@cleocode/core 2026.9.16 → 2026.9.18

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

@@ -9,8 +9,10 @@
  * @epic T9833
  * @task T10062
  */
-import type { GraphIndexAssessment, GraphPublicationRows, ParserExecutionLimits } from '@cleocode/contracts';
+import type { GraphIndexAssessment, GraphIndexRunSummary, GraphParseCacheEntry, GraphPublicationRows, ParserExecutionLimits } from '@cleocode/contracts';
 import type { NodeSQLiteDatabase } from 'drizzle-orm/node-sqlite';
+/** Read the parse cache committed with the current generation (T12315). */
+export declare function readNexusParseCache(db: NodeSQLiteDatabase): GraphParseCacheEntry[];
 /**
  * Atomically publish staged rows if the graph has not changed since assessment.
  * Failed inserts, FTS repair, or stale generations roll back the entire replacement.
@@ -37,7 +39,16 @@ export interface NexusAnalysisParams {
     projectRoot?: string;
     /** Explicit existing identity override; otherwise require persisted parent identity. */
     projectIdOverride?: string;
-    /** When true, skip unchanged indexes and atomically rebuild changed generations. */
+    /**
+     * Parse every file instead of reusing the previous generation's extractions.
+     * When omitted, an analysis reuses what is provably current (T12315) and
+     * falls back to a full parse — reporting why — when it cannot.
+     */
+    full?: boolean;
+    /**
+     * @deprecated Incremental reuse is the default since T12315; this flag is
+     * accepted for compatibility and has no effect. Use `full` to force a rebuild.
+     */
     incremental?: boolean;
     /** Explicit relative paths of nested repositories authorized for source inclusion. */
     includedRepositories?: readonly string[];
@@ -51,12 +62,18 @@ export interface NexusAnalysisParams {
 export interface NexusAnalysisResult {
     projectId: string;
     repoPath: string;
+    /** Whether this run reused previous extractions (mode `incremental` or `unchanged`). */
     incremental: boolean;
+    /** Mode, reason, per-file counts and phase costs of this run. */
+    summary: GraphIndexRunSummary;
     nodeCount: number;
     relationCount: number;
     fileCount: number;
     durationMs: number;
-    /** Committed per-file outcomes and source provenance. */
+    /**
+     * Committed per-file outcomes and source provenance, as a summary: the
+     * reference list is reported as `referenceCount` (T12348).
+     */
     assessment: GraphIndexAssessment | null;
 }
 /**

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

@@ -1 +1 @@
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package/dist/nexus/analyze-orchestrator.js

@@ -18,6 +18,8 @@ import { worktreeScope } from '../paths.js';
 import { getProjectInfo } from '../project-info.js';
 import { createParserExecutionPort } from '../resources/spawn-wrapper.js';
 import { nexusNodes, nexusRelations } from '../store/schema/cleo-project/nexus-graph.js';
+import { assessmentSummary, writeAssessment } from './assessment-store.js';
+import { buildFileManifest, clearFileManifest, writeFileManifest, writeRunCost, } from './graph-manifest.js';
 import { generateProjectHash } from './hash.js';
 import { readKnowledgeIndexAssessment } from './knowledge.js';
 import { resolveSourceRoots } from './source-roots.js';
@@ -38,6 +40,60 @@ function rootFingerprint(roots) {
         })),
     });
 }
+/**
+ * Compare source OWNERSHIP only — never the observed revision.
+ *
+ * Reusing a file's extraction depends on its bytes (content hash), not on which
+ * commit produced them, so a new commit must not by itself force a full
+ * rebuild (T12315). The revision is still recorded as provenance and still
+ * guards against concurrent change via {@link rootFingerprint}.
