@cleocode/core 2026.9.16 → 2026.9.17

package/dist/store/exodus/on-open.js

@@ -62,8 +62,9 @@
  * @see packages/core/src/store/exodus/verify-migration.ts — verifyMigration parity gate (T11551)
  * @see packages/core/src/store/dual-scope-db.ts — the open chokepoint that calls this
  */
-import { existsSync } from 'node:fs';
-import { resolve } from 'node:path';
+import { existsSync, mkdtempSync, rmSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { join, resolve } from 'node:path';
 import { getLogger } from '../../logger.js';
 import { withLock } from '../lock.js';
 import { archiveMigratedSources, hasExodusCompleteMarker } from './archive.js';
@@ -77,6 +78,43 @@ const log = getLogger('exodus-on-open');
  * migration is already in flight.
  */
 let _exodusInProgress = false;
+/**
+ * Stores an explicit `cleo doctor superseded-store --reconcile` is working on
+ * in this process, by resolved path (T12355). exodus-on-open must never fire
+ * for such a store mid-reconcile: it would migrate and ARCHIVE the very legacy
+ * files the reconcile already planned to read ("unable to open database
+ * …/.cleo/tasks.db", found by the v2026.9.17 Stage A gate with
+ * CLEO_DISABLE_EXODUS_ON_OPEN unset). Scoped to the store and the reconcile's
+ * lifetime — never the env var, never other stores.
+ */
+const _reconcileInProgress = new Map();
+/**
+ * Run `fn` with exodus-on-open suppressed for the store at `dbPath`.
+ *
+ * Whichever runs first, the two converge: if on-open already migrated (and
+ * archived) the legacy files, the reconcile finds no legacy source and reports
+ * nothing to do; if the reconcile ran first, the store is populated and on-open
+ * skips it. Both place every row in the table the runtime reads.
+ *
+ * @param dbPath - The project `cleo.db` being reconciled.
+ * @param fn - The reconcile.
+ * @returns `fn`'s result.
+ * @task T12355
+ */
+export async function withExodusOnOpenSuppressed(dbPath, fn) {
+    const key = resolve(dbPath);
+    _reconcileInProgress.set(key, (_reconcileInProgress.get(key) ?? 0) + 1);
+    try {
+        return await fn();
+    }
+    finally {
+        const left = (_reconcileInProgress.get(key) ?? 1) - 1;
+        if (left <= 0)
+            _reconcileInProgress.delete(key);
+        else
+            _reconcileInProgress.set(key, left);
+    }
+}
 /**
  * Opt-out env flag. Set `CLEO_DISABLE_EXODUS_ON_OPEN=1` to skip the lazy
  * auto-migration entirely (e.g. for tooling that intentionally inspects an
@@ -115,6 +153,32 @@ function safeRowCount(nativeDb, table) {
 function consolidatedIsEmpty(nativeDb, scope) {
     return safeRowCount(nativeDb, baseTableForScope(scope)) === 0;
 }
+/** Stranding warnings already emitted this process, keyed by target path. */
+const _strandedWarned = new Set();
+/** Log a stranded-data warning once per target per process (every open would repeat it). */
+function warnStrandedOnce(dbPath, reason) {
+    if (_strandedWarned.has(dbPath))
+        return;
+    _strandedWarned.add(dbPath);
+    log.warn({ dbPath }, `exodus-on-open: STRANDED LEGACY DATA — ${reason}`);
+}
+/** The supported remedy for a stranded scope. */
+function remedyFor(scope) {
+    return scope === 'project'
+        ? 'Run `cleo doctor superseded-store --reconcile --dry-run`, then `--reconcile`, to copy it in.'
+        : 'Run `cleo doctor exodus-health` and `cleo exodus migrate` to consolidate it.';
+}
+/**
+ * Names of this scope's legacy sources that still hold copyable rows. Only
