@cleocode/core 2026.9.7 → 2026.9.9

package/dist/memory/retrieval/search.d.ts

@@ -20,6 +20,11 @@ export type { BudgetedEntry, BudgetedResult, BudgetedRetrievalOptions } from '@c
  * @param projectRoot - Project root directory
  * @param params - Search parameters
  * @returns Compact search results with token estimate
+ * @remarks Explicit project ownership and the inherited operation lifetime are
+ * captured before asynchronous reads. Optional citation and retrieval-log writes
+ * are registered before return so the existing background barrier can await them.
+ * Session attribution is resolved before scheduling. Telemetry remains best-effort;
+ * this result does not claim durable telemetry outcomes or complete runtime callers.
  *
  * @example
  * ```ts
@@ -55,13 +60,21 @@ export declare function searchBrainCompact(projectRoot: string, params: SearchBr
  *   - Walk list, accumulate token cost (≈ textLen/4), stop at budget.
  *   - Episodic entries dropped first when budget is tight.
  *
- * Citation tracking: increments citationCount for returned entries in background (setImmediate).
+ * Citation tracking uses the existing background lifecycle barrier.
  *
  * @param projectRoot - Project root directory
  * @param query - Text to search for
  * @param tokenBudget - Maximum tokens to spend on results (default 500)
  * @param options - Optional filters (types, tiers, verified)
  * @returns Retrieved entries within budget with token accounting
+ * @remarks Explicit project scope and inherited execution are captured before
+ * reads. Citation writes retain that original deadline and cancellation; no new
+ * maintenance budget is created. Underlying telemetry remains best-effort and is
+ * not represented as a durable receipt in this result.
+ * @example
+ * ```ts
+ * const result = await retrieveWithBudget(projectRoot, 'authentication', 500);
+ * ```
  */
 export declare function retrieveWithBudget(projectRoot: string, query: string, tokenBudget?: number, options?: BudgetedRetrievalOptions): Promise<BudgetedResult>;
 //# sourceMappingURL=search.d.ts.map

package/dist/memory/retrieval/search.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../../src/memory/retrieval/search.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAGV,cAAc,EACd,wBAAwB,EACxB,wBAAwB,EACxB,wBAAwB,EACzB,MAAM,qBAAqB,CAAC;AAS7B,YAAY,EAAE,aAAa,EAAE,cAAc,EAAE,wBAAwB,EAAE,MAAM,qBAAqB,CAAC;AAMnG;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AACH,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,wBAAwB,GAC/B,OAAO,CAAC,wBAAwB,CAAC,CAmTnC;AASD;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AACH,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,MAAM,EACb,WAAW,SAAuB,EAClC,OAAO,CAAC,EAAE,wBAAwB,GACjC,OAAO,CAAC,cAAc,CAAC,CA0RzB"}
+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../../src/memory/retrieval/search.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAGV,cAAc,EACd,wBAAwB,EACxB,wBAAwB,EACxB,wBAAwB,EACzB,MAAM,qBAAqB,CAAC;AAS7B,YAAY,EAAE,aAAa,EAAE,cAAc,EAAE,wBAAwB,EAAE,MAAM,qBAAqB,CAAC;AAMnG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AACH,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,wBAAwB,GAC/B,OAAO,CAAC,wBAAwB,CAAC,CAGnC;AA4XD;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgCG;AACH,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,MAAM,EACb,WAAW,SAAuB,EAClC,OAAO,CAAC,EAAE,wBAAwB,GACjC,OAAO,CAAC,cAAc,CAAC,CAKzB"}

package/dist/memory/retrieval/search.js

@@ -9,11 +9,11 @@
  * @epic T5149
  */
 import { memoryFindHitNext } from '../../mvi-helpers.js';
+import { captureProjectScope, worktreeScope } from '../../project-scope.js';
 import { hybridSearch, searchBrain } from '../brain-search.js';
 import { searchSimilar } from '../brain-similarity.js';
-import { getCurrentSessionId } from './get-current-session-id.js';
-import { incrementCitationCounts } from './increment-citation-counts.js';
-import { logRetrieval } from './log-retrieval.js';
+import { isCurrentMemoryEntry, memoryEligibilityClause } from '../eligibility.js';
+import { scheduleCitationTracking, scheduleRetrievalTelemetry } from './telemetry.js';
 // ============================================================================
 // Layer 1: Compact Search
 // ============================================================================
@@ -27,6 +27,11 @@ import { logRetrieval } from './log-retrieval.js';
  * @param projectRoot - Project root directory
  * @param params - Search parameters
  * @returns Compact search results with token estimate
+ * @remarks Explicit project ownership and the inherited operation lifetime are
+ * captured before asynchronous reads. Optional citation and retrieval-log writes
+ * are registered before return so the existing background barrier can await them.
