@cleocode/core 2026.9.7 → 2026.9.9

package/dist/memory/brain-backfill.d.ts

@@ -18,12 +18,14 @@
  *
  * T1003: Staged backfill functions (stagedBackfillRun, approveBackfillRun,
  * rollbackBackfillRun, listBackfillRuns) are appended below the graph
- * back-fill core. Staged runs write row IDs to brain_backfill_runs first;
- * actual mutations happen only on approve.
+ * back-fill core. Staged runs capture exact source/version and incident-edge
+ * preconditions in brain_backfill_runs; approval reconstructs only those missing
+ * nodes, without synthesizing edges or invoking the broad graph back-fill.
  *
  * @task T530
  * @epic T523
  */
+import type { KnowledgeBackfillOptions } from '@cleocode/contracts';
 import type { BrainBackfillRunRow } from '../store/schema/memory-schema.js';
 /** Result returned by backfillBrainGraph. */
 export interface BrainBackfillResult {
@@ -84,8 +86,9 @@ export interface StagedBackfillRunResult {
  *
  * Discovers all candidate node IDs from typed tables (decisions, patterns,
  * learnings, observations, sticky notes) that are NOT yet in brain_page_nodes.
- * Writes the list to `rollback_snapshot_json` and creates a `brain_backfill_runs`
- * row with status='staged'. No rows are inserted into brain tables.
+ * Captures exact nodes, source hashes, incident-edge fingerprints and project binding in
+ * `rollback_snapshot_json`, and creates a `brain_backfill_runs`
+ * row with status='staged'. The ledger is written, but derived graph rows are unchanged.
  *
  * Pass `source` as a human-readable descriptor (e.g. a file path or session ID).
  * Pass `kind` as the backfill kind (e.g. 'graph-backfill', 'observation-promotion').
@@ -95,18 +98,20 @@ export interface StagedBackfillRunResult {
  * @returns StagedBackfillRunResult with the staged run record.
  *
  * @task T1003
+ * @remarks The snapshot captures exact source and relationship preconditions without mutating derived nodes.
+ * @example
+ * ```ts
+ * const staged = await stagedBackfillRun(projectRoot, undefined);
+ * ```
  */
-export declare function stagedBackfillRun(projectRoot: string, opts?: {
-    source?: string;
-    kind?: string;
-    targetTable?: string;
-}): Promise<StagedBackfillRunResult>;
+export declare function stagedBackfillRun(projectRoot: string, opts?: KnowledgeBackfillOptions): Promise<StagedBackfillRunResult>;
 /**
  * Approve a staged backfill run, committing its rows to live brain tables.
  *
- * Reads the run record, validates that it is in 'staged' status, then triggers
- * `backfillBrainGraph` to perform the actual INSERT OR IGNORE work. Finally,
- * updates the run row to status='approved' with the current timestamp.
+ * Reads the staged run under a writer transaction, validates its exact source
+ * and graph preconditions, then inserts only its reviewed derived nodes. The
+ * same transaction records created-row hashes and approval metadata for recovery.
+ * Historical edges remain unchanged.
  *
  * Double-approve is idempotent: returns `{ alreadySettled: true }` if the run
  * is already approved or rolled-back.
@@ -117,6 +122,11 @@ export declare function stagedBackfillRun(projectRoot: string, opts?: {
  * @returns Result with the updated run record and graph backfill stats.
  *
  * @task T1003
+ * @remarks Approval inserts only the reviewed nodes and records recovery hashes atomically; stale source or graph state is rejected.
+ * @example
+ * ```ts
+ * const applied = await approveBackfillRun(projectRoot, runId, 'calling-agent');
+ * ```
  */
 export declare function approveBackfillRun(projectRoot: string, runId: string, approvedBy?: string): Promise<{
     run: BrainBackfillRunRow;
@@ -140,6 +150,11 @@ export declare function approveBackfillRun(projectRoot: string, runId: string, a
  * @returns Result with the updated run record and optional delete count.
  *
  * @task T1003
+ * @remarks Recovery removes only unchanged nodes created by this run and refuses concurrent node or edge edits.
