@cleocode/core 2026.10.5 → 2026.10.6-rc.ci.673

package/dist/store/exodus/archive.d.ts

@@ -91,6 +91,13 @@ export interface ExodusCompleteMarker {
     readonly targetDbPath?: string;
     /** Persisted cutover token; prevents a replaced/restored database inheriting this marker. */
     readonly databaseIdentity?: string;
+    /**
+     * What `verifyMigration` reported at the cutover beyond the data-continuity
+     * gate (content digests that differ, values outside an enum), surfaced by
+     * `cleo doctor exodus-health` so a FAILED verify is never silent (T12711).
+     * Absent when the verify passed.
+     */
+    readonly verifyIssues?: readonly string[];
 }
 /**
  * Return `true` if a scope's exodus completion marker exists on disk.
@@ -107,6 +114,17 @@ export interface ExodusCompleteMarker {
  * @returns Whether `<scopeBase>/exodus-complete` exists.
  */
 export declare function hasExodusCompleteMarker(scope: ExodusScope, cwd?: string, targetDbPath?: string, nativeDb?: DatabaseSync): boolean;
+/**
+ * What a scope's completion marker records `verifyMigration` reported at the
+ * cutover beyond data continuity (T12711); empty when the verify passed, the
+ * marker is absent or unreadable.
+ *
+ * @param scope - Target scope.
+ * @param cwd   - Working directory used to resolve the project `.cleo/` dir.
+ * @param targetDbPath - Explicit target database; its directory owns metadata, overriding discovery.
+ * @returns The recorded issues.
+ */
+export declare function readExodusVerifyIssues(scope: ExodusScope, cwd?: string, targetDbPath?: string): string[];
 /**
  * Write a scope's exodus completion marker atomically (write-then-rename).
  *
@@ -119,11 +137,32 @@ export declare function hasExodusCompleteMarker(scope: ExodusScope, cwd?: string
  * @param cwd             - Working directory used to resolve the project dir.
  * @param targetDbPath - Explicit target database; its directory owns metadata, overriding discovery.
  * @param databaseIdentity - Token committed on the verified database generation before publication.
+ * @param verifyIssues - What the cutover's verify reported beyond data continuity (T12711).
  * @returns The marker's absolute path.
  *
  * @task T11777
  */
-export declare function writeExodusCompleteMarker(scope: ExodusScope, archivedSources: readonly string[], cwd?: string, targetDbPath?: string, databaseIdentity?: string): string;
+export declare function writeExodusCompleteMarker(scope: ExodusScope, archivedSources: readonly string[], cwd?: string, targetDbPath?: string, databaseIdentity?: string, verifyIssues?: readonly string[]): string;
+/**
+ * Certify a scope as sealed (`cleo exodus seal`), MERGING into an existing
+ * completion marker rather than rebuilding it (T13375).
+ *
+ * Seal runs only count parity, never a cutover, so it has nothing to say about
+ * the fields a cutover recorded: `databaseIdentity` (which
+ * {@link hasExodusCompleteMarker} certifies a database handle against),
+ * `targetDbPath`, `verifyIssues`, `completedAt`, `cleoVersion`, or any field a
+ * later format adds. Every one is kept; `archivedSources` gains the sources
+ * this seal archived. Without a marker, or with one that is not a version-1
+ * marker of this scope, a fresh marker is written as before.
+ *
+ * @param scope           - Scope being certified as migrated.
+ * @param archivedSources - Logical names of the sources this seal archived.
+ * @param cwd             - Working directory used to resolve the project dir.
+ * @returns The marker's absolute path.
+ *
+ * @task T13375
+ */
+export declare function sealExodusCompleteMarker(scope: ExodusScope, archivedSources: readonly string[], cwd?: string): string;
 /**
  * Outcome of archiving one source DB.
  */
@@ -182,8 +221,9 @@ export interface ArchiveMigratedSourcesResult {
  *
  * @task T11777
  * @param identities - Persisted cutover tokens for the exact verified target generations.
+ * @param verifyIssues - What the cutover's verify reported beyond data continuity, recorded in each marker (T12711).
  */
-export declare function archiveMigratedSources(consumed: readonly LegacyDbDescriptor[], cwd?: string, targets?: Pick<ExodusPlan, 'projectDbPath' | 'globalDbPath'>, identities?: Partial<Record<ExodusScope, string>>): ArchiveMigratedSourcesResult;
+export declare function archiveMigratedSources(consumed: readonly LegacyDbDescriptor[], cwd?: string, targets?: Pick<ExodusPlan, 'projectDbPath' | 'globalDbPath'>, identities?: Partial<Record<ExodusScope, string>>, verifyIssues?: readonly string[]): ArchiveMigratedSourcesResult;
 /**
  * A legacy source DB that is still present on disk AFTER its scope's exodus
  * completion marker was written — i.e. stranded residue that should have been