+ * Session attribution is resolved before scheduling. Telemetry remains best-effort;
+ * this result does not claim durable telemetry outcomes or complete runtime callers.
  *
  * @example
  * ```ts
@@ -45,7 +50,67 @@ import { logRetrieval } from './log-retrieval.js';
  * ```
  */
 export async function searchBrainCompact(projectRoot, params) {
-    const { query, limit, tables, dateStart, dateEnd, agent, useRRF = true, peerId, includeGlobal, mode, since, } = params;
+    const scope = captureProjectScope(projectRoot, worktreeScope.getStore());
+    return worktreeScope.run(scope, () => searchBrainCompactScoped(scope.worktreeRoot, params));
+}
+async function searchBrainCompactScoped(projectRoot, params) {
+    if (params.agent && params.tables?.some((table) => table !== 'observations'))
+        throw new Error('Agent provenance filtering only supports observations');
+    const result = await searchBrainCompactCurrent(projectRoot, params);
+    if (params.includeHistory ||
+        params.agent ||
+        (params.tables && !params.tables.includes('decisions')) ||
+        !params.query.trim())
+        return result;
+    const historical = await searchBrain(projectRoot, params.query, {
+        tables: ['decisions'],
+        limit: Math.max(params.limit ?? 10, 10),
+        includeHistory: true,
+        peerId: params.peerId,
+        includeGlobal: params.includeGlobal,
+    });
+    const { getBrainAccessor } = await import('../../store/memory-accessor.js');
+    const accessor = await getBrainAccessor(projectRoot);
+    for (const match of historical.decisions) {
+        let decision = await accessor.getDecision(match.id);
+        const seen = new Set();
+        while (decision?.supersededBy && !seen.has(decision.id) && seen.size < 32) {
+            seen.add(decision.id);
+            decision = await accessor.getDecision(decision.supersededBy);
+        }
+        if (!decision || decision.id === match.id || !isCurrentMemoryEntry(decision))
+            continue;
+        if (params.peerId &&
+            decision.peerId !== params.peerId &&
+            !(params.includeGlobal !== false && decision.peerId === 'global'))
+            continue;
+        const date = decision.createdAt ?? '';
+        if ((params.since && date < params.since) ||
+            (params.dateStart && date < params.dateStart) ||
+            (params.dateEnd && date > params.dateEnd))
+            continue;
+        const existing = result.results.find((hit) => hit.id === decision.id && hit.type === 'decision');
+        if (existing) {
+            existing.matchedHistoricalIds = [...(existing.matchedHistoricalIds ?? []), match.id];
+        }
+        else {
+            result.results.unshift({
+                id: decision.id,
+                type: 'decision',
+                title: decision.decision.slice(0, 80),
+                date,
+                matchedHistoricalIds: [match.id],
+                _next: memoryFindHitNext(decision.id),
+            });
+        }
+    }
+    result.results = result.results.slice(0, params.limit ?? 10);
+    result.total = result.results.length;
+    result.tokensEstimated = result.total * 50;
+    return result;
+}
+async function searchBrainCompactCurrent(projectRoot, params) {
+    const { query, limit, tables, dateStart, dateEnd, agent, useRRF = true, peerId, includeGlobal, mode, since, includeHistory = false, } = params;
     if (!query?.trim()) {
         return { results: [], total: 0, tokensEstimated: 0 };
     }
@@ -61,41 +126,54 @@ export async function searchBrainCompact(projectRoot, params) {
             return { results: [], total: 0, tokensEstimated: 0 };
         }
         // Determine which tables to query
-        const targetTables = tables && tables.length > 0 ? tables : ['observations', 'learnings', 'patterns', 'decisions'];
-        const sinceClause = since ? ` AND created_at >= '${since}'` : '';
-        const dateStartClause = dateStart ? ` AND created_at >= '${dateStart}'` : '';
-        const dateEndClause = dateEnd ? ` AND created_at <= '${dateEnd}'` : '';
-        const perTableLimit = effectiveLimit * 2;
+        const targetTables = tables && tables.length > 0
+            ? tables
+            : ['observations', 'learnings', 'patterns', 'decisions'];
         const results = [];