+ */
+function ownershipFingerprint(roots) {
+    return JSON.stringify({
+        projectId: roots.projectId,
+        projectRoot: roots.projectRoot,
+        sourceRoot: roots.sourceRoot,
+        roots: roots.roots.map((root) => ({
+            requestedPath: root.requestedPath,
+            canonicalPath: root.canonicalPath,
+            graphPrefix: root.graphPrefix,
+            explicitlyIncluded: root.explicitlyIncluded,
+            status: root.status,
+        })),
+    });
+}
+/** Read the parse cache committed with the current generation (T12315). */
+export function readNexusParseCache(db) {
+    return db
+        .values(sql `SELECT path, content_hash, fingerprint, generation, payload FROM main._nexus_parse_cache`)
+        .map((row) => {
+        const [path, contentHash, fingerprint, generation, payload] = row;
+        if (typeof path !== 'string' ||
+            typeof contentHash !== 'string' ||
+            typeof fingerprint !== 'string' ||
+            typeof generation !== 'string' ||
+            !(payload instanceof Uint8Array))
+            throw new Error('Invalid nexus parse cache row');
+        return { path, contentHash, fingerprint, generation, payload };
+    });
+}
+/** Apply a parse-cache mutation inside the caller's publication transaction. */
+function applyParseCacheUpdate(tx, update) {
+    if (update.reset)
+        tx.run(sql `DELETE FROM main._nexus_parse_cache`);
+    for (let offset = 0; offset < update.deletePaths.length; offset += 500) {
+        const batch = update.deletePaths.slice(offset, offset + 500);
+        tx.run(sql `DELETE FROM main._nexus_parse_cache WHERE path IN (${sql.join(batch.map((path) => sql `${path}`), sql `, `)})`);
+    }
+    for (const entry of update.upserts) {
+        if (entry.fingerprint !== update.fingerprint)
+            throw new Error(`Parse cache entry ${entry.path} carries a foreign extractor fingerprint`);
+        tx.run(sql `INSERT INTO main._nexus_parse_cache (path, content_hash, fingerprint, generation, payload)
+      VALUES (${entry.path}, ${entry.contentHash}, ${entry.fingerprint}, ${entry.generation}, ${entry.payload})
+      ON CONFLICT(path) DO UPDATE SET content_hash = excluded.content_hash,
+        fingerprint = excluded.fingerprint, generation = excluded.generation, payload = excluded.payload`);
+    }
+}
 /** Fail closed when a required root observation did not finish successfully. */
 function requireObservedRoots(roots) {
     const failed = roots.roots.filter((root) => root.status !== 'available' && root.status !== 'unversioned');
@@ -81,11 +137,59 @@ function includedRepositoryScope(db, repoPath) {
         return repository;
     });
 }
+/** Read the extractor fingerprint recorded with the committed generation (T12315). */
+function publishedExtractorFingerprint(db) {
+    const value = db.values(sql `SELECT value FROM main._nexus_meta WHERE key = 'graph_extractor_fingerprint'`)[0]?.[0];
+    return typeof value === 'string' ? value : null;
+}
 /** Read the last committed graph generation without opening a write transaction. */
 function graphGeneration(db) {
     const value = db.values(sql `SELECT value FROM main._nexus_meta WHERE key = 'graph_generation'`)[0]?.[0];
     return typeof value === 'string' ? value : null;
 }
+/**
+ * Page-cache ceiling for a graph write transaction, in KiB (T12348).
+ *
+ * A one-shot CLI open gets an 8 MB cache (T11829). A publication dirties every
+ * row, index and FTS page of the graph — ~290 MB on this repository — so with
+ * 8 MB SQLite spills pages to the WAL mid-transaction and reads them back,
+ * repeatedly: replacing the rows cost 340k read and 328k write syscalls at
+ * 8 MB, 124k/223k at 256 MB, and 40k/146k (the floor: each page written once)
+ * at 512 MB. On a FUSE mount every syscall costs ~0.5–1.5 ms. This is a
+ * ceiling, not an allocation: SQLite grows the cache only as pages are
+ * touched, and the previous size is restored when the transaction ends.
+ */
+const GRAPH_WRITE_CACHE_KIB = 524_288;
+/**
+ * Run a graph write in a transaction that write-locks the PROJECT store only.