+ * @example
+ * ```ts
+ * const restored = await rollbackBackfillRun(projectRoot, runId);
+ * ```
  */
 export declare function rollbackBackfillRun(projectRoot: string, runId: string): Promise<{
     run: BrainBackfillRunRow;

package/dist/memory/brain-backfill.d.ts.map

@@ -1 +1 @@
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package/dist/memory/brain-backfill.js

@@ -18,13 +18,16 @@
  *
  * T1003: Staged backfill functions (stagedBackfillRun, approveBackfillRun,
  * rollbackBackfillRun, listBackfillRuns) are appended below the graph
- * back-fill core. Staged runs write row IDs to brain_backfill_runs first;
- * actual mutations happen only on approve.
+ * back-fill core. Staged runs capture exact source/version and incident-edge
+ * preconditions in brain_backfill_runs; approval reconstructs only those missing
+ * nodes, without synthesizing edges or invoking the broad graph back-fill.
  *
  * @task T530
  * @epic T523
  */
 import { createHash, randomBytes } from 'node:crypto';
+import { realpathSync } from 'node:fs';
+import { z } from 'zod';
 import { getBrainAccessor } from '../store/memory-accessor.js';
 import { getBrainDb, getBrainNativeDb } from '../store/memory-sqlite.js';
 import * as brainSchema from '../store/schema/memory-schema.js';
@@ -403,13 +406,116 @@ function generateRunId() {
     const rand = randomBytes(2).toString('hex');
     return `bfr-${ts}-${rand}`;
 }
+const stagedSourceTableSchema = z.enum([
+    'brain_decisions',
+    'brain_patterns',
+    'brain_learnings',
+    'brain_observations',
+    'brain_sticky_notes',
+]);
+const stagedNodeSchema = z.object({
+    id: z.string(),
+    node_type: z.string(),
+    label: z.string(),
+    quality_score: z.number(),
+    content_hash: z.string(),
+    metadata_json: z.string(),
+    created_at: z.string(),
+    last_activity_at: z.string(),
+    updated_at: z.null(),
+});
+const stagedSnapshotSchema = z.object({
+    version: z.literal(2),
+    projectRoot: z.string(),
+    candidates: z
+        .array(z.object({
+        id: z.string(),
+        sourceTable: stagedSourceTableSchema,
+        sourceId: z.string(),
+        sourceHash: z.string(),
+        edgeHash: z.string(),
+        node: stagedNodeSchema,
+    }))
+        .max(500),
+    created: z
+        .array(z.object({ id: z.string(), rowHash: z.string(), edgeHash: z.string() }))
+        .max(500),
+});
+const stagedRunSchema = z.object({
+    id: z.string(),
+    kind: z.string(),
+    status: z.string(),
+    created_at: z.string(),
+    approved_at: z.string().nullable(),
+    rows_affected: z.number(),
+    rollback_snapshot_json: z.string().nullable(),
+    source: z.string(),
+    target_table: z.string(),
+    approved_by: z.string().nullable(),
+});
+const typedSourceSchema = z.record(z.string(), z.union([z.string(), z.number(), z.null()]));
+const sourceKinds = {
+    brain_decisions: 'decision',
+    brain_patterns: 'pattern',
+    brain_learnings: 'learning',
+    brain_observations: 'observation',
+    brain_sticky_notes: 'sticky',
+};
+const volatileSourceFields = new Set([
+    'access_count',
+    'last_accessed_at',
+    'citation_count',
+    'last_cited_at',
+    'updated_at',
+    'retrieval_count',
+    'last_retrieved_at',
+    'last_activity_at',
+    'reinforcement_count',
+]);
+/** Hash source content and provenance without treating retrieval counters as an edit. */
+function stagedSourceHash(row) {
+    return createHash('sha256')
+        .update(JSON.stringify(Object.entries(row)
+        .filter(([key]) => !volatileSourceFields.has(key))
+        .sort(([a], [b]) => a.localeCompare(b))))
+        .digest('hex');
+}
+/** Fingerprint exact graph rows, including concurrent relationship changes. */
+function stagedGraphHash(value) {
+    return createHash('sha256').update(JSON.stringify(value)).digest('hex');
+}
+/** Read all incident edges without modifying historical relationships. */
+function stagedEdgesHash(db, id) {
+    return stagedGraphHash(db
+        .prepare('SELECT * FROM main.brain_page_edges WHERE from_id = ? OR to_id = ? ORDER BY from_id, to_id, edge_type')
+        .all(id, id));
+}
+/** Reject legacy and cross-project snapshots rather than guessing which rows may be removed. */
+function readStagedSnapshot(raw, projectRoot) {
+    if (raw.target_table !== 'brain_page_nodes')