         for (const table of targetTables) {
-            let sql;
-            if (table === 'observations') {
-                sql = `SELECT id, title, created_at FROM brain_observations WHERE 1=1${sinceClause}${dateStartClause}${dateEndClause} ORDER BY created_at DESC LIMIT ${perTableLimit}`;
-            }
-            else if (table === 'learnings') {
-                sql = `SELECT id, insight AS title, created_at FROM brain_learnings WHERE 1=1${sinceClause}${dateStartClause}${dateEndClause} ORDER BY created_at DESC LIMIT ${perTableLimit}`;
-            }
-            else if (table === 'patterns') {
-                sql = `SELECT id, pattern AS title, extracted_at AS created_at FROM brain_patterns WHERE 1=1${since ? ` AND extracted_at >= '${since}'` : ''}${dateStart ? ` AND extracted_at >= '${dateStart}'` : ''}${dateEnd ? ` AND extracted_at <= '${dateEnd}'` : ''} ORDER BY extracted_at DESC LIMIT ${perTableLimit}`;
+            const titleColumn = table === 'decisions'
+                ? 'decision'
+                : table === 'learnings'
+                    ? 'insight'
+                    : table === 'patterns'
+                        ? 'pattern'
+                        : 'title';
+            const dateColumn = table === 'patterns' ? 'extracted_at' : 'created_at';
+            const filters = [];
+            const values = [];
+            for (const lower of [since, dateStart]) {
+                if (lower) {
+                    filters.push(`${dateColumn} >= ?`);
+                    values.push(lower);
+                }
             }
-            else {
-                // decisions
-                sql = `SELECT id, decision AS title, created_at FROM brain_decisions WHERE 1=1${sinceClause}${dateStartClause}${dateEndClause} ORDER BY created_at DESC LIMIT ${perTableLimit}`;
+            if (dateEnd) {
+                filters.push(`${dateColumn} <= ?`);
+                values.push(dateEnd);
             }
-            try {
-                const rows = nativeDb.prepare(sql).all();
-                for (const row of rows) {
-                    results.push({
-                        id: row.id,
-                        type: table.replace(/s$/, ''),
-                        title: (row.title ?? '').slice(0, 80),
-                        date: row.created_at ?? '',
-                        relevance: 0,
-                    });
+            const dates = filters.length ? ` AND ${filters.join(' AND ')}` : '';
+            const rows = nativeDb
+                .prepare(`SELECT id, ${titleColumn} AS title, ${dateColumn} AS created_at FROM main.brain_${table} WHERE 1=1${memoryEligibilityClause(table, undefined, includeHistory)}${dates} ORDER BY ${dateColumn} DESC LIMIT ?`)
+                .all(...values, effectiveLimit * 2);
+            for (const row of rows) {
+                if (typeof row.id !== 'string' ||
+                    typeof row.title !== 'string' ||
+                    typeof row.created_at !== 'string') {
+                    throw new Error(`Invalid source row in brain_${table}`);
                 }
-            }
-            catch {
-                // table missing or DB error — skip
+                results.push({
+                    id: row.id,
+                    type: table === 'decisions'
+                        ? 'decision'
+                        : table === 'patterns'
+                            ? 'pattern'
+                            : table === 'learnings'
+                                ? 'learning'
+                                : 'observation',
+                    title: row.title.slice(0, 80),
+                    date: row.created_at,
+                    relevance: 0,
+                });
             }
         }
         // Sort globally by date descending, then trim to limit
@@ -107,7 +185,8 @@ export async function searchBrainCompact(projectRoot, params) {
         return { results: trimmed, total: trimmed.length, tokensEstimated: trimmed.length * 50 };
     }
     // ----- RRF path (default or mode=hybrid) -----
-    if ((useRRF && !agentFilter && mode !== 'lexical') || (mode === 'hybrid' && !agentFilter)) {
+    if (!includeHistory &&
+        ((useRRF && !agentFilter && mode !== 'lexical') || (mode === 'hybrid' && !agentFilter))) {
         // Run FTS (for dates + table-level data) and RRF fusion in parallel.