+ *
+ * The project handle carries the global `cleo.db` ATTACHed as `nexus_global`
+ * (see `ensureGlobalRegistryAttached`), and `BEGIN IMMEDIATE` takes the write
+ * lock of EVERY attached database. An immediate publication therefore held the
+ * global store's write lock for its whole duration — while it ran, a
+ * concurrent `cleo nexus projects clean` gave up with "database is locked"
+ * after 180 s. A deferred transaction whose first statement writes `main`
+ * acquires main's lock alone, with the same busy handling and a fresh snapshot,
+ * so the generation check that follows still reads under the write lock (T12348).
+ *
+ * @param db - Owning project graph database.
+ * @param write - Transaction body; every statement in it must target `main`.
+ */
+function writeGraphTransaction(db, write) {
+    const previous = db.values(sql `PRAGMA main.cache_size`)[0]?.[0];
+    db.run(sql.raw(`PRAGMA main.cache_size = -${GRAPH_WRITE_CACHE_KIB}`));
+    try {
+        db.transaction((tx) => {
+            // A write that matches no row still takes main's RESERVED lock, and only main's.
+            tx.run(sql `DELETE FROM main._nexus_meta WHERE 0`);
+            return write(tx);
+        }, { behavior: 'deferred' });
+    }
+    finally {
+        if (typeof previous === 'number')
+            db.run(sql.raw(`PRAGMA main.cache_size = ${previous}`));
+    }
+}
 /**
  * Atomically publish staged rows if the graph has not changed since assessment.
  * Failed inserts, FTS repair, or stale generations roll back the entire replacement.
@@ -113,18 +217,20 @@ export function publishNexusGraph(db, rows, expectedGeneration) {
             reference.publicationGeneration !== generation))
             throw new Error('Staged reference publication generation does not match rows');
     }
-    db.transaction((tx) => {
+    writeGraphTransaction(db, (tx) => {
         if (graphGeneration(tx) !== expectedGeneration) {
             throw new Error('Nexus graph changed during indexing; discard staged generation and retry.');
         }
-        tx.delete(nexusRelations).run();
-        tx.delete(nexusNodes).run();
         // The optional FTS shadow can contain orphaned rowids; reset it inside
         // the same transaction so trigger failures restore the previous generation.
-        if (tx.values(sql `SELECT name FROM main.sqlite_master WHERE name = 'nexus_symbols_fts'`)
-            .length > 0) {
+        // Reset it FIRST (T12348): the per-row delete trigger then finds nothing
+        // to remove, instead of re-tokenizing every old node's text to delete it.
+        if (tx.values(sql `SELECT name FROM main.sqlite_master WHERE name = 'nexus_symbols_fts'`).length >
+            0) {
             tx.run(sql `DELETE FROM main.nexus_symbols_fts`);
         }
+        tx.delete(nexusRelations).run();
+        tx.delete(nexusNodes).run();
         for (let offset = 0; offset < rows.nodes.length; offset += 500) {
             tx.insert(nexusNodes)
                 .values(rows.nodes.slice(offset, offset + 500))
@@ -144,13 +250,49 @@ export function publishNexusGraph(db, rows, expectedGeneration) {
       `).length > 0) {
             throw new Error('Staged lexical declaration publication generation does not match rows');
         }
-        if (rows.assessment) {
-            tx.run(sql `INSERT INTO main._nexus_meta (key, value) VALUES ('graph_assessment', ${JSON.stringify(rows.assessment)})
+        if (rows.parseCache)
+            applyParseCacheUpdate(tx, rows.parseCache);
+        // The fingerprint names the extractor build that produced these rows; a
+        // publisher without a parse cache leaves the build unproven.
+        if (rows.parseCache?.fingerprint) {
+            tx.run(sql `INSERT INTO main._nexus_meta (key, value) VALUES ('graph_extractor_fingerprint', ${rows.parseCache.fingerprint})
         ON CONFLICT(key) DO UPDATE SET value = excluded.value, updated_at = strftime('%s', 'now')`);
         }
+        else {
+            tx.run(sql `DELETE FROM main._nexus_meta WHERE key = 'graph_extractor_fingerprint'`);
+        }
+        if (rows.assessment)
+            writeFileManifest(tx, buildFileManifest(rows.assessment, rows.assessment.files));
+        else
+            clearFileManifest(tx);
+        // T12348: summary and reference list are written together, separately.