+        throw new Error('Staged backfill supports derived brain_page_nodes only.');
+    const parsed = stagedSnapshotSchema.safeParse(JSON.parse(raw.rollback_snapshot_json ?? 'null'));
+    if (!parsed.success)
+        throw new Error('Backfill snapshot lacks exact source and recovery preconditions; discard this staged run and stage a new run. Legacy approved runs require their canonical backup.');
+    if (parsed.data.projectRoot !== realpathSync(projectRoot))
+        throw new Error('Backfill project binding changed.');
+    return parsed.data;
+}
+/** Read a validated ledger row while the caller holds the writer transaction. */
+function readStagedRun(db, runId) {
+    const row = db.prepare('SELECT * FROM main.brain_backfill_runs WHERE id = ?').get(runId);
+    if (!row)
+        throw new Error(`Backfill run '${runId}' not found`);
+    return stagedRunSchema.parse(row);
+}
 /**
  * Stage a graph backfill run against brain_page_nodes / brain_page_edges.
  *
  * Discovers all candidate node IDs from typed tables (decisions, patterns,
  * learnings, observations, sticky notes) that are NOT yet in brain_page_nodes.
- * Writes the list to `rollback_snapshot_json` and creates a `brain_backfill_runs`
- * row with status='staged'. No rows are inserted into brain tables.
+ * Captures exact nodes, source hashes, incident-edge fingerprints and project binding in
+ * `rollback_snapshot_json`, and creates a `brain_backfill_runs`
+ * row with status='staged'. The ledger is written, but derived graph rows are unchanged.
  *
  * Pass `source` as a human-readable descriptor (e.g. a file path or session ID).
  * Pass `kind` as the backfill kind (e.g. 'graph-backfill', 'observation-promotion').
@@ -419,61 +525,108 @@ function generateRunId() {
  * @returns StagedBackfillRunResult with the staged run record.
  *
  * @task T1003
+ * @remarks The snapshot captures exact source and relationship preconditions without mutating derived nodes.
+ * @example
+ * ```ts
+ * const staged = await stagedBackfillRun(projectRoot, undefined);
+ * ```
  */
 export async function stagedBackfillRun(projectRoot, opts) {
-    const db = await getBrainDb(projectRoot);
-    const accessor = await getBrainAccessor(projectRoot);
-    const source = opts?.source ?? 'staged-run';
-    const kind = opts?.kind ?? 'graph-backfill';
-    const targetTable = opts?.targetTable ?? 'brain_page_nodes';
-    // Gather candidate IDs not yet in brain_page_nodes
-    const [decisions, patterns, learnings, observations, stickyNotes] = await Promise.all([
-        accessor.findDecisions(),
-        accessor.findPatterns(),
-        accessor.findLearnings(),
-        accessor.findObservations(),
-        accessor.findStickyNotes(),
-    ]);
-    // Collect candidate node IDs
-    const candidates = [
-        ...decisions.map((d) => `decision:${d.id}`),
-        ...patterns.map((p) => `pattern:${p.id}`),
-        ...learnings.map((l) => `learning:${l.id}`),
-        ...observations.map((o) => `observation:${o.id}`),
-        ...stickyNotes.map((s) => `sticky:${s.id}`),
-    ];
-    // Filter out IDs already present in brain_page_nodes
-    const existingNodes = await db
-        .select({ id: brainSchema.brainPageNodes.id })
-        .from(brainSchema.brainPageNodes);
-    const existingSet = new Set(existingNodes.map((n) => n.id));
-    const pendingIds = candidates.filter((id) => !existingSet.has(id));
-    const runId = generateRunId();
-    const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
-    const run = {
-        id: runId,
-        kind,
-        status: 'staged',
-        createdAt: now,
-        approvedAt: null,
-        rowsAffected: pendingIds.length,
-        rollbackSnapshotJson: JSON.stringify(pendingIds),
-        source,
-        targetTable,
-        approvedBy: null,
-    };
-    await db.insert(brainSchema.brainBackfillRuns).values(run);
-    return {
-        run,
-        empty: pendingIds.length === 0,
-    };
+    await getBrainDb(projectRoot);
+    const db = getBrainNativeDb(projectRoot);
+    if (!db)
+        throw new Error('brain.db native handle unavailable');
+    if (opts?.targetTable && opts.targetTable !== 'brain_page_nodes')
+        throw new Error('Staged backfill supports derived brain_page_nodes only.');
+    const selected = opts?.nodeIds === undefined