         // FTS gives us row-level dates; RRF gives us the fused ranking order.
         const [ftsResult, rrfResults] = await Promise.all([
@@ -116,12 +195,7 @@ export async function searchBrainCompact(projectRoot, params) {
                 tables,
                 peerId,
                 includeGlobal,
-            }).catch(() => ({
-                decisions: [],
-                patterns: [],
-                learnings: [],
-                observations: [],
-            })),
+            }),
             hybridSearch(query, projectRoot, { limit: effectiveLimit * 2 }),
         ]);
         // Build a date map from FTS rows (id -> date string)
@@ -192,14 +266,7 @@ export async function searchBrainCompact(projectRoot, params) {
         }
         if (results.length > 0) {
             const returnedIds = results.map((r) => r.id);
-            setImmediate(() => {
-                incrementCitationCounts(projectRoot, returnedIds).catch(() => { });
-                getCurrentSessionId(projectRoot)
-                    .then((sessionId) => {
-                    return logRetrieval(projectRoot, query, returnedIds, 'find-rrf', results.length * 50, sessionId);
-                })
-                    .catch(() => { });
-            });
+            await scheduleRetrievalTelemetry(projectRoot, query, returnedIds, 'find-rrf', results.length * 50);
         }
         return { results, total: results.length, tokensEstimated: results.length * 50 };
     }
@@ -212,6 +279,7 @@ export async function searchBrainCompact(projectRoot, params) {
         tables: effectiveTables,
         peerId,
         includeGlobal,
+        includeHistory,
     });
     // Project full results to compact format.
     // Note: searchBrain() returns rows from raw SQL (nativeDb) which use
@@ -276,14 +344,7 @@ export async function searchBrainCompact(projectRoot, params) {
     // Citation tracking + retrieval logging (non-blocking)
     if (results.length > 0) {
         const returnedIds = results.map((r) => r.id);
-        setImmediate(() => {
-            incrementCitationCounts(projectRoot, returnedIds).catch(() => { });
-            getCurrentSessionId(projectRoot)
-                .then((sessionId) => {
-                return logRetrieval(projectRoot, query, returnedIds, 'find', results.length * 50, sessionId);
-            })
-                .catch(() => { });
-        });
+        await scheduleRetrievalTelemetry(projectRoot, query, returnedIds, 'find', results.length * 50);
     }
     return {
         results,
@@ -313,15 +374,27 @@ const DEFAULT_TOKEN_BUDGET = 500;
  *   - Walk list, accumulate token cost (≈ textLen/4), stop at budget.
  *   - Episodic entries dropped first when budget is tight.
  *
- * Citation tracking: increments citationCount for returned entries in background (setImmediate).
+ * Citation tracking uses the existing background lifecycle barrier.
  *
  * @param projectRoot - Project root directory
  * @param query - Text to search for
  * @param tokenBudget - Maximum tokens to spend on results (default 500)
  * @param options - Optional filters (types, tiers, verified)
  * @returns Retrieved entries within budget with token accounting
+ * @remarks Explicit project scope and inherited execution are captured before
+ * reads. Citation writes retain that original deadline and cancellation; no new
+ * maintenance budget is created. Underlying telemetry remains best-effort and is
+ * not represented as a durable receipt in this result.
+ * @example
+ * ```ts
+ * const result = await retrieveWithBudget(projectRoot, 'authentication', 500);
+ * ```
  */
 export async function retrieveWithBudget(projectRoot, query, tokenBudget = DEFAULT_TOKEN_BUDGET, options) {
+    const scope = captureProjectScope(projectRoot, worktreeScope.getStore());
+    return worktreeScope.run(scope, () => retrieveWithBudgetScoped(scope.worktreeRoot, query, tokenBudget, options));
+}
+async function retrieveWithBudgetScoped(projectRoot, query, tokenBudget, options) {
     if (!query?.trim()) {
         return { entries: [], tokensUsed: 0, tokensRemaining: tokenBudget, excluded: 0 };
     }
@@ -330,12 +403,7 @@ export async function retrieveWithBudget(projectRoot, query, tokenBudget = DEFAU
     // -------------------------------------------------------------------------
     const [ftsResult, vecResults, graphNeighbors] = await Promise.all([
         // A. FTS5
-        searchBrain(projectRoot, query, { limit: 30 }).catch(() => ({
-            decisions: [],
-            patterns: [],
-            learnings: [],
-            observations: [],
-        })),
+        searchBrain(projectRoot, query, { limit: 30 }),
         // B. Vector KNN (degrades gracefully when unavailable)
         searchSimilar(query, projectRoot, 20).catch(() => []),
         // C. Graph neighbors from top FTS hit
@@ -550,11 +618,7 @@ export async function retrieveWithBudget(projectRoot, query, tokenBudget = DEFAU
     // -------------------------------------------------------------------------
     if (result.length > 0) {
         const returnedIds = result.map((e) => e.id);
-        setImmediate(() => {
-            incrementCitationCounts(projectRoot, returnedIds).catch(() => {
-                /* best-effort */
-            });
-        });
+        scheduleCitationTracking(projectRoot, returnedIds);
     }
     return {
         entries: result,

package/dist/memory/retrieval/search.js.map

@@ -1 +1 @@
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package/dist/memory/retrieval/telemetry.d.ts

@@ -0,0 +1,31 @@
+/**
+ * Register optional citation writes within the caller's captured ownership.