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

@@ -1 +1 @@
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+{"version":3,"file":"archive.d.ts","sourceRoot":"","sources":["../../../src/store/exodus/archive.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAmDG;AAYH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAMhD,OAAO,KAAK,EAAE,UAAU,EAAE,WAAW,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAsC9E;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,WAAW,EAAE,GAAG,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,MAAM,CAEhG;AAED;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,WAAW,EAAE,GAAG,CAAC,EAAE,MAAM,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,MAAM,CAQhG;AAED;;;;;GAKG;AACH,MAAM,WAAW,oBAAoB;IACnC,6BAA6B;IAC7B,QAAQ,CAAC,OAAO,EAAE,CAAC,CAAC;IACpB,+CAA+C;IAC/C,QAAQ,CAAC,KAAK,EAAE,WAAW,CAAC;IAC5B,uDAAuD;IACvD,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,yCAAyC;IACzC,QAAQ,CAAC,WAAW,EAAE,MAAM,CAAC;IAC7B,2EAA2E;IAC3E,QAAQ,CAAC,eAAe,EAAE,SAAS,MAAM,EAAE,CAAC;IAC5C,iFAAiF;IACjF,QAAQ,CAAC,YAAY,CAAC,EAAE,MAAM,CAAC;IAC/B,6FAA6F;IAC7F,QAAQ,CAAC,gBAAgB,CAAC,EAAE,MAAM,CAAC;IACnC;;;;;OAKG;IACH,QAAQ,CAAC,YAAY,CAAC,EAAE,SAAS,MAAM,EAAE,CAAC;CAC3C;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,uBAAuB,CACrC,KAAK,EAAE,WAAW,EAClB,GAAG,CAAC,EAAE,MAAM,EACZ,YAAY,CAAC,EAAE,MAAM,EACrB,QAAQ,CAAC,EAAE,YAAY,GACtB,OAAO,CAuBT;AAED;;;;;;;;;GASG;AACH,wBAAgB,sBAAsB,CACpC,KAAK,EAAE,WAAW,EAClB,GAAG,CAAC,EAAE,MAAM,EACZ,YAAY,CAAC,EAAE,MAAM,GACpB,MAAM,EAAE,CASV;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,yBAAyB,CACvC,KAAK,EAAE,WAAW,EAClB,eAAe,EAAE,SAAS,MAAM,EAAE,EAClC,GAAG,CAAC,EAAE,MAAM,EACZ,YAAY,CAAC,EAAE,MAAM,EACrB,gBAAgB,CAAC,EAAE,MAAM,EACzB,YAAY,GAAE,SAAS,MAAM,EAAO,GACnC,MAAM,CAmBR;AASD;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,wBAAwB,CACtC,KAAK,EAAE,WAAW,EAClB,eAAe,EAAE,SAAS,MAAM,EAAE,EAClC,GAAG,CAAC,EAAE,MAAM,GACX,MAAM,CAyBR;AAED;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,uDAAuD;IACvD,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,qCAAqC;IACrC,QAAQ,CAAC,UAAU,EAAE,MAAM,CAAC;IAC5B,6EAA6E;IAC7E,QAAQ,CAAC,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;IACnC,6EAA6E;IAC7E,QAAQ,CAAC,MAAM,EAAE,UAAU,GAAG,QAAQ,CAAC;CACxC;AAiCD;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,eAAe,CAC7B,MAAM,EAAE,kBAAkB,EAC1B,GAAG,CAAC,EAAE,MAAM,EACZ,YAAY,CAAC,EAAE,MAAM,GACpB,oBAAoB,CAkCtB;AAED;;GAEG;AACH,MAAM,WAAW,4BAA4B;IAC3C,mCAAmC;IACnC,QAAQ,CAAC,OAAO,EAAE,SAAS,oBAAoB,EAAE,CAAC;IAClD,wDAAwD;IACxD,QAAQ,CAAC,cAAc,EAAE,SAAS,WAAW,EAAE,CAAC;CACjD;AAED;;;;;;;;;;;;;;;;;;;;;GAqBG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,SAAS,kBAAkB,EAAE,EACvC,GAAG,CAAC,EAAE,MAAM,EACZ,OAAO,CAAC,EAAE,IAAI,CAAC,UAAU,EAAE,eAAe,GAAG,cAAc,CAAC,EAC5D,UAAU,CAAC,EAAE,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,CAAC,EACjD,YAAY,GAAE,SAAS,MAAM,EAAO,GACnC,4BAA4B,CA2B9B;AAED;;;;GAIG;AACH,MAAM,WAAW,oBAAoB;IACnC,2BAA2B;IAC3B,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,oDAAoD;IACpD,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC;IACtB,gDAAgD;IAChD,QAAQ,CAAC,KAAK,EAAE,WAAW,CAAC;CAC7B;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,qBAAqB,CACnC,OAAO,EAAE,SAAS,kBAAkB,EAAE,EACtC,GAAG,CAAC,EAAE,MAAM,GACX,oBAAoB,EAAE,CAexB;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,sBAAsB,CACpC,QAAQ,EAAE,SAAS,oBAAoB,EAAE,EACzC,OAAO,EAAE,SAAS,kBAAkB,EAAE,EACtC,GAAG,CAAC,EAAE,MAAM,GACX,oBAAoB,EAAE,CASxB"}