+        ? undefined
+        : z.array(z.string().min(1)).min(1).max(500).parse(opts.nodeIds);
+    if (selected && new Set(selected).size !== selected.length)
+        throw new Error('Backfill nodeIds must not contain duplicates.');
+    db.exec('BEGIN IMMEDIATE');
+    try {
+        const now = new Date().toISOString();
+        const snapshot = {
+            version: 2,
+            projectRoot: realpathSync(projectRoot),
+            candidates: [],
+            created: [],
+        };
+        for (const sourceTable of stagedSourceTableSchema.options) {
+            const kind = sourceKinds[sourceTable];
+            const selection = selected
+                ? ` AND (? || ':' || source.id) IN (${selected.map(() => '?').join(',')})`
+                : '';
+            const rows = db
+                .prepare(`SELECT source.* FROM main.${sourceTable} source
+        LEFT JOIN main.brain_page_nodes node ON node.id = ? || ':' || source.id
+        WHERE node.id IS NULL${selection} ORDER BY source.id LIMIT 501`)
+                .all(kind, ...(selected ? [kind, ...selected] : []));
+            for (const value of rows) {
+                const source = typedSourceSchema.parse(value);
+                if (typeof source.id !== 'string')
+                    throw new Error('Backfill source identifier is invalid');
+                const id = `${kind}:${source.id}`;
+                if (selected &&
+                    (source.invalid_at != null ||
+                        (kind === 'decision' &&
+                            (source.superseded_by != null || source.confirmation_state === 'superseded'))))
+                    throw new Error(`Selected backfill source ${id} is not currently eligible.`);
+                const sourceHash = stagedSourceHash(source);
+                const label = source.decision ?? source.pattern ?? source.insight ?? source.title ?? source.content;
+                if (typeof label !== 'string' || !label.trim())
+                    throw new Error(`Backfill source ${id} has no substantive label; resolve it before staging.`);
+                snapshot.candidates.push({
+                    id,
+                    sourceId: source.id,
+                    sourceTable,
+                    sourceHash,
+                    edgeHash: stagedEdgesHash(db, id),
+                    node: {
+                        id,
+                        node_type: kind,
+                        label: label.slice(0, 200),
+                        quality_score: typeof source.quality_score === 'number' ? source.quality_score : 0.5,
+                        content_hash: sourceHash,
+                        metadata_json: JSON.stringify({
+                            sourceTable,
+                            sourceId: source.id,
+                            sourceHash,
+                            derived: true,
+                        }),
+                        created_at: now,
+                        last_activity_at: now,
+                        updated_at: null,
+                    },
+                });
+                if (snapshot.candidates.length > 500)
+                    throw new Error('More than 500 missing nodes require a bounded source selection before staging.');
+            }
+        }
+        if (selected && snapshot.candidates.length !== selected.length) {
+            const found = new Set(snapshot.candidates.map((candidate) => candidate.id));
+            throw new Error(`Selected backfill IDs are missing, already indexed, or unsupported: ${selected.filter((id) => !found.has(id)).join(', ')}`);
+        }
+        const id = generateRunId();
+        db.prepare(`INSERT INTO main.brain_backfill_runs
+      (id, kind, status, created_at, rows_affected, rollback_snapshot_json, source, target_table)
+      VALUES (?, ?, 'staged', ?, ?, ?, ?, 'brain_page_nodes')`).run(id, opts?.kind ?? 'graph-backfill', now, snapshot.candidates.length, JSON.stringify(snapshot), opts?.source ?? 'staged-run');
+        const run = mapRunRow(readStagedRun(db, id));
+        db.exec('COMMIT');
+        return { run, empty: snapshot.candidates.length === 0 };
+    }
+    catch (error) {
+        db.exec('ROLLBACK');
+        throw error;
+    }
 }
 /**
  * Approve a staged backfill run, committing its rows to live brain tables.