+        if (rows.assessment)
+            writeAssessment(tx, rows.assessment);
         tx.run(sql `INSERT INTO main._nexus_meta (key, value) VALUES ('graph_generation', ${generation})
       ON CONFLICT(key) DO UPDATE SET value = excluded.value, updated_at = strftime('%s', 'now')`);
-    }, { behavior: 'immediate' });
+    });
+}
+/**
+ * Re-record source provenance for a generation whose files were just verified
+ * byte-identical to the current tree, without replacing any graph rows.
+ * @param db - Owning project graph database.
+ * @param assessment - The previous assessment with current roots and revision, or
+ *   `null` when only the file manifest needs re-recording.
+ * @param manifest - File manifest re-observed from the verified tree.
+ * @param expectedGeneration - Generation the verification was performed against.
+ * @returns The recorded assessment, or `null` when none was re-recorded.
+ * @throws When the generation changed since verification.
+ */
+function recordVerifiedProvenance(db, assessment, manifest, expectedGeneration) {
+    writeGraphTransaction(db, (tx) => {
+        if (graphGeneration(tx) !== expectedGeneration)
+            throw new Error('Nexus graph changed during verification; provenance not updated.');
+        // A re-recorded summary keeps the stored reference list of this generation.
+        if (assessment)
+            writeAssessment(tx, assessment);
+        writeFileManifest(tx, manifest);
+    });
+    return assessment;
 }
 // ---------------------------------------------------------------------------
 // Public API
@@ -193,7 +335,7 @@ export async function runNexusAnalysis(params) {
 }
 /** Keep the entire asynchronous analysis bound to its captured identity parent. */
 async function runScopedNexusAnalysis(params, projectRoot) {
-    const { projectIdOverride, incremental = false, onProgress } = params;
+    const { projectIdOverride, full = false, onProgress } = params;
     const execution = worktreeScope.getStore()?.execution;
     execution?.assertActive();
     const signals = [params.parserLimits?.signal, execution?.signal].filter((signal) => signal !== undefined);
@@ -233,9 +375,18 @@ async function runScopedNexusAnalysis(params, projectRoot) {
     execution?.assertActive();
     const repoPath = sourceRoots.sourceRoot;
     const assessedRevision = sourceRoots.roots[0]?.revision ?? null;
-    const unchangedRoots = previousAssessment?.sourceRoots !== undefined &&
-        rootFingerprint(previousAssessment.sourceRoots) === rootFingerprint(sourceRoots);
-    const useIncremental = incremental && expectedGeneration !== null && unchangedRoots;
+    const unchangedOwnership = previousAssessment?.sourceRoots !== undefined &&
+        ownershipFingerprint(previousAssessment.sourceRoots) === ownershipFingerprint(sourceRoots);
+    const fullReason = full
+        ? 'full rebuild requested (--full)'
+        : expectedGeneration === null
+            ? 'no previous generation to reuse'
+            : previousAssessment?.sourceRoots === undefined
+                ? 'the previous generation predates source-root provenance'
+                : !unchangedOwnership
+                    ? 'source ownership (project root, source root or included repositories) changed since the previous generation'
+                    : undefined;
+    const useIncremental = fullReason === undefined;
     let committedAssessment = null;
     const recheckRoots = async () => {
         execution?.assertActive();
@@ -263,15 +414,20 @@ async function runScopedNexusAnalysis(params, projectRoot) {
             currentFiles.length !== recorded.size ||
             currentFiles.some((file) => !file.contentHash || recorded.get(file.path) !== file.contentHash))
             throw new Error('Source files changed before publication; previous graph retained.');
+        return currentFiles;
     };
     const result = await runPipeline(repoPath, projectId, db, tables, onProgress, {
         parserExecution: createParserExecutionPort(),
         parserLimits: { ...params.parserLimits, signal },
         incremental: useIncremental,
+        ...(fullReason ? { fullReason } : {}),
+        loadParseCache: () => readNexusParseCache(db),
+        publishedFingerprint: publishedExtractorFingerprint(db),
         assessedRevision,
         sourceRoots,