package/dist/store/exodus/archive.js

@@ -63,6 +63,7 @@ const markerIdentity = z.object({
     scope: z.enum(['project', 'global']),
     targetDbPath: z.string().optional(),
     databaseIdentity: z.string().optional(),
+    verifyIssues: z.array(z.string()).optional(),
 });
 /** Per-scope archive directory name (sibling of the migrated DBs). */
 const ARCHIVE_DIR_NAME = '_archive';
@@ -150,6 +151,28 @@ export function hasExodusCompleteMarker(scope, cwd, targetDbPath, nativeDb) {
             !marker.targetDbPath ||
             resolve(marker.targetDbPath) === resolve(targetDbPath)));
 }
+/**
+ * What a scope's completion marker records `verifyMigration` reported at the
+ * cutover beyond data continuity (T12711); empty when the verify passed, the
+ * marker is absent or unreadable.
+ *
+ * @param scope - Target scope.
+ * @param cwd   - Working directory used to resolve the project `.cleo/` dir.
+ * @param targetDbPath - Explicit target database; its directory owns metadata, overriding discovery.
+ * @returns The recorded issues.
+ */
+export function readExodusVerifyIssues(scope, cwd, targetDbPath) {
+    try {
+        const markerPath = exodusMarkerPath(scope, cwd, targetDbPath);
+        if (!existsSync(markerPath))
+            return [];
+        const marker = markerIdentity.safeParse(JSON.parse(readFileSync(markerPath, 'utf8')));
+        return marker.success ? (marker.data.verifyIssues ?? []) : [];
+    }
+    catch {
+        return [];
+    }
+}
 /**
  * Write a scope's exodus completion marker atomically (write-then-rename).
  *
@@ -162,11 +185,12 @@ export function hasExodusCompleteMarker(scope, cwd, targetDbPath, nativeDb) {
  * @param cwd             - Working directory used to resolve the project dir.
  * @param targetDbPath - Explicit target database; its directory owns metadata, overriding discovery.
  * @param databaseIdentity - Token committed on the verified database generation before publication.
+ * @param verifyIssues - What the cutover's verify reported beyond data continuity (T12711).
  * @returns The marker's absolute path.
  *
  * @task T11777
  */
-export function writeExodusCompleteMarker(scope, archivedSources, cwd, targetDbPath, databaseIdentity) {
+export function writeExodusCompleteMarker(scope, archivedSources, cwd, targetDbPath, databaseIdentity, verifyIssues = []) {
     const markerPath = exodusMarkerPath(scope, cwd, targetDbPath);
     const baseDir = scopeBaseDir(scope, cwd, targetDbPath);
     mkdirSync(baseDir, { recursive: true });
@@ -178,11 +202,63 @@ export function writeExodusCompleteMarker(scope, archivedSources, cwd, targetDbP
         archivedSources: [...archivedSources],
         targetDbPath: resolve(targetDbPath ?? join(baseDir, 'cleo.db')),
         ...(databaseIdentity ? { databaseIdentity } : {}),
+        ...(verifyIssues.length > 0 ? { verifyIssues: [...verifyIssues] } : {}),
     };
+    publishMarker(markerPath, marker);
+    log.info({ scope, markerPath, archivedSources }, 'exodus: wrote completion marker');
+    return markerPath;
+}
+/** Write a marker object atomically (write-then-rename). */
+function publishMarker(markerPath, marker) {
     const tmpPath = `${markerPath}.tmp`;
     writeFileSync(tmpPath, JSON.stringify(marker, null, 2) + '\n', 'utf8');
     renameSync(tmpPath, markerPath);
-    log.info({ scope, markerPath, archivedSources }, 'exodus: wrote completion marker');
