ checks: [...], prMetadata: {...} }` — matches the classifier
  * input contract in stop-matrix.mjs.
+ *
+ * Production seam: when `--payload-file <path>` is passed, the tick path
+ * reads the gh payload from that file. Same shape as the stub. The
+ * orchestrator skill (apt-watch-ci §3) captures `gh pr checks ...` +
+ * `gh pr view ...` into the payload file BEFORE invoking the cmd — the cmd
+ * itself never shells out to gh.
  */
 
 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
@@ -113,12 +140,14 @@ 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,
@@ -255,6 +284,21 @@ function summarize(s) {
 // ---------------------------------------------------------------------------
 
 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
 	const pr = prCheck
@@ -290,7 +334,8 @@ function doTick(root, flags) {
 			})
 		}
 
-		const payload = fetchGhPayload(pr)
+		const payloadFile = flags.get('payload-file')
+		const payload = payloadFile ? loadPayloadFile(resolve(root, payloadFile)) : fetchGhPayload(pr)
 		if (payload.error) {
 			// gh CLI not available / auth failed → infra-backoff. Don't count it,
 			// double the next-tick interval (capped at MAX_TICK_INTERVAL_MS), and reschedule.
@@ -480,10 +525,34 @@ function fetchGhPayload(_pr) {
 	// Real gh shell-out lives in the skill body. The cmd's tick treats
 	// "no stub + no payload" as infra-backoff so unit tests can exercise the
 	// path without a live gh binary. The orchestrator skill is responsible
-	// for pre-fetching and re-invoking with APT_TEST_GH_STUB set, OR for
-	// passing real data via a future --payload-file flag (out of scope here).
+	// for pre-fetching and re-invoking with APT_TEST_GH_STUB set (tests) OR
+	// `--payload-file <path>` (production — see loadPayloadFile below).
 	return {
-		error: 'gh shell-out is the skill orchestrator boundary — set APT_TEST_GH_STUB for unit tests',
+		error:
+			'gh shell-out is the skill orchestrator boundary — set APT_TEST_GH_STUB for unit tests or pass --payload-file for production',
+	}
+}
+
+/**
+ * Read a gh payload from disk for the production path (FRAMEWORK-BUG-010).
+ * Returns the same shape as fetchGhPayload's stub branch on success, or an
+ * { error } envelope on missing path / parse failure — the existing
+ * infra-backoff branch surfaces the error cleanly.
+ *
+ * @param {string} path absolute or already-resolved path
+ */
+function loadPayloadFile(path) {
+	try {
+		if (!existsSync(path)) {
+			return { error: `payload-file path not found: ${path}` }
+		}
+		const data = JSON.parse(readFileSync(path, 'utf-8'))
+		return {
+			checks: data.checks || [],
+			prMetadata: data.prMetadata || { state: 'OPEN' },
+		}
+	} catch (e) {
+		return { error: `payload-file parse error: ${e.message}` }
 	}
 }
 

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

@@ -140,7 +140,7 @@ 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/src/cli/commands/init.mjs

@@ -41,6 +41,7 @@ import {
 	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,
@@ -48,6 +49,7 @@ import {
 	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'
@@ -82,8 +84,21 @@ const TRANSFORM_LOADERS = new Map(
  * a missing runtimes flag should block (no flag, no `--yes`) or not
  * (flag passed, or `--yes`).
  *
+ * 0.6.7 — `--force-runtimes` (Bug 2 fix) bypasses the `upgrade_noop`
+ * short-circuit so `/apt:update` can re-stamp runtime manifests even
+ * when `.aperant/config.json` is at the current schema. Strictly
+ * 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 }}
+ * @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('--')))
@@ -96,12 +111,26 @@ export function parseInstallFlags(args) {
 	// C47 D-04 — opt out of the PROJECT.md auto-chain. Forwarded as
 	// `answers.skipBootstrap` into both interview paths.
 	const skipBootstrap = flagSet.has('--skip-bootstrap')
+	// 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,
@@ -326,6 +355,33 @@ function applyCollapsedClassAToMigration(
 	}
 }
 