+ * @param projectRoot - Explicit owning project root.
+ * @param entryIds - Returned evidence identities copied before scheduling.
+ * @returns No durable receipt; the existing background barrier observes completion.
+ * @remarks Reuses the inherited execution deadline and cancellation without a new
+ * budget or queue. Underlying citation failures remain best-effort.
+ * @example
+ * ```ts
+ * scheduleCitationTracking(projectRoot, ['O-example']);
+ * ```
+ */
+export declare function scheduleCitationTracking(projectRoot: string, entryIds: string[]): void;
+/**
+ * Capture attribution, then independently register citations and a retrieval log.
+ * @param projectRoot - Explicit owning project root.
+ * @param query - Original search query or exact fetched identity list.
+ * @param entryIds - Returned evidence identities copied before asynchronous work.
+ * @param source - Existing retrieval path label retained in the log.
+ * @param tokensUsed - Existing estimated token count, without recalculating policy.
+ * @returns Completion of session capture and scheduling, not a durable telemetry receipt.
+ * @remarks Both writers retain the original operation lifetime. A failed sibling
+ * cannot release the barrier over pending work. No global session is resolved
+ * after scheduling; underlying telemetry failures remain best-effort.
+ * @example
+ * ```ts
+ * await scheduleRetrievalTelemetry(projectRoot, 'auth', ['O-example'], 'find', 50);
+ * ```
+ */
+export declare function scheduleRetrievalTelemetry(projectRoot: string, query: string, entryIds: string[], source: string, tokensUsed: number): Promise<void>;
+//# sourceMappingURL=telemetry.d.ts.map

package/dist/memory/retrieval/telemetry.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"telemetry.d.ts","sourceRoot":"","sources":["../../../src/memory/retrieval/telemetry.ts"],"names":[],"mappings":"AAWA;;;;;;;;;;;GAWG;AACH,wBAAgB,wBAAwB,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,IAAI,CAOtF;AAED;;;;;;;;;;;;;;;GAeG;AACH,wBAAsB,0BAA0B,CAC9C,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,MAAM,EAAE,EAClB,MAAM,EAAE,MAAM,EACd,UAAU,EAAE,MAAM,GACjB,OAAO,CAAC,IAAI,CAAC,CAcf"}

package/dist/memory/retrieval/telemetry.js

@@ -0,0 +1,53 @@
+/**
+ * Optional retrieval telemetry registered with the existing operation lifecycle.
+ * Code placed in `packages/core/` per Package-Boundary Check — verified against AGENTS.md.
+ * @packageDocumentation
+ */
+import { captureProjectScope, worktreeScope } from '../../project-scope.js';
+import { trackBackgroundOp } from '../../store/background-ops.js';
+import { getCurrentSessionId } from './get-current-session-id.js';
+import { incrementCitationCounts } from './increment-citation-counts.js';
+import { logRetrieval } from './log-retrieval.js';
+/**
+ * Register optional citation writes within the caller's captured ownership.
+ * @param projectRoot - Explicit owning project root.
+ * @param entryIds - Returned evidence identities copied before scheduling.
+ * @returns No durable receipt; the existing background barrier observes completion.
+ * @remarks Reuses the inherited execution deadline and cancellation without a new
+ * budget or queue. Underlying citation failures remain best-effort.
+ * @example
+ * ```ts
+ * scheduleCitationTracking(projectRoot, ['O-example']);
+ * ```
+ */
+export function scheduleCitationTracking(projectRoot, entryIds) {
+    const scope = captureProjectScope(projectRoot, worktreeScope.getStore());
+    const ids = [...entryIds];
+    trackBackgroundOp(() => worktreeScope.run(scope, () => incrementCitationCounts(scope.worktreeRoot, ids)), scope.execution);
+}
+/**
+ * Capture attribution, then independently register citations and a retrieval log.