  *
- * Reads the run record, validates that it is in 'staged' status, then triggers
- * `backfillBrainGraph` to perform the actual INSERT OR IGNORE work. Finally,
- * updates the run row to status='approved' with the current timestamp.
+ * Reads the staged run under a writer transaction, validates its exact source
+ * and graph preconditions, then inserts only its reviewed derived nodes. The
+ * same transaction records created-row hashes and approval metadata for recovery.
+ * Historical edges remain unchanged.
  *
  * Double-approve is idempotent: returns `{ alreadySettled: true }` if the run
  * is already approved or rolled-back.
@@ -484,43 +637,91 @@ export async function stagedBackfillRun(projectRoot, opts) {
  * @returns Result with the updated run record and graph backfill stats.
  *
  * @task T1003
+ * @remarks Approval inserts only the reviewed nodes and records recovery hashes atomically; stale source or graph state is rejected.
+ * @example
+ * ```ts
+ * const applied = await approveBackfillRun(projectRoot, runId, 'calling-agent');
+ * ```
  */
 export async function approveBackfillRun(projectRoot, runId, approvedBy) {
     await getBrainDb(projectRoot);
-    const nativeDb = getBrainNativeDb(projectRoot);
-    if (!nativeDb) {
+    const db = getBrainNativeDb(projectRoot);
+    if (!db)
         throw new Error('brain.db native handle unavailable');
+    db.exec('BEGIN IMMEDIATE');
+    try {
+        const raw = readStagedRun(db, runId);
+        if (raw.status === 'approved' || raw.status === 'rolled-back') {
+            db.exec('COMMIT');
+            return { run: mapRunRow(raw), alreadySettled: true };
+        }
+        if (raw.status !== 'staged')
+            throw new Error('Backfill run is not staged.');
+        const snapshot = readStagedSnapshot(raw, projectRoot);
+        if (snapshot.created.length)
+            throw new Error('Staged backfill unexpectedly contains committed nodes.');
+        const beforeNodes = Number(db.prepare('SELECT COUNT(*) AS count FROM main.brain_page_nodes').get()?.count);
+        const beforeEdges = Number(db.prepare('SELECT COUNT(*) AS count FROM main.brain_page_edges').get()?.count);
+        const typedCounts = Object.fromEntries(stagedSourceTableSchema.options.map((table) => [
+            table,
+            Number(db.prepare(`SELECT COUNT(*) AS count FROM main.${table}`).get()?.count),
+        ]));
+        for (const candidate of snapshot.candidates) {
+            const current = typedSourceSchema.parse(db
+                .prepare(`SELECT * FROM main.${candidate.sourceTable} WHERE id = ?`)
+                .get(candidate.sourceId));
+            if (candidate.id !== `${sourceKinds[candidate.sourceTable]}:${candidate.sourceId}` ||
+                candidate.node.id !== candidate.id ||
+                stagedSourceHash(current) !== candidate.sourceHash ||
+                db.prepare('SELECT id FROM main.brain_page_nodes WHERE id = ?').get(candidate.id) ||
+                stagedEdgesHash(db, candidate.id) !== candidate.edgeHash)
+                throw new Error(`Backfill proposal is stale for ${candidate.id}; stage a new run.`);
+        }
+        const insert = db.prepare(`INSERT INTO main.brain_page_nodes
+      (id, node_type, label, quality_score, content_hash, metadata_json, created_at, last_activity_at, updated_at)
+      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)`);
+        const byType = {};
+        for (const candidate of snapshot.candidates) {