+ * called once the consolidated store is known to be empty.
+ */
+async function strandedLegacySources(scope, cwd) {
+    const { buildExodusPlan, legacySourcesHoldRows } = await import('./index.js');
+    return buildExodusPlan(cwd)
+        .sources.filter((s) => s.targetScope === scope && existsSync(s.path))
+        .filter((s) => legacySourcesHoldRows([s]))
+        .map((s) => s.name);
+}
 /** Recover only the inserted resources recorded by this staging operation. */
 async function rollbackBothScopes(plan) {
     const { getDualScopeNativeDb, openDualScopeDbAtPath } = await import('../dual-scope-db.js');
@@ -293,20 +357,50 @@ async function runExodusOnOpen(scope, dbPath, nativeDb, cwd) {
     if (_exodusInProgress) {
         return { outcome: 'skipped', reason: 're-entrant open during active migration' };
     }
-    if (isDisabledByEnv()) {
-        return { outcome: 'skipped', reason: 'CLEO_DISABLE_EXODUS_ON_OPEN set' };
+    if (_reconcileInProgress.has(resolve(dbPath))) {
+        return {
+            outcome: 'skipped',
+            reason: 'an explicit superseded-store reconcile of this store is in progress',
+        };
     }
     // Fast path (unlocked): if the consolidated DB already has data, nothing to do.
     // This makes the second-open case a cheap COUNT(*) with no lock acquisition.
     if (!consolidatedIsEmpty(nativeDb, scope)) {
         return { outcome: 'skipped', reason: 'consolidated cleo.db already populated' };
     }
+    // Kill-switch (T12319): honoured, but never SILENTLY. Exported machine-wide
+    // as an incident stopgap on 2026-06-04, it left ~21 projects running on an
+    // empty cleo.db while their legacy stores held every task — and nothing said
+    // so. Skip as asked, but when the skip strands real rows, say so loudly.
+    if (isDisabledByEnv()) {
+        const stranded = await strandedLegacySources(scope, cwd);
+        if (stranded.length === 0) {
+            return { outcome: 'skipped', reason: 'CLEO_DISABLE_EXODUS_ON_OPEN set' };
+        }
+        const reason = `CLEO_DISABLE_EXODUS_ON_OPEN set while the consolidated ${scope} cleo.db is EMPTY and ` +
+            `legacy ${stranded.join(', ')} still hold rows — CLEO is running WITHOUT that data. ` +
+            remedyFor(scope);
+        warnStrandedOnce(dbPath, reason);
+        return { outcome: 'skipped', reason };
+    }
     // Completion-marker gate (T11777): once this scope's cutover is recorded, the
     // migration has already happened and the legacy sources have been archived.
     // Gate on the committed MARKER rather than (only) the source-file existsSync,
     // so a re-appearing or stranded legacy DB can NEVER re-arm exodus-on-open even
     // if the consolidated base table momentarily reads empty (DHQ-052 · T11662).
+    //
+    // T12319: the marker must never HIDE data, though. An empty consolidated
+    // store beside legacy files that still hold rows contradicts the marker's own
+    // claim, so this is an abort (writes refuse via `assertWriteDurable`), not a
+    // skip — re-arming stays forbidden, and the operator gets the explicit remedy.
     if (hasExodusCompleteMarker(scope, cwd, dbPath, nativeDb)) {
+        const stranded = await strandedLegacySources(scope, cwd);
+        if (stranded.length > 0) {
+            const reason = `exodus completion marker claims the ${scope} scope migrated, but its cleo.db is EMPTY ` +
+                `while legacy ${stranded.join(', ')} still hold rows. ${remedyFor(scope)}`;