+ * @param projectRoot - Explicit owning project root.
+ * @param query - Original search query or exact fetched identity list.
+ * @param entryIds - Returned evidence identities copied before asynchronous work.
+ * @param source - Existing retrieval path label retained in the log.
+ * @param tokensUsed - Existing estimated token count, without recalculating policy.
+ * @returns Completion of session capture and scheduling, not a durable telemetry receipt.
+ * @remarks Both writers retain the original operation lifetime. A failed sibling
+ * cannot release the barrier over pending work. No global session is resolved
+ * after scheduling; underlying telemetry failures remain best-effort.
+ * @example
+ * ```ts
+ * await scheduleRetrievalTelemetry(projectRoot, 'auth', ['O-example'], 'find', 50);
+ * ```
+ */
+export async function scheduleRetrievalTelemetry(projectRoot, query, entryIds, source, tokensUsed) {
+    const scope = captureProjectScope(projectRoot, worktreeScope.getStore());
+    const ids = [...entryIds];
+    return worktreeScope.run(scope, async () => {
+        const sessionId = await getCurrentSessionId(scope.worktreeRoot);
+        scheduleCitationTracking(scope.worktreeRoot, ids);
+        trackBackgroundOp(() => worktreeScope.run(scope, () => logRetrieval(scope.worktreeRoot, query, ids, source, tokensUsed, sessionId)), scope.execution);
+    });
+}
+//# sourceMappingURL=telemetry.js.map

package/dist/memory/retrieval/telemetry.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"telemetry.js","sourceRoot":"","sources":["../../../src/memory/retrieval/telemetry.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AACH,OAAO,EAAE,mBAAmB,EAAE,aAAa,EAAE,MAAM,wBAAwB,CAAC;AAC5E,OAAO,EAAE,iBAAiB,EAAE,MAAM,+BAA+B,CAAC;AAClE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAC;AAClE,OAAO,EAAE,uBAAuB,EAAE,MAAM,gCAAgC,CAAC;AACzE,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAElD;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,wBAAwB,CAAC,WAAmB,EAAE,QAAkB;IAC9E,MAAM,KAAK,GAAG,mBAAmB,CAAC,WAAW,EAAE,aAAa,CAAC,QAAQ,EAAE,CAAC,CAAC;IACzE,MAAM,GAAG,GAAG,CAAC,GAAG,QAAQ,CAAC,CAAC;IAC1B,iBAAiB,CACf,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,EAAE,CAAC,uBAAuB,CAAC,KAAK,CAAC,YAAY,EAAE,GAAG,CAAC,CAAC,EACtF,KAAK,CAAC,SAAS,CAChB,CAAC;AACJ,CAAC;AAED;;;;;;;;;;;;;;;GAeG;AACH,MAAM,CAAC,KAAK,UAAU,0BAA0B,CAC9C,WAAmB,EACnB,KAAa,EACb,QAAkB,EAClB,MAAc,EACd,UAAkB;IAElB,MAAM,KAAK,GAAG,mBAAmB,CAAC,WAAW,EAAE,aAAa,CAAC,QAAQ,EAAE,CAAC,CAAC;IACzE,MAAM,GAAG,GAAG,CAAC,GAAG,QAAQ,CAAC,CAAC;IAC1B,OAAO,aAAa,CAAC,GAAG,CAAC,KAAK,EAAE,KAAK,IAAI,EAAE;QACzC,MAAM,SAAS,GAAG,MAAM,mBAAmB,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC;QAChE,wBAAwB,CAAC,KAAK,CAAC,YAAY,EAAE,GAAG,CAAC,CAAC;QAClD,iBAAiB,CACf,GAAG,EAAE,CACH,aAAa,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,EAAE,CAC5B,YAAY,CAAC,KAAK,CAAC,YAAY,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,UAAU,EAAE,SAAS,CAAC,CAC5E,EACH,KAAK,CAAC,SAAS,CAChB,CAAC;IACJ,CAAC,CAAC,CAAC;AACL,CAAC"}

package/dist/nexus/analyze-orchestrator.d.ts

@@ -1,23 +1,46 @@
 /**
  * Nexus analyze orchestrator — business logic extracted from `cleo nexus analyze`.
