@cleocode/core 2026.10.12 → 2026.10.13-rc.ci.682

package/dist/docs/legacy-doc-migration.js

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+/**
+ * T13360 — honest migration of legacy docs into the re-keyed store
+ * (spec `cleodocs-rearch-design` §5, D11165).
+ *
+ * Imports every legacy CleoDocs document (`docs_attachments` rows — the
+ * D11-collapse twin of the legacy `attachments` registry) into the T13354
+ * re-keyed conduit history family, inside the T13448 migration safety
+ * harness:
+ *
+ *   backup → BEGIN IMMEDIATE → before-fingerprints → step → verify →
+ *   COMMIT (only when every check passed) / ROLLBACK
+ *
+ * Honesty contract (the spec's words are the ACs):
+ *
+ *   - **Every imported history row is labeled `origin: 'migrated'`** — no
+ *     imported row poses as native (AC1).
+ *   - **No fabricated authors, no invented version numbers** — authors come
+ *     from the legacy docs audit log's real `actor`; when no provenance
+ *     exists the row is system-attributed (`system:migration`), the AC's
+ *     sanctioned "system attribution", never an invented human (AC2).
+ *     Version ordinals are derived from the real audit-event order.
+ *   - **Dangling-pointer docs are content-captured or marked dangling** —
+ *     a doc whose recorded path is missing or ephemeral (worktree/tmp) gets
+ *     its bytes recovered from the content-addressed blob store when
+ *     possible (captured); otherwise it is recorded in
+ *     `conduit_doc_migration_ledger` with `status: 'dangling'`, the legacy
+ *     pointer and the reason — never silently imported (AC3).
+ *   - **Idempotent** — every write carries a NATURAL uid (doc slug; (doc
+ *     uid, content hash, event timestamp); ledger slug), so a re-run derives
+ *     the same uids and `ON CONFLICT DO NOTHING` turns it into a verified
+ *     no-op; docs already in the ledger are skipped. The second run's
+ *     harness verification proves zero deltas and unchanged hashes (AC4).
+ *
+ * The migration is exposed as `cleo docs migrate` (dispatch op
+ * `docs.migrate`); it takes its own pre-step VACUUM INTO backup through the
+ * harness and needs no `--force` (it is additive — nothing is deleted).
+ *
+ * Cross-device identity (T13638): the audit log (`docs-audit.jsonl`) is a
+ * DEVICE-LOCAL file — it never syncs. Version identity therefore CANNOT
+ * derive from a row's position in it (`evt-<i>` was v1 and diverged across
+ * devices). Every imported version's natural uid is instead a pure function
+ * of the version's real facts — (doc uid, content hash, event timestamp) —
+ * so two devices migrating the same synced legacy doc derive IDENTICAL uids
+ * for the same content whatever their local audit logs hold, and two
+ * different contents can never collide on one uid. The doc uid, the ledger
+ * receipt, and the head projection were already device-independent.
+ *
+ * Existing installs: a store that already ran the t13360 import keeps its
+ * position-derived version uids — the ledger receipt makes the migration
+ * one-shot per doc, so the content-derived derivation applies to newly
+ * migrated rows only (accepted mixed state, per the task's (a) option; no
+ * re-key migration, since the spec does not mandate one).
+ *
+ * @module
+ * @task T13360
+ * @task T13633 — review round 2: leaf HLC constant, native-conflict count,
+ *   cross-device caveat
+ * @task T13638 — version uids derived from (doc uid, content hash, event
+ *   timestamp), never from the device-local audit position
+ * @epic T13340
+ * @saga T13339
+ */
+import { createHash } from 'node:crypto';
+import { existsSync, readFileSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { isAbsolute, resolve, sep } from 'node:path';
+import { getCleoWorktreesRoot } from '@cleocode/paths';
+import { eq, isNotNull } from 'drizzle-orm';
+import { getCleoDir } from '../paths.js';
+import { blobContentExists, blobFilePath } from '../store/blob-keep.js';
+import { findConduitDocMigration, importMigratedConduitDoc, importMigratedConduitVersion, recordConduitDocMigration, upsertConduitDocHead, } from '../store/conduit-doc-history.js';
+import { runMigrationSteps, } from '../store/migration-safety.js';
+import { conduitAttachments } from '../store/schema/cleo-project/conduit.js';
+import { getDb } from '../store/sqlite.js';
+import { encodeHlc, PRE_HLC_REPLICA } from '../store/sync/hlc.js';
+import { docsAttachments } from '../store/tasks-schema.js';
+import { readAuditLog } from './docs-audit.js';
+/**
+ * The honest system attribution for migrated rows with no real author
+ * provenance (spec §5 "system attribution"). Never an invented human name.