+}
+/**
+ * Certify a scope as sealed (`cleo exodus seal`), MERGING into an existing
+ * completion marker rather than rebuilding it (T13375).
+ *
+ * Seal runs only count parity, never a cutover, so it has nothing to say about
+ * the fields a cutover recorded: `databaseIdentity` (which
+ * {@link hasExodusCompleteMarker} certifies a database handle against),
+ * `targetDbPath`, `verifyIssues`, `completedAt`, `cleoVersion`, or any field a
+ * later format adds. Every one is kept; `archivedSources` gains the sources
+ * this seal archived. Without a marker, or with one that is not a version-1
+ * marker of this scope, a fresh marker is written as before.
+ *
+ * @param scope           - Scope being certified as migrated.
+ * @param archivedSources - Logical names of the sources this seal archived.
+ * @param cwd             - Working directory used to resolve the project dir.
+ * @returns The marker's absolute path.
+ *
+ * @task T13375
+ */
+export function sealExodusCompleteMarker(scope, archivedSources, cwd) {
+    const markerPath = exodusMarkerPath(scope, cwd);
+    let prior = null;
+    if (existsSync(markerPath)) {
+        try {
+            const raw = JSON.parse(readFileSync(markerPath, 'utf8'));
+            const known = markerIdentity.safeParse(raw);
+            if (known.success && known.data.scope === scope && typeof raw === 'object' && raw !== null)
+                prior = { ...raw };
+        }
+        catch {
+            prior = null;
+        }
+        if (prior === null)
+            log.warn({ scope, markerPath }, 'exodus seal: unreadable completion marker rewritten');
+    }
+    if (prior === null)
+        return writeExodusCompleteMarker(scope, archivedSources, cwd);
+    const before = Array.isArray(prior.archivedSources)
+        ? prior.archivedSources.filter((n) => typeof n === 'string')
+        : [];
+    publishMarker(markerPath, {
+        ...prior,
+        archivedSources: [...new Set([...before, ...archivedSources])],
+    });
+    log.info({ scope, markerPath, archivedSources }, 'exodus: merged into completion marker');
     return markerPath;
 }
 /**
@@ -278,8 +354,9 @@ export function archiveSourceDb(source, cwd, targetDbPath) {
  *
  * @task T11777
  * @param identities - Persisted cutover tokens for the exact verified target generations.
+ * @param verifyIssues - What the cutover's verify reported beyond data continuity, recorded in each marker (T12711).
  */
-export function archiveMigratedSources(consumed, cwd, targets, identities) {
+export function archiveMigratedSources(consumed, cwd, targets, identities, verifyIssues = []) {
     const results = [];
     const scopes = new Set();
     for (const source of consumed) {
@@ -291,7 +368,7 @@ export function archiveMigratedSources(consumed, cwd, targets, identities) {
     for (const scope of scopes) {
         const archivedForScope = consumed.filter((s) => s.targetScope === scope).map((s) => s.name);
         const target = scope === 'project' ? targets?.projectDbPath : targets?.globalDbPath;
-        writeExodusCompleteMarker(scope, archivedForScope, cwd, target, identities?.[scope]);
+        writeExodusCompleteMarker(scope, archivedForScope, cwd, target, identities?.[scope], verifyIssues);
         markersWritten.push(scope);
     }
     return { sources: results, markersWritten };