  *
- * Runs the code-intelligence pipeline, clears the existing index for full runs,
+ * Stages a replacement code graph and publishes it atomically,
  * refreshes the nexus-bridge, updates the multi-project registry, and sweeps
- * the git log for task–symbol links. All side-effects are best-effort and do
- * not fail the pipeline on error.
+ * the git log for task–symbol links. Post-publication hooks are best-effort.
  *
  * @module nexus/analyze-orchestrator
  * @epic T9833
  * @task T10062
  */
+import type { GraphIndexAssessment, GraphPublicationRows, ParserExecutionLimits } from '@cleocode/contracts';
+import type { NodeSQLiteDatabase } from 'drizzle-orm/node-sqlite';
+/**
+ * Atomically publish staged rows if the graph has not changed since assessment.
+ * Failed inserts, FTS repair, or stale generations roll back the entire replacement.
+ * Code placed in `packages/core/` per Package-Boundary Check — verified against AGENTS.md.
+ * @param db - Owning project graph database with the canonical schema installed.
+ * @param rows - Validated staged nodes, relations and source assessment to publish.
+ * @param expectedGeneration - Previously observed generation; null for the first publication.
+ * @remarks The transaction rejects stale generation preconditions and restores the
+ * prior live rows on failure. Successful replacement does not itself retain an
+ * independently recoverable historical generation.
+ * @example
+ * ```ts
+ * publishNexusGraph(db, stagedRows, expectedGeneration);
+ * ```
+ */
+export declare function publishNexusGraph(db: NodeSQLiteDatabase, rows: GraphPublicationRows, expectedGeneration: string | null): void;
 /** Parameters for {@link runNexusAnalysis}. */
 export interface NexusAnalysisParams {
+    /** Per-file parser bounds and cancellation; native RSS containment is unverified. */
+    parserLimits?: ParserExecutionLimits;
     /** Absolute path to the repository to analyze. */
     repoPath: string;
-    /** Override the project ID (default: `base64url(repoPath).slice(0, 32)`). */
+    /** Stable identity parent; defaults to repoPath and can differ from the analyzed source. */
+    projectRoot?: string;
+    /** Explicit existing identity override; otherwise require persisted parent identity. */
     projectIdOverride?: string;
-    /** When true, only re-index files that changed since the last run. */
+    /** When true, skip unchanged indexes and atomically rebuild changed generations. */
     incremental?: boolean;
+    /** Explicit relative paths of nested repositories authorized for source inclusion. */
+    includedRepositories?: readonly string[];
     /**
      * Progress callback invoked every 50 files (and on completion).
      * Omit for JSON output mode.
@@ -33,21 +56,30 @@ export interface NexusAnalysisResult {
     relationCount: number;
     fileCount: number;
     durationMs: number;
+    /** Committed per-file outcomes and source provenance. */
+    assessment: GraphIndexAssessment | null;
 }
 /**
  * Run the nexus code-intelligence pipeline on a repository.
  *
  * This function:
- * 1. Derives the project ID.
- * 2. For full runs, clears the existing nexus index.
- * 3. Runs `@cleocode/nexus` pipeline.
+ * 1. Captures the existing parent identity and explicit source roots.
+ * 2. Captures the current graph generation for concurrent-write detection.
+ * 3. Stages and atomically publishes the `@cleocode/nexus` pipeline output.
  * 4. Best-effort: refreshes `nexus-bridge.md`.
  * 5. Best-effort: updates the multi-project registry.
  * 6. Best-effort: sweeps the git log for task–symbol links.
  *
  * @param params - Analysis configuration
  * @returns Pipeline result with node/relation/file counts and duration
- * @throws {Error} When the pipeline itself fails (best-effort steps never throw)
+ * @throws {Error} When identity, source preconditions or the pipeline fail.
+ * @remarks Root revisions and file hashes are optimistic preconditions, not a
+ * filesystem lock. Publication uses the owning store's synchronous generation CAS;
+ * optional post-publication hooks cannot replace its committed result.
+ * @example
+ * ```ts
+ * const result = await runNexusAnalysis({ repoPath: '/identity', includedRepositories: ['app'] });
+ * ```
  */
 export declare function runNexusAnalysis(params: NexusAnalysisParams): Promise<NexusAnalysisResult>;
 //# sourceMappingURL=analyze-orchestrator.d.ts.map

package/dist/nexus/analyze-orchestrator.d.ts.map

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