+            warnStrandedOnce(dbPath, reason);
+            return { outcome: 'aborted', reason };
+        }
         return {
             outcome: 'skipped',
             reason: 'exodus completion marker present — scope already migrated (cutover sealed)',
@@ -352,9 +446,23 @@ async function runExodusOnOpen(scope, dbPath, nativeDb, cwd) {
             sources: plan.sources.filter((s) => existsSync(s.path)).map((s) => s.name),
         }, 'exodus-on-open: consolidated cleo.db is empty and legacy data present — auto-migrating');
         _exodusInProgress = true;
+        const bareScratch = mkdtempSync(join(tmpdir(), 'cleo-exodus-bare-'));
         try {
             // 1. Run the migration engine (copies BOTH scopes; idempotent + journaled).
-            const migrateResult = await runExodusMigrate(plan, false, (msg) => log.debug({ scope }, `exodus-on-open: ${msg}`));
+            // T12355: land every row where the RUNTIME reads it — the same targets
+            // `cleo doctor superseded-store --reconcile` uses — creating the
+            // runtime-bound tables first, since several exist only once the
+            // tasks-domain lineage has run.
+            const { buildRuntimeTargetResolver } = await import('./runtime-targets.js');
+            const resolveTarget = await buildRuntimeTargetResolver();
+            // The same unmigrated-bare-family source the reconcile reads, so the two
+            // converge whichever runs first. Never archived: it is not a legacy file.
+            const { unmigratedBareSources } = await import('./reconcile.js');
+            const bare = scope === 'project'
+                ? await unmigratedBareSources(dbPath, resolveTarget, plan.sources.find((s) => s.name === 'tasks' && existsSync(s.path))?.path, bareScratch)
+                : { first: [], last: [] };
+            const migratePlan = { ...plan, sources: [...bare.first, ...plan.sources, ...bare.last] };
+            const migrateResult = await runExodusMigrate(migratePlan, false, (msg) => log.debug({ scope }, `exodus-on-open: ${msg}`), { resolveTarget, ensureRuntimeTables: true });
             if (!migrateResult.ok) {
                 // Revert only migration-owned rows; retain conflicts and their evidence.
                 const recovery = await rollbackBothScopes(plan);
@@ -374,7 +482,7 @@ async function runExodusOnOpen(scope, dbPath, nativeDb, cwd) {
             }
             // 2. PARITY GATE (AC2): verifyMigration (T11551) — row-count + content
             //    digest + FK integrity + enum-drift equivalence legacy↔consolidated.
-            const verifyResult = verifyMigration(plan.sources, plan.projectDbPath, plan.globalDbPath, (msg) => log.debug({ scope }, `exodus-on-open verify: ${msg}`));
+            const verifyResult = verifyMigration(migratePlan.sources, plan.projectDbPath, plan.globalDbPath, (msg) => log.debug({ scope }, `exodus-on-open verify: ${msg}`), resolveTarget);
             // Surface diagnostics (hash mismatch / source enum-drift) but do NOT
             // abort on them — see isDataContinuityOk(). A correct normalising
             // migration legitimately produces both; only a row-count deficit or an
@@ -459,6 +567,7 @@ async function runExodusOnOpen(scope, dbPath, nativeDb, cwd) {
         }
         finally {
             _exodusInProgress = false;
+            rmSync(bareScratch, { recursive: true, force: true });
         }
     }, 
     // Tolerate a slow migration: a large fleet copy can take a while, so allow a