+ */
+export const MIGRATION_SYSTEM_AUTHOR = 'system:migration';
+/** True when `absPath` is ephemeral — inside a CLEO/Claude worktree or tmp. */
+function isEphemeralPath(absPath) {
+    const worktreesRoot = getCleoWorktreesRoot();
+    if (absPath === worktreesRoot || absPath.startsWith(`${worktreesRoot}${sep}`)) {
+        return 'worktree';
+    }
+    if (absPath.includes(`${sep}.claude${sep}worktrees${sep}`))
+        return 'worktree';
+    const tmp = tmpdir();
+    if (absPath.startsWith(`${tmp}${sep}`) || absPath.startsWith(`${sep}tmp${sep}`))
+        return 'tmp';
+    return null;
+}
+/** Read the content-addressed blob bytes for a sha/mime, or null. */
+function readBlobBytes(cleoDir, sha256, mime) {
+    const primary = blobFilePath(cleoDir, sha256, mime);
+    try {
+        return readFileSync(primary);
+    }
+    catch {
+        return null;
+    }
+}
+/** Cheap whitespace token count — a measurement, never an invention. */
+function countTokens(bytes) {
+    let count = 0;
+    let inWs = true;
+    for (let i = 0; i < bytes.length; i++) {
+        const c = bytes[i] ?? 0;
+        const ws = c === 32 || c === 9 || c === 10 || c === 13;
+        if (!ws && inWs)
+            count += 1;
+        inWs = ws;
+    }
+    return count;
+}
+function sha256Hex(bytes) {
+    return createHash('sha256').update(bytes).digest('hex');
+}
+function parsePayload(raw) {
+    try {
+        const parsed = JSON.parse(raw);
+        if (parsed !== null && typeof parsed === 'object' && !Array.isArray(parsed)) {
+            return parsed;
+        }
+        return null;
+    }
+    catch {
+        return null;
+    }
+}
+function formatFromMime(mime, slug) {
+    if (mime?.includes('markdown'))
+        return 'markdown';
+    if (slug.toLowerCase().endsWith('.md'))
+        return 'markdown';
+    return 'text';
+}
+/**
+ * Derive the import plan for every legacy doc — the SAME derivation runs in
+ * `planLegacyDocMigration` (to declare the harness's expected deltas) and
+ * inside the step (inside the transaction), so the deltas match by
+ * construction and any divergence fails verification and rolls back.
+ *
+ * Read-only: never writes; reads the store, the blob files and the audit
+ * log.
+ *
+ * @internal Exported for tests.
+ */
+export async function deriveLegacyDocMigrationPlan(projectRoot) {
+    const cleoDir = getCleoDir(projectRoot);
+    const db = await getDb(projectRoot);
+    const rows = await db.select().from(docsAttachments).where(isNotNull(docsAttachments.slug)).all();
+    const audit = readAuditLog(projectRoot);
+    const docs = [];
+    let skipped = 0;
+    let nativeConflicts = 0;
+    for (const row of rows) {
+        const slug = row.slug;
+        // Idempotency: a doc already receipted (captured or dangling) is done.
+        if ((await findConduitDocMigration(projectRoot, slug)) !== null) {
+            skipped += 1;
+            continue;
+        }
+        // Never clobber a native conduit doc that happens to share the slug —
+        // counted explicitly so the operator can reconcile it (T13633).