+/**
+ * Resolve the effective runtimes list from flags, with fallback to
+ * `suggestRuntimes` and a final fallback to `['claude']`.
+ *
+ * Shared by the `nonInteractiveAnswers` upgrade path and the
+ * `--force-runtimes` synthesis block in `cmdInit` to avoid duplication.
+ *
+ * Emits a one-line stderr warning when the final fallback fires (no
+ * explicit flags and `suggestRuntimes` returned empty) so the choice is
+ * visible without breaking automated callers.
+ *
+ * @param {string} targetDir
+ * @param {ReturnType<typeof parseInstallFlags>} parsedFlags
+ * @returns {string[]}
+ */
+function selectRuntimes(targetDir, parsedFlags) {
+	if (parsedFlags.runtimes_explicit) return parsedFlags.runtimes
+	const suggested = new Set(suggestRuntimes(targetDir))
+	if (suggested.size === 0) {
+		process.stderr.write(
+			'[apt-tools] No runtime specified and config has no suggestRuntimes; defaulting to claude.\n',
+		)
+		suggested.add('claude')
+	}
+	return [...suggested]
+}
+
 /**
  * Non-TTY / scripted path — derive answers from flags + sensible defaults,
  * gated by the Class A/B classifier (spec R2 + R3).
@@ -427,9 +483,7 @@ function nonInteractiveAnswers(targetDir, canonicalRoot, archetype, parsedFlags)
 		const visibility = migration.migrated?.share?.visibility === 'team' ? 'team' : 'solo'
 		const autonomyDefault = migration.migrated?.autonomy?.default ?? 1
 		const xverify = migration.migrated?.multi_model?.cross_verification?.tools ?? []
-		const suggested = new Set(suggestRuntimes(targetDir))
-		if (suggested.size === 0) suggested.add('claude')
-		const runtimes = parsedFlags.runtimes_explicit ? parsedFlags.runtimes : [...suggested]
+		const runtimes = selectRuntimes(targetDir, parsedFlags)
 		return {
 			runtimes,
 			autonomyDefault,
@@ -599,6 +653,12 @@ async function interactiveInterview(targetDir, version, canonicalRoot, archetype
 			migration.applied_defaults.length === 0 &&
 			migration.auto_added.length === 0
 		if (noDrift) {
+			// 0.6.7 (Bug 2 fix) — `--force-runtimes` bypasses the TTY
+			// "Nothing to do." outro so the runtime walker re-stamps every
+			// manifest; cmdInit's force-runtimes synthesis path takes over.
+			if (parsedFlags.forceRuntimes) {
+				return { upgrade_noop: true, skipBootstrap, migration }
+			}
 			process.stdout.write(`\n${aperantBanner(version)}\n\n`)
 			clack.intro('install')
 			clack.note(`Already up to date — v${version}`, 'No drift')
@@ -907,6 +967,22 @@ function applyInterviewAnswers(config, answers) {
 	}
 	config.project_type =
 		answers.archetype.type === 'brownfield' ? 'unknown' : config.project_type || 'unknown'
+
+	// Onboarding marker (task 15-05-26_apt-setup-onboarding-marker-7q9c).
+	// `/apt:setup` dispatches on this marker to decide review-mode vs full
+	// Batch 1-8 flow — file existence alone cannot disambiguate "fresh seed
+	// from template" from "fully tuned by setup" because templates/config.json
+	// ships with every key populated. Only the fresh-seed branch reaches this
+	// function (finishInit:1331); the upgrade branch (finishInit:1338-1357)
+	// writes answers.migration.migrated directly and never calls
+	// applyInterviewAnswers, so legacy unmarked configs correctly stay
+	// unmarked on upgrade. --yes / --accept-new-defaults walk this same fresh
+	// path but do NOT walk Batch 1-8 questions, so completed stays false.
+	config.onboarding = {
+		completed: false,
+		seeded_from_template: true,
+		seeded_at: new Date().toISOString(),
+	}
 }
 