+            const node = candidate.node;
+            insert.run(node.id, node.node_type, node.label, node.quality_score, node.content_hash, node.metadata_json, node.created_at, node.last_activity_at, node.updated_at);
+            const created = db.prepare('SELECT * FROM main.brain_page_nodes WHERE id = ?').get(node.id);
+            if (!created)
+                throw new Error('Created backfill node is unreadable');
+            snapshot.created.push({
+                id: node.id,
+                rowHash: stagedGraphHash(created),
+                edgeHash: stagedEdgesHash(db, node.id),
+            });
+            byType[node.node_type] = (byType[node.node_type] ?? 0) + 1;
+        }
+        db.prepare(`UPDATE main.brain_backfill_runs SET status = 'approved', approved_at = ?, approved_by = ?, rollback_snapshot_json = ? WHERE id = ?`).run(new Date().toISOString(), approvedBy ?? 'owner', JSON.stringify(snapshot), runId);
+        const run = mapRunRow(readStagedRun(db, runId));
+        db.exec('COMMIT');
+        return {
+            run,
+            alreadySettled: false,
+            backfillResult: {
+                before: {
+                    nodes: beforeNodes,
+                    edges: beforeEdges,
+                    decisions: typedCounts['brain_decisions'] ?? 0,
+                    patterns: typedCounts['brain_patterns'] ?? 0,
+                    learnings: typedCounts['brain_learnings'] ?? 0,
+                    observations: typedCounts['brain_observations'] ?? 0,
+                    stickyNotes: typedCounts['brain_sticky_notes'] ?? 0,
+                },
+                after: { nodes: beforeNodes + snapshot.created.length, edges: beforeEdges },
+                nodesInserted: snapshot.created.length,
+                edgesInserted: 0,
+                stubsCreated: 0,
+                byType,
+            },
+        };
     }
-    const rawRun = nativeDb
-        .prepare('SELECT * FROM brain_backfill_runs WHERE id = ? LIMIT 1')
-        .get(runId);
-    if (!rawRun) {
-        throw new Error(`Backfill run '${runId}' not found`);
-    }
-    // If already settled, return as-is
-    if (rawRun.status === 'approved' || rawRun.status === 'rolled-back') {
-        const run = mapRunRow(rawRun);
-        return { run, alreadySettled: true };
+    catch (error) {
+        db.exec('ROLLBACK');
+        throw error;
     }
-    // Execute the actual backfill
-    const backfillResult = await backfillBrainGraph(projectRoot);
-    // Mark run as approved
-    const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
-    const approver = approvedBy ?? 'owner';
-    nativeDb
-        .prepare(`UPDATE brain_backfill_runs
-       SET status = 'approved', approved_at = ?, approved_by = ?
-       WHERE id = ?`)
-        .run(now, approver, runId);
-    // Re-fetch updated run
-    const updatedRaw = nativeDb
-        .prepare('SELECT * FROM brain_backfill_runs WHERE id = ? LIMIT 1')
-        .get(runId);
-    return {
-        run: mapRunRow(updatedRaw),
-        alreadySettled: false,
-        backfillResult,
-    };
 }
 /**
  * Rollback a staged backfill run, discarding staged rows.
@@ -539,64 +740,54 @@ export async function approveBackfillRun(projectRoot, runId, approvedBy) {
  * @returns Result with the updated run record and optional delete count.
  *
  * @task T1003
+ * @remarks Recovery removes only unchanged nodes created by this run and refuses concurrent node or edge edits.