package/dist/store/exodus/archive.js.map

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

@@ -0,0 +1,104 @@
+/**
+ * The live store's own bare legacy family as a reconcile source.
+ *
+ * A `cleo.db` from before consolidation can hold rows in bare tables
+ * (`tasks`, `task_labels`, `sessions`, …) that the runtime no longer reads.
+ * Two reconcile modes carry them into the prefixed tables:
+ *
+ * - full mode, while `tasks_tasks` is still EMPTY (the project never ran on
+ *   the consolidated store): every bare row (T12346);
+ * - bare-strands mode (T13309), once `tasks_tasks` is populated: only bare
+ *   rows whose key the prefixed twin lacks, plus bare tasks whose id a
+ *   DIFFERENT live task took (renumbered by the caller). A row that is, or
+ *   refers to, a task the live store recorded as deleted is skipped and named,
+ *   never resurrected, and so is a row referring to a task neither side holds.
+ *
+ * @module
+ * @task T12346
+ * @task T13309
+ */
+import type { SupersededStoreBareAccount, SupersededStoreConflict } from '@cleocode/contracts';
+import type { TargetResolver } from './runtime-targets.js';
+import { type TaskIdRemapResult } from './task-id-remap.js';
+import { type LegacyDbDescriptor } from './types.js';
+/**
+ * The live store's own dead bare task-core family as a reconcile source — item
+ * 2 of T12319, found real by the T12346 sweep: a stranded `cleo.db` can hold
+ * rows in bare tables the runtime no longer reads that exist in NO legacy file
+ * (llmtxt: 1,972 `task_labels`; versionguard: 20 `task_dependencies`).
+ *
+ * Offered ONLY while the prefixed `tasks_tasks` is still empty — i.e. the
+ * project never ran on the consolidated store. Once it has, a bare row missing
+ * from the prefixed family may be one the runtime deliberately removed; the
+ * bare-strands mode ({@link bareStrandSource}) handles that case.
+ *
+ * @returns The descriptor (path = the materialised file), or `null`.
+ */
+export declare function bareTaskCoreSource(liveStorePath: string, resolveTarget: TargetResolver, outDir: string): Promise<LegacyDbDescriptor | null>;
+/** Result of {@link bareStrandSource}. */
+export interface BareStrandSource {
+    /** The materialised stranded rows, or `null` when none is left to copy. */
+    readonly source: LegacyDbDescriptor | null;
+    /** Rows deliberately left uncopied, per table and reason. */
+    readonly skipped: SupersededStoreConflict[];
+    /** Every bare table with rows, as the run found it (recorded on success). */
+    readonly accounted: SupersededStoreBareAccount[];
+    /** `false` when the live task graph is empty: full mode's case, not this one. */
+    readonly populated: boolean;
+    /**
+     * The renumbering of bare tasks a different live task shadows, applied
+     * BEFORE any row was judged present or skipped (T13333), so each row is
+     * judged by the key it is copied under. Its `sources` is `source`.
+     */
+    readonly remap: TaskIdRemapResult;
+    /**
+     * Every stranded row the run did NOT list in `skipped`, renumbered: the
+     * rows it copies plus those it judged already present. Each must be in the
+     * live store once the run is over, or the run is refused (T13333).
+     * `null` when the live task graph is empty or no bare table holds rows.
+     */
+    readonly accountingPath: string | null;
+}
+/**
+ * The live store's stranded bare rows as a reconcile source (T13309): for a
+ * project already running on the consolidated store, the bare rows whose key
+ * the prefixed twin lacks, and the bare tasks a different live task shadows by
+ * id (kept so the caller's renumbering recovers them).
+ *
+ * The shadowed tasks are renumbered first, with every reference re-pointed,
+ * so a child row is judged by the key it is copied under, never by the key of
+ * the live holder's child (T13333). An undecided collision is not renumbered:
+ * the caller withholds the task graph.
+ *
+ * Skipped, and named in `skipped`: a row that is, or whose task reference
+ * points at, a task the live store recorded as deleted (`tasks_audit_log`
+ * action `task_deleted`), a row whose task reference neither the live store
+ * nor the copy holds (`parent-absent`), and, to a fixed point, a row whose
+ * task reference is a bare task this run skipped (`parent-skipped`, T13334).
+ * A deletion record of a shadowed id, or of a fresh id a renumbering took,
+ * belongs to another task and skips nothing. A table whose twin key the bare
+ * table cannot produce keeps every row, and the post-copy verification judges
+ * it.
+ *
+ * @param liveStorePath - The live project `cleo.db` (read only).
+ * @param resolveTarget - Runtime target resolver.
+ * @param outDir - Scratch directory for the materialised file.
+ * @param cleoDir - The project's `.cleo`, where earlier receipts live.
+ */
+export declare function bareStrandSource(liveStorePath: string, resolveTarget: TargetResolver, outDir: string, cleoDir: string): Promise<BareStrandSource>;
+/**
+ * Task references in the copied strands source that the live store cannot
+ * resolve after the copy: `table.column -> id` for each (T13334). Empty when
+ * every reference a copied row carries names a live task.
+ *
+ * Only scalar references are judged. A JSON array of task ids (a session's
+ * `tasks_completed_json`, `tasks_created_json`) is history: an id in it whose
+ * task is gone is valid, as the runtime keeps it (deleting a task leaves it
+ * listed) and the sync wire drops it rather than rejecting the row (T12798).
+ * A copied session listing a deleted task is therefore copied (T13377).
+ *
+ * @param liveStorePath - The live project `cleo.db` (read only).
+ * @param sourcePath - The strands source the run copied from.
+ */
+export declare function danglingStrandReferences(liveStorePath: string, sourcePath: string): string[];
+//# sourceMappingURL=bare-family.d.ts.map

package/dist/store/exodus/bare-family.d.ts.map

@@ -0,0 +1 @@
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