package/dist/store/exodus/on-open.js.map

@@ -1 +1 @@
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package/dist/store/exodus/reconcile.d.ts

@@ -0,0 +1,103 @@
+/**
+ * Explicit, verified reconcile of stranded legacy project stores into `cleo.db`.
+ *
+ * ## Why this exists (T12319)
+ *
+ * Measured 2026-09-24: ~21 projects ran on an EMPTY consolidated `cleo.db`
+ * while their legacy `.cleo/tasks.db` / `.cleo/brain.db` still held everything
+ * (llmtxt: 849 tasks + 1,696 observations; claude-todo: 5,330 + 5,148). Two
+ * things kept exodus-on-open from ever copying them: a machine-wide
+ * `CLEO_DISABLE_EXODUS_ON_OPEN=1` incident kill-switch (skip, silently), and —
+ * with the switch off — a copy engine that aborted on real legacy data (FK
+ * order, pre-T1408 archive reasons, pre-T877 stages, grandfathered hierarchy
+ * rows, NULL `valid_at`). `cleo doctor superseded-store` saw the rows but
+ * could only say "reconcile the contents first", with no command to do it.
+ *
+ * This module is that command's engine. It does NOT write a second copier: the
+ * copy is {@link runExodusMigrate} (same transforms, receipts and recovery),
+ * restricted to the project target. What it adds is the envelope:
+ *
+ * - **Assessment by key, not count.** For every legacy table the number of
+ *   source rows whose primary key is ABSENT from the live table. A count can
+ *   look complete while unrelated rows written into the empty shell mask real
+ *   gaps; a key cannot.
+ * - **Additive only.** `INSERT OR IGNORE` never overwrites or duplicates a row
+ *   already in `cleo.db`; the legacy files are read-only inputs and are never
+ *   moved, archived or deleted.
+ * - **Verified or reverted.** After the copy the assessment is re-run; any
+ *   missing key (or a live table that shrank) reverts exactly the rows this run
+ *   inserted, via their receipts, and the outcome is `refused`.
+ * - **Idempotent.** A fully reconciled project is a no-op: nothing is written.
+ *
+ * @module
+ * @task T12319
+ * @see ./migrate.ts — the single copy engine
+ * @see ../../doctor/superseded-store.ts — the survey that points here
+ */
+import type { SupersededStoreReconcileResult, SupersededStoreTableCount } from '@cleocode/contracts';
+import { type TargetResolver } from './runtime-targets.js';
+import type { LegacyDbDescriptor } from './types.js';
+/**
+ * Account for every data-bearing legacy project table against the live store.
+ *
+ * Read-only on both sides: the live store is opened `readOnly` and each legacy
+ * file is ATTACHed to that connection, which SQLite opens read-only too.
+ *
+ * @param liveStorePath - Absolute path of the live project `cleo.db`.
+ * @param sources - Existing project-scope legacy sources.
+ * @param resolveTarget - Where each legacy table lands; a reconcile passes the
+ *   runtime-read targets ({@link buildRuntimeTargetResolver}).
+ * @returns One entry per legacy table holding rows, in copy order.
+ * @task T12319
+ */
+export declare function assessSupersededProjectStores(liveStorePath: string, sources: readonly LegacyDbDescriptor[], resolveTarget?: TargetResolver): SupersededStoreTableCount[];
+/**
+ * Whether any of `sources` holds at least one row in a table exodus would copy.
+ *
+ * Cheap by construction — stops at the first non-empty table — because it runs
+ * on the open path whenever a consolidated store is empty and its migration is
+ * being skipped, to decide whether that skip is stranding real data.
+ *
+ * @param sources - Legacy source descriptors of ONE scope.
+ * @returns `true` when a legacy file still holds copyable rows.
+ * @task T12319
+ */
+export declare function legacySourcesHoldRows(sources: readonly LegacyDbDescriptor[]): boolean;
+/**
+ * The unmigrated `cleo.db`'s own dead bare task-core family as exodus sources,
+ * for exodus-on-open (T12355): the same source the reconcile reads, so the two
+ * converge whichever runs first — without it, on-open left e.g. llmtxt's 1,972
+ * bare-only `task_labels` behind while a reconcile recovered them.
+ *
+ * @param liveStorePath - The project `cleo.db` being migrated.
+ * @param resolveTarget - The runtime target resolver.
+ * @param legacyTasksPath - The legacy `tasks.db`, if present (its fresher-row comparison).
+ * @param outDir - Scratch directory the materialised sources are written to.
+ * @returns Sources to copy BEFORE the legacy files (bare rows newer than their
+ *   legacy copy) and AFTER them (the rest of the bare family); both empty when
+ *   the bare family is not a source.
+ * @task T12355
+ */
+export declare function unmigratedBareSources(liveStorePath: string, resolveTarget: TargetResolver, legacyTasksPath: string | undefined, outDir: string): Promise<{
+    first: LegacyDbDescriptor[];
+    last: LegacyDbDescriptor[];
+}>;
+/**
+ * Reconcile a project's stranded legacy stores into its live `cleo.db`.
+ *
+ * @param projectRoot - Absolute project root.
+ * @param options - `dryRun` assesses and reports without writing anything.
+ * @returns The receipt; `outcome: 'refused'` means the copy did not verify and
+ *   every row it inserted was reverted.
+ * @example
+ * ```ts
+ * const plan = await reconcileSupersededStores('/mnt/projects/llmtxt', { dryRun: true });
+ * for (const t of plan.before) console.log(t.targetTable, t.missingInLive);
+ * ```
+ * @task T12319
+ */
+export declare function reconcileSupersededStores(projectRoot: string, options?: {
+    readonly dryRun?: boolean;
+    readonly additive?: boolean;
+}): Promise<SupersededStoreReconcileResult>;
+//# sourceMappingURL=reconcile.d.ts.map

package/dist/store/exodus/reconcile.d.ts.map

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