+        const existing = await db
+            .select({ slug: conduitAttachments.slug })
+            .from(conduitAttachments)
+            .where(eq(conduitAttachments.slug, slug))
+            .get();
+        if (existing !== undefined && existing !== null) {
+            nativeConflicts += 1;
+            continue;
+        }
+        const payload = parsePayload(row.attachmentJson);
+        const mime = payload?.mime;
+        const fmt = formatFromMime(mime, slug);
+        // ── dangling classification (doctor parity: missing OR ephemeral path) ──
+        const pointerPath = payload !== null && typeof payload.path === 'string' && payload.path.length > 0
+            ? payload.path
+            : null;
+        let danglingReason = null;
+        if (payload === null) {
+            danglingReason = 'unparseable-payload';
+        }
+        else if (payload.kind !== 'blob' && payload.kind !== 'local-file') {
+            danglingReason = `no-local-content:${payload.kind}`;
+        }
+        else if (pointerPath !== null) {
+            const abs = isAbsolute(pointerPath) ? pointerPath : resolve(projectRoot, pointerPath);
+            const ephemeral = isEphemeralPath(abs);
+            if (!existsSync(abs)) {
+                danglingReason = 'path-missing';
+            }
+            else if (ephemeral !== null) {
+                danglingReason = `path-ephemeral:${ephemeral}`;
+            }
+        }
+        // ── content capture ──
+        let content = null;
+        let capturedReason = 'captured';
+        if (danglingReason === null) {
+            if (payload?.kind === 'local-file' && pointerPath !== null) {
+                const abs = isAbsolute(pointerPath) ? pointerPath : resolve(projectRoot, pointerPath);
+                try {
+                    content = readFileSync(abs);
+                }
+                catch {
+                    danglingReason = 'path-unreadable';
+                }
+            }
+            else {
+                content = readBlobBytes(cleoDir, row.sha256, mime ?? 'application/octet-stream');
+                if (content === null)
+                    danglingReason = 'blob-bytes-missing';
+            }
+            if (content !== null && danglingReason !== null) {
+                // Dangling pointer, bytes recovered from the content-addressed store.
+                capturedReason = `recovered:${danglingReason}`;
+                danglingReason = null;
+            }
+        }
+        else if (danglingReason !== 'unparseable-payload' && payload?.kind !== undefined) {
+            // Dangling pointer — try to recover the bytes by sha from the blob store.
+            if (blobContentExists(cleoDir, row.sha256, mime ?? 'application/octet-stream')) {
+                content = readBlobBytes(cleoDir, row.sha256, mime ?? 'application/octet-stream');
+                if (content !== null) {
+                    capturedReason = `recovered:${danglingReason}`;
+                    danglingReason = null;
+                }
+            }
+        }
+        if (danglingReason !== null || content === null) {
+            docs.push({
+                slug,
+                status: 'dangling',
+                reason: danglingReason ?? 'blob-bytes-missing',
+                legacyPath: pointerPath,
+                legacySha256: row.sha256,
+                content: null,
+                format: fmt,
+                title: row.summary ?? null,
+                createdAt: row.createdAt,
+                versions: [],
+                fromAgentId: MIGRATION_SYSTEM_AUTHOR,
+            });
+            continue;
+        }
+        // ── history reconstruction from the real audit log ──
+        const events = audit.entries.filter((e) => e.slug === slug && (e.op === 'docs.add' || e.op === 'docs.update'));
+        const versions = [];
+        // T13638: two events with the SAME content at the SAME instant are one
+        // logical version — the content-derived natural uid cannot tell them
+        // apart, so a repeat would either no-op away honest history or parent a
+        // version to itself. The first occurrence is kept; each repeat is a
+        // collapsed duplicate write, counted into the survivor's summary.