 /**
@@ -1061,7 +1137,13 @@ export async function cmdInit(projectDir, extraArgs = []) {
 		// idempotent — preserves PROJECT.md, refreshes sidecar from it).
 		// In TTY mode clack already rendered "Nothing to do." to stdout,
 		// so suppress the JSON envelope (matches the cancelled path).
-		if (answers?.upgrade_noop) {
+		//
+		// 0.6.7 (Bug 2 fix) — `--force-runtimes` bypasses this short-circuit
+		// so `/apt:update` can re-stamp every runtime manifest even when
+		// `.aperant/config.json` is at the current schema. We synthesize a
+		// real InstallAnswers shape from the existing config so
+		// installRuntimes + finishInit run their normal upgrade path.
+		if (answers?.upgrade_noop && !parsedFlags.forceRuntimes) {
 			if (interactiveTty) return rawText('', 0)
 			const bootstrap = answers.skipBootstrap
 				? { status: 'skipped', reason: '--skip-bootstrap flag' }
@@ -1077,7 +1159,57 @@ export async function cmdInit(projectDir, extraArgs = []) {
 			})
 		}
 
-		const results = await installRuntimes(answers.runtimes, canonicalRoot, installTarget, version)
+		// 0.6.7 (Bug 2 fix) — when forceRuntimes is set on a no-drift run,
+		// synthesize a real InstallAnswers shape from the existing config so
+		// the runtime walker re-stamps every manifest. Visibility/autonomy/
+		// cross-verification are read from answers.migration.migrated (already
+		// in memory from nonInteractiveAnswers — avoids a second config read);
+		// runtimes resolved via selectRuntimes helper shared with the upgrade path.
+		let effectiveAnswers = answers
+		if (answers?.upgrade_noop && parsedFlags.forceRuntimes) {
+			const existing = answers.migration?.migrated || {}
+			const runtimes = selectRuntimes(installTarget, parsedFlags)
+			effectiveAnswers = {
+				runtimes,
+				autonomyDefault: existing?.autonomy?.default ?? 1,
+				visibility: existing?.share?.visibility === 'team' ? 'team' : 'solo',
+				crossVerificationTools: existing?.multi_model?.cross_verification?.tools ?? [],
+				scanNow: false,
+				skipBootstrap: answers.skipBootstrap,
+				archetype: detectArchetype(installTarget),
+				agent_runtime: detectAgentRuntime(),
+				applied_defaults: [],
+				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
@@ -1089,14 +1221,21 @@ export async function cmdInit(projectDir, extraArgs = []) {
 			installTarget,
 			canonicalRoot,
 			version,
-			answers.runtimes,
+			effectiveAnswers.runtimes,
 			results,
-			answers,
+			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(answers, results, version, kernelResult)
+			await renderOutro(effectiveAnswers, results, version, kernelResult)
 			// TTY mode: envelope was persisted to disk + suppressed from stdout
 			// because the clack outro already rendered the user-facing summary.
 			// Return the rawText shape with empty payload so wrap() routes us
@@ -1273,6 +1412,19 @@ 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,
@@ -1284,6 +1436,8 @@ function finishInit(
 	answers,
 	suppressStdout = false,
 	kernelResult = null,
+	forceOverwriteCatalog = false,
+	legacyCleanup = null,
 ) {
 	writeLastInstallSummary(targetDir, runtimeResults, version)
 
@@ -1414,7 +1568,40 @@ function finishInit(
 	if (existsSync(claudeMdPath)) instructionFile = claudeMdPath
 	else if (existsSync(agentsMdPath)) 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
@@ -1525,6 +1712,11 @@ function finishInit(
 					...(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) {