         includedRepositories,
         publishGraph: async (rows) => {
+            const recheckStart = Date.now();
             await recheckRoots();
             if (!rows.assessment?.sourceRoots ||
                 rootFingerprint(rows.assessment.sourceRoots) !== rootFingerprint(sourceRoots))
@@ -279,17 +435,52 @@ async function runScopedNexusAnalysis(params, projectRoot) {
             await recheckFiles(rows.assessment);
             execution?.assertActive();
             signal?.throwIfAborted();
+            const commitStart = Date.now();
             publishNexusGraph(db, rows, expectedGeneration);
-            committedAssessment = rows.assessment;
+            const timing = `[nexus] Publication: source recheck ${commitStart - recheckStart}ms, atomic commit of ` +
+                `${rows.nodes.length} nodes + ${rows.relations.length} relations ${Date.now() - commitStart}ms\n`;
+            process.stderr.write(timing); // json-stream-hygiene-allowed: analyze progress telemetry on stderr, same channel as the pipeline phase log
+            committedAssessment = rows.assessment ? assessmentSummary(rows.assessment) : null;
         },
     });
     if (!committedAssessment && previousAssessment) {
         // Incremental no-op still needs current provenance: Git or source bytes can
         // change while the pipeline scans without ever invoking the publisher.
         await recheckRoots();
-        await recheckFiles(previousAssessment);
+        const verifiedFiles = await recheckFiles(previousAssessment);
         execution?.assertActive();
         signal?.throwIfAborted();
+        // T12315: a new commit with byte-identical sources no longer forces a full
+        // rebuild, so the unchanged graph must still record the revision it was
+        // just verified against — otherwise knowledge coverage would report it
+        // stale forever. The files were re-hashed above, so the claim is exact.
+        const provenance = previousAssessment.sourceRoots &&
+            rootFingerprint(previousAssessment.sourceRoots) !== rootFingerprint(sourceRoots)
+            ? {
+                ...previousAssessment,
+                sourceRoots,
+                assessedRevision,
+                assessedAt: new Date().toISOString(),
+            }
+            : null;
+        // T12316: re-record current mtimes as well, so freshness checks keep taking
+        // the metadata fast path after a checkout or `touch` that changed no bytes.
+        committedAssessment =
+            recordVerifiedProvenance(db, provenance, buildFileManifest(provenance ?? previousAssessment, verifiedFiles), expectedGeneration) ?? committedAssessment;
+    }
+    // Advisory: remember what a publishing run cost, so a later freshness check
+    // can estimate a refresh before starting one (T12316).
+    if (result.summary.mode !== 'unchanged') {
+        try {
+            writeRunCost(db, {
+                summary: result.summary,
+                durationMs: Date.now() - startTime,
+                recordedAt: new Date().toISOString(),
+            });
+        }
+        catch {
+            // non-fatal: estimates degrade to "unknown cost"
+        }
     }
     // Best-effort: refresh nexus-bridge.md
     try {
@@ -322,15 +513,18 @@ async function runScopedNexusAnalysis(params, projectRoot) {
     catch {
         // non-fatal
     }
+    const reportedAssessment = committedAssessment ?? previousAssessment;
     return {
         projectId,
         repoPath,
-        incremental: useIncremental,
+        incremental: result.summary.mode !== 'full',
+        summary: result.summary,
         nodeCount: result.nodeCount,
         relationCount: result.relationCount,
         fileCount: result.fileCount,
         durationMs: Date.now() - startTime,
-        assessment: committedAssessment ?? previousAssessment,
+        // T12348: the summary; the reference list is detail (`nexus status --references`).
+        assessment: reportedAssessment ? assessmentSummary(reportedAssessment) : null,
     };
 }
 //# sourceMappingURL=analyze-orchestrator.js.map

package/dist/nexus/analyze-orchestrator.js.map

@@ -1 +1 @@
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package/dist/nexus/assessment-store.d.ts

@@ -0,0 +1,86 @@
+/**
+ * Storage layout of the published graph assessment (T12348).