+        const seenVersionKeys = new Map();
+        const collapsedDuplicates = new Map();
+        for (const event of events) {
+            if (event.sha256 === undefined)
+                continue;
+            const eventMime = mime ?? 'application/octet-stream';
+            if (!blobContentExists(cleoDir, event.sha256, eventMime))
+                continue; // bytes gone — honest omission
+            const bytes = readBlobBytes(cleoDir, event.sha256, eventMime);
+            if (bytes === null)
+                continue;
+            const versionKey = `${event.sha256}|${event.ts}`;
+            const prior = seenVersionKeys.get(versionKey);
+            if (prior !== undefined) {
+                collapsedDuplicates.set(versionKey, (collapsedDuplicates.get(versionKey) ?? 0) + 1);
+                continue;
+            }
+            seenVersionKeys.set(versionKey, versions.length);
+            versions.push({
+                authorAgentId: typeof event.actor === 'string' && event.actor.length > 0
+                    ? event.actor
+                    : MIGRATION_SYSTEM_AUTHOR,
+                contentHash: event.sha256,
+                sizeBytes: bytes.length,
+                tokens: countTokens(bytes),
+                createdAt: event.ts,
+                changeSummary: `migrated from the legacy docs store (audit ${event.op} @ ${event.ts})`,
+            });
+        }
+        for (const [versionKey, count] of collapsedDuplicates) {
+            const index = seenVersionKeys.get(versionKey);
+            if (index === undefined)
+                continue;
+            const survivor = versions[index];
+            if (survivor === undefined)
+                continue;
+            versions[index] = {
+                ...survivor,
+                changeSummary: `${survivor.changeSummary}; collapsed ${count} duplicate audit event(s) with identical content and timestamp`,
+            };
+        }
+        if (versions.length === 0) {
+            // No recoverable audit history — one content-capture version, honestly
+            // system-attributed. Never invented authors or ordinals.
+            versions.push({
+                authorAgentId: MIGRATION_SYSTEM_AUTHOR,
+                contentHash: row.sha256,
+                sizeBytes: content.length,
+                tokens: countTokens(content),
+                createdAt: row.createdAt,
+                changeSummary: 'migrated from the legacy docs store (content capture; no audit provenance)',
+            });
+        }
+        docs.push({
+            slug,
+            status: 'captured',
+            reason: capturedReason,
+            legacyPath: pointerPath,
+            legacySha256: row.sha256,
+            content,
+            format: fmt,
+            title: row.summary ?? null,
+            createdAt: row.createdAt,
+            versions,
+            fromAgentId: versions[versions.length - 1]?.authorAgentId ?? MIGRATION_SYSTEM_AUTHOR,
+        });
+    }
+    const expectedDelta = {
+        conduit_attachments: 0,
+        conduit_attachment_versions: 0,
+        conduit_doc_heads: 0,
+        conduit_doc_migration_ledger: 0,
+    };
+    for (const doc of docs) {
+        expectedDelta['conduit_doc_migration_ledger'] += 1;
+        if (doc.status === 'captured') {
+            expectedDelta['conduit_attachments'] += 1;
+            expectedDelta['conduit_attachment_versions'] += doc.versions.length;
+            expectedDelta['conduit_doc_heads'] += 1;
+        }
+    }
+    return { docs, skipped, nativeConflicts, expectedDelta };
+}
+/**
+ * Plan the migration: derive the work, declare the harness's expected deltas,
+ * and build the single harness step. Call immediately before
+ * {@link runLegacyDocMigration} — the plan and the step re-derive from the
+ * same state, and the harness fails verification (rolling back) if a
+ * concurrent write lands in between.
+ *
+ * @param projectRoot - Absolute path to the CLEO project root.
+ * @returns The plan (step + declared deltas + per-doc decisions).