+ * @example
+ * ```ts
+ * const restored = await rollbackBackfillRun(projectRoot, runId);
+ * ```
  */
 export async function rollbackBackfillRun(projectRoot, runId) {
     await getBrainDb(projectRoot);
-    const nativeDb = getBrainNativeDb(projectRoot);
-    if (!nativeDb) {
+    const db = getBrainNativeDb(projectRoot);
+    if (!db)
         throw new Error('brain.db native handle unavailable');
-    }
-    const rawRun = nativeDb
-        .prepare('SELECT * FROM brain_backfill_runs WHERE id = ? LIMIT 1')
-        .get(runId);
-    if (!rawRun) {
-        throw new Error(`Backfill run '${runId}' not found`);
-    }
-    // Already rolled back — idempotent no-op
-    if (rawRun.status === 'rolled-back') {
-        return { run: mapRunRow(rawRun), alreadySettled: true, deletedRows: 0 };
-    }
-    let deletedRows = 0;
-    // If already approved, we need to DELETE committed rows from the target table
-    if (rawRun.status === 'approved' && rawRun.rollback_snapshot_json) {
-        let ids = [];
-        try {
-            ids = JSON.parse(rawRun.rollback_snapshot_json);
-        }
-        catch {
-            // Malformed snapshot — proceed without deleting
+    db.exec('BEGIN IMMEDIATE');
+    try {
+        const raw = readStagedRun(db, runId);
+        if (raw.status === 'rolled-back') {
+            db.exec('COMMIT');
+            return { run: mapRunRow(raw), alreadySettled: true, deletedRows: 0 };
         }
-        if (ids.length > 0) {
-            const targetTable = rawRun.target_table;
-            // Validate table name against known brain tables (prevent SQL injection)
-            const allowedTables = [
-                'brain_page_nodes',
-                'brain_observations',
-                'brain_decisions',
-                'brain_patterns',
-                'brain_learnings',
-                'brain_transcript_events',
-            ];
-            if (allowedTables.includes(targetTable)) {
-                // SQLite has a limit of ~999 bound params — chunk if needed
-                const CHUNK = 200;
-                for (let i = 0; i < ids.length; i += CHUNK) {
-                    const chunk = ids.slice(i, i + CHUNK);
-                    const placeholders = chunk.map(() => '?').join(',');
-                    const result = nativeDb
-                        .prepare(`DELETE FROM ${targetTable} WHERE id IN (${placeholders})`)
-                        .run(...chunk);
-                    deletedRows += result.changes ?? 0;
-                }
+        let deletedRows = 0;
+        if (raw.status === 'approved') {
+            const snapshot = readStagedSnapshot(raw, projectRoot);
+            if (snapshot.created.length !== snapshot.candidates.length)
+                throw new Error('Backfill receipt does not cover every created node.');
+            for (const created of snapshot.created) {
+                const current = db
+                    .prepare('SELECT * FROM main.brain_page_nodes WHERE id = ?')
+                    .get(created.id);
+                if (!current ||
+                    stagedGraphHash(current) !== created.rowHash ||
+                    stagedEdgesHash(db, created.id) !== created.edgeHash)
+                    throw new Error(`Backfill rollback is stale for ${created.id}; preserve concurrent changes and inspect the canonical backup.`);
+            }
+            for (const created of snapshot.created) {
+                const result = db.prepare('DELETE FROM main.brain_page_nodes WHERE id = ?').run(created.id);
+                deletedRows += Number(result.changes);
             }
         }
+        else if (raw.status !== 'staged')
+            throw new Error('Backfill run cannot be rolled back from its current state.');
+        db.prepare("UPDATE main.brain_backfill_runs SET status = 'rolled-back' WHERE id = ?").run(runId);
+        const run = mapRunRow(readStagedRun(db, runId));
+        db.exec('COMMIT');
+        return { run, alreadySettled: false, deletedRows };
+    }
+    catch (error) {
+        db.exec('ROLLBACK');
+        throw error;
     }
-    // Mark run as rolled-back
-    nativeDb.prepare(`UPDATE brain_backfill_runs SET status = 'rolled-back' WHERE id = ?`).run(runId);
-    const updatedRaw = nativeDb
-        .prepare('SELECT * FROM brain_backfill_runs WHERE id = ? LIMIT 1')
-        .get(runId);
-    return { run: mapRunRow(updatedRaw), alreadySettled: false, deletedRows };
 }
 /**
  * List backfill runs, optionally filtered by status.