+ *
+ * The assessment used to be ONE `_nexus_meta` JSON value holding every
+ * retained unresolved/unmodeled reference with its full evidence — 472 MB on
+ * this repository, 647k references against a 3.75 MB remainder. Every reader
+ * paid to parse and validate all of it: `cleo nexus status` took ~10 s and
+ * returned a 472 MB envelope, and every analysis re-read it before starting.
+ *
+ * The summary (`graph_assessment`) now carries everything except the
+ * reference list, plus `referenceCount`; the list lives under
+ * `graph_assessment_references` and is read only when asked for. Both are
+ * written in the publishing transaction, so they always describe the same
+ * generation. A historical value with inline `references` stays readable.
+ *
+ * The list is stored gzip-compressed (a BLOB), because every publication
+ * rewrites it: 453 MB of JSON is 116k pages written to the WAL and 116k more
+ * at checkpoint — measured at 0.6 ms per page write on this repository's FUSE
+ * mount, most of a 49-minute publication. At gzip level 1 it is 28 MB, costs
+ * ~0.6 s to compress and ~0.55 s to inflate. A historical plain-text list is
+ * still read as stored.
+ *
+ * Code placed in `packages/core/` per Package-Boundary Check — verified against AGENTS.md.
+ *
+ * @task T12348
+ * @module nexus/assessment-store
+ */
+import type { GraphIndexAssessment, GraphIndexReferenceReport } from '@cleocode/contracts';
+import type { NodeSQLiteDatabase } from 'drizzle-orm/node-sqlite';
+/** `_nexus_meta` key of the assessment summary. */
+export declare const ASSESSMENT_KEY = "graph_assessment";
+/** `_nexus_meta` key of the separately stored reference list. */
+export declare const ASSESSMENT_REFERENCES_KEY = "graph_assessment_references";
+/**
+ * Encode a reference list for storage under {@link ASSESSMENT_REFERENCES_KEY}.
+ *
+ * @param references - The generation's retained references.
+ * @returns gzip-compressed JSON, stored as a BLOB.
+ */
+export declare function encodeStoredReferences(references: readonly GraphIndexReferenceReport[]): Uint8Array;
+/**
+ * Decode a stored reference list back to its JSON text.
+ *
+ * Accepts the compressed BLOB written since T12348 and the plain JSON text
+ * written before it; anything else is malformed metadata.
+ *
+ * @param value - The raw `_nexus_meta.value` of {@link ASSESSMENT_REFERENCES_KEY}.
+ * @returns The list's JSON text.
+ * @throws When the value is neither text nor a compressed list.
+ * @example
+ * ```ts
+ * const references = JSON.parse(decodeStoredReferences(row.value));
+ * ```
+ */
+export declare function decodeStoredReferences(value: unknown): string;
+/**
+ * Return the summary form of an assessment: the reference list removed and
+ * its length recorded as `referenceCount`.
+ *
+ * An assessment without a `references` list is returned unchanged, so a
+ * summary stays a summary and a historical index without references keeps
+ * its shape.
+ *
+ * @param assessment - Full or summary assessment.
+ * @returns The summary a reader of `graph_assessment` observes.
+ * @example
+ * ```ts
+ * const head = assessmentSummary(stagedAssessment);
+ * ```
+ */
+export declare function assessmentSummary(assessment: GraphIndexAssessment): GraphIndexAssessment;
+/**
+ * Write an assessment inside the caller's transaction.
+ *
+ * - A full assessment writes its summary and replaces the reference list.
+ * - A summary that already carries `referenceCount` (for example a provenance
+ *   re-record of an unchanged generation) rewrites the summary only, keeping
+ *   the stored list of that same generation.
+ * - An assessment with neither removes any stale list.
+ *
+ * @param tx - Graph database handle or open transaction.
+ * @param assessment - Assessment to persist.
+ * @returns The summary as written.
+ */
+export declare function writeAssessment(tx: Pick<NodeSQLiteDatabase, 'run'>, assessment: GraphIndexAssessment): GraphIndexAssessment;
+//# sourceMappingURL=assessment-store.d.ts.map

package/dist/nexus/assessment-store.d.ts.map

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