+ * @task T13360
+ */
+export async function planLegacyDocMigration(opts) {
+    const derived = await deriveLegacyDocMigrationPlan(opts.projectRoot);
+    const verify = {
+        expectedDelta: derived.expectedDelta,
+    };
+    const step = {
+        name: 'migrate-legacy-docs',
+        description: 'import legacy docs + history into the re-keyed conduit store (T13360, spec §5)',
+        verify,
+        run: async ({ db: _db, projectRoot, log }) => {
+            const plan = await deriveLegacyDocMigrationPlan(projectRoot);
+            for (const doc of plan.docs) {
+                if (doc.status === 'dangling') {
+                    await recordConduitDocMigration(projectRoot, {
+                        slug: doc.slug,
+                        docUid: null,
+                        status: 'dangling',
+                        reason: doc.reason,
+                        ...(doc.legacyPath !== null ? { legacyPath: doc.legacyPath } : {}),
+                        legacySha256: doc.legacySha256,
+                        versionsImported: 0,
+                    });
+                    log(`marked dangling: ${doc.slug} (${doc.reason})`);
+                    continue;
+                }
+                const content = doc.content ?? Buffer.alloc(0);
+                const contentHash = sha256Hex(content);
+                const { uid: docUid } = await importMigratedConduitDoc(projectRoot, {
+                    slug: doc.slug,
+                    fromAgentId: doc.fromAgentId,
+                    content,
+                    contentHash,
+                    format: doc.format,
+                    ...(doc.title !== null ? { title: doc.title } : {}),
+                    tokens: countTokens(content),
+                    createdAt: doc.createdAt,
+                    versionCount: doc.versions.length,
+                });
+                let parentUid = null;
+                let lastVersionUid = '';
+                let ordinal = 0;
+                for (const version of doc.versions) {
+                    ordinal += 1;
+                    const { uid } = await importMigratedConduitVersion(projectRoot, {
+                        attachmentUid: docUid,
+                        parentVersionUid: parentUid,
+                        authorAgentId: version.authorAgentId,
+                        storageKey: `sha256:${version.contentHash}`,
+                        contentHash: version.contentHash,
+                        sizeBytes: version.sizeBytes,
+                        tokens: version.tokens,
+                        versionNumber: ordinal,
+                        createdAt: version.createdAt,
+                        changeSummary: version.changeSummary,
+                        slug: doc.slug,
+                    });
+                    parentUid = uid;
+                    lastVersionUid = uid;
+                }
+                // Head projection: a deterministic HLC (pre-replica, phys = the last
+                // version's real timestamp) so a re-run's upsert is a stable no-op on
+                // every device — no spurious conflict records (AC4).
+                const lastVersion = doc.versions[doc.versions.length - 1];
+                if (lastVersion !== undefined && lastVersionUid.length > 0) {
+                    await upsertConduitDocHead(projectRoot, {
+                        attachmentUid: docUid,
+                        headVersionUid: lastVersionUid,
+                        headHlc: encodeHlc({
+                            phys: Date.parse(lastVersion.createdAt),
+                            ctr: ordinal,
+                            replica: PRE_HLC_REPLICA,
+                        }),
+                    });
+                }
+                await recordConduitDocMigration(projectRoot, {
+                    slug: doc.slug,
+                    docUid,
+                    status: 'captured',
+                    reason: doc.reason,
+                    ...(doc.legacyPath !== null ? { legacyPath: doc.legacyPath } : {}),
+                    legacySha256: doc.legacySha256,
+                    versionsImported: doc.versions.length,
+                });
+                log(`captured: ${doc.slug} (${doc.versions.length} version(s))`);
+            }
+            log(`legacy docs migration applied: ${plan.docs.filter((d) => d.status === 'captured').length} captured, ` +
+                `${plan.docs.filter((d) => d.status === 'dangling').length} dangling, ` +
+                `${plan.skipped} already migrated, ${plan.nativeConflicts} native-conflict skips`);
+        },
+    };
+    return {
+        step,
+        expectedDelta: derived.expectedDelta,
+        docs: derived.docs,
+        counts: {
+            toCapture: derived.docs.filter((d) => d.status === 'captured').length,
+            toMarkDangling: derived.docs.filter((d) => d.status === 'dangling').length,
+            toSkip: derived.skipped,
+            nativeConflicts: derived.nativeConflicts,
+            versions: derived.docs.reduce((n, d) => n + d.versions.length, 0),
+        },
+    };
+}
+/**
+ * Run the legacy docs migration inside the T13448 harness: pre-step VACUUM
+ * INTO backup → BEGIN IMMEDIATE → before-fingerprints → import → verify →
+ * COMMIT, or ROLLBACK on any failure (the failed step is never visible).
+ * Additive only — nothing is deleted, so no `force` is required.
+ *
+ * @param opts.projectRoot - Absolute path to the CLEO project root.
+ * @param opts.db - Live native handle on the project store (chokepoint-opened).
+ * @param opts.cwd - Invocation directory (the restore path's worktree guard).
+ * @param opts.onStepReport - Optional per-step report sink.
+ * @returns The harness report plus plan counts.
+ * @task T13360
+ */
+export async function runLegacyDocMigration(opts) {
+    const plan = await planLegacyDocMigration({ projectRoot: opts.projectRoot });
+    const report = await runMigrationSteps([plan.step], {
+        db: opts.db,
+        projectRoot: opts.projectRoot,
+        cwd: opts.cwd,
+        onStepReport: opts.onStepReport,
+    });
+    return { report, counts: plan.counts };
+}
+//# sourceMappingURL=legacy-doc-migration.js.map

package/dist/docs/legacy-doc-migration.js.map

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package/dist/docs/publications-store.d.ts

@@ -0,0 +1,67 @@
+/**
+ * Publications ledger store accessors (T13362) — the store-backed replacement
+ * for the deprecated `.cleo/docs-publications.json` sidecar.
+ *
+ * Every read/write of the docs publication ledger goes through this module on
+ * the `openDualScopeDb` chokepoint's drizzle handle ({@link getDb}) — gate 3
+ * (no raw opens) and gate 28 (no raw SQL writes to the syncing
+ * `docs_publications` table; the drizzle upsert compiles to the sanctioned
+ * `INSERT … ON CONFLICT … DO UPDATE` form).
+ *
+ * Semantics:
+ *
+ *   - Identity is NATURAL over (owner_id, blob_name, published_path): both
+ *     devices derive the same row uid for one triple, so a re-publish
+ *     coalesces onto one row (gate 37 declaration in
+ *     `row-identity-registry.ts`).
+ *   - {@link upsertDocsPublication} refreshes `last_blob_sha` /
+ *     `published_at` on conflict (latest-publish-wins); nothing is ever
+ *     DELETEd here.
+ *   - {@link readDocsPublications} carries a one-time, idempotent migration
+ *     shim: when the store table is empty and the legacy
+ *     `.cleo/docs-publications.json` still holds entries, they are seeded
+ *     into the table on first access. The shim is marked for follow-up in
+ *     T13362: once the JSON shim has shipped one release, drop the seed path.
+ *
+ * @module
+ * @task T13362
+ * @epic T13340
+ * @saga T13339
+ */
+import type { DocsPublicationRecord } from './docs-ops.js';
+/**
+ * Record (or refresh) one publication in the store ledger.
+ *
+ * Upserts on (ownerId, blobName, publishedPath). A conflicting row gets the
+ * fresh `lastBlobSha`/`publishedAt` so the ledger always reflects the latest
+ * known good publication; the row uid is the natural identity over the triple,
+ * so a concurrent publish on another device coalesces onto the same row.
+ *
+ * @param projectRoot - Absolute path to the CLEO project root.
+ * @param record - The publication facts; `publishedAt` is stamped here.
+ */
+export declare function upsertDocsPublication(projectRoot: string, record: Omit<DocsPublicationRecord, 'publishedAt'>): Promise<void>;
+/**
+ * Read every publication row from the store ledger.
+ *
+ * Legacy shim (T13362 follow-up: remove one release after ship): when the
+ * table is empty and `.cleo/docs-publications.json` still holds entries, the
+ * entries are seeded idempotently (natural-key insert, `ON CONFLICT DO
+ * NOTHING`) and a `.seeded` marker is written so the seed runs once. When the
+ * table already holds rows they are authoritative and the JSON is ignored.
+ *
+ * @param projectRoot - Absolute path to the CLEO project root.
+ * @returns All recorded publications (empty when none exist).
+ */
+export declare function readDocsPublications(projectRoot: string): Promise<DocsPublicationRecord[]>;
+/**
+ * Read the set of blob SHA-256 hashes named by any publication row.
+ *
+ * Used by the attachment janitor so a published blob is never declared
+ * unreferenced (and GC'd) while its publication lives.
+ *
+ * @param projectRoot - Absolute path to the CLEO project root.
+ * @returns Distinct `last_blob_sha` values across all publications.
+ */
+export declare function readDocsPublicationSha256Set(projectRoot: string): Promise<Set<string>>;
+//# sourceMappingURL=publications-store.d.ts.map

package/dist/docs/publications-store.d.ts.map

@@ -0,0 +1 @@
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