@optave/codegraph 3.4.1 → 3.6.0

package/dist/domain/graph/builder/stages/collect-files.js

@@ -2,12 +2,66 @@
  * Stage: collectFiles
  *
  * Collects all source files to process. Handles both normal and scoped rebuilds.
+ * For incremental builds with a valid journal, reconstructs the file list from
+ * the DB's file_hashes table + journal deltas, skipping the filesystem scan.
  */
 import fs from 'node:fs';
 import path from 'node:path';
-import { info } from '../../../../infrastructure/logger.js';
+import { debug, info } from '../../../../infrastructure/logger.js';
 import { normalizePath } from '../../../../shared/constants.js';
+import { readJournal } from '../../journal.js';
 import { collectFiles as collectFilesUtil } from '../helpers.js';
+/**
+ * Reconstruct allFiles from DB file_hashes + journal deltas.
+ * Returns null when the fast path isn't applicable (first build, no journal, etc).
+ */
+function tryFastCollect(ctx) {
+    const { db, rootDir } = ctx;
+    // 1. Check that file_hashes table exists and has entries
+    let dbFileCount;
+    try {
+        dbFileCount = db.prepare('SELECT COUNT(*) as c FROM file_hashes').get().c;
+    }
+    catch {
+        return null;
+    }
+    if (dbFileCount === 0)
+        return null;
+    // 2. Read the journal — only use fast path when journal has entries,
+    // proving the watcher was active and tracking changes. An empty-but-valid
+    // journal (no watcher) could miss file deletions.
+    const journal = readJournal(rootDir);
+    if (!journal.valid)
+        return null;
+    const hasEntries = (journal.changed && journal.changed.length > 0) ||
+        (journal.removed && journal.removed.length > 0);
+    if (!hasEntries)
+        return null;
+    // 3. Load existing file list from file_hashes (relative paths)
+    const dbFiles = db.prepare('SELECT file FROM file_hashes').all().map((r) => r.file);
+    // 4. Apply journal deltas: remove deleted files, add new/changed files
+    const fileSet = new Set(dbFiles);
+    if (journal.removed) {
+        for (const removed of journal.removed) {
+            fileSet.delete(removed);
+        }
+    }
+    if (journal.changed) {
+        for (const changed of journal.changed) {
+            fileSet.add(changed);
+        }
+    }
+    // 5. Convert to absolute paths and compute directories
+    const files = [];
+    const directories = new Set();
+    for (const relPath of fileSet) {
+        const absPath = path.join(rootDir, relPath);
+        files.push(absPath);
+        directories.add(path.dirname(absPath));
+    }
+    debug(`collectFiles fast path: ${dbFiles.length} from DB, journal: +${journal.changed?.length ?? 0}/-${journal.removed?.length ?? 0} → ${files.length} files`);
+    return { files, directories };
+}
 export async function collectFiles(ctx) {
     const { rootDir, config, opts } = ctx;
     if (opts.scope) {
@@ -31,12 +85,22 @@ export async function collectFiles(ctx) {
         ctx.removed = missing;
         ctx.isFullBuild = false;
         info(`Scoped rebuild: ${existing.length} files to rebuild, ${missing.length} to purge`);
+        return;
     }
-    else {
-        const collected = collectFilesUtil(rootDir, [], config, new Set());
-        ctx.allFiles = collected.files;
-        ctx.discoveredDirs = collected.directories;
-        info(`Found ${ctx.allFiles.length} files to parse`);
+    // Incremental fast path: reconstruct file list from DB + journal deltas
+    // instead of full recursive filesystem scan (~8ms savings on 473 files).
+    if (ctx.incremental && !ctx.forceFullRebuild) {
+        const fast = tryFastCollect(ctx);
+        if (fast) {
+            ctx.allFiles = fast.files;
+            ctx.discoveredDirs = fast.directories;
+            info(`Found ${ctx.allFiles.length} files (cached)`);
+            return;
+        }
     }
+    const collected = collectFilesUtil(rootDir, [], config, new Set());
+    ctx.allFiles = collected.files;
+    ctx.discoveredDirs = collected.directories;
+    info(`Found ${ctx.allFiles.length} files to parse`);
 }
 //# sourceMappingURL=collect-files.js.map

package/dist/domain/graph/builder/stages/collect-files.js.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/stages/detect-changes.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"detect-changes.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/detect-changes.ts"],"names":[],"mappings":"AAeA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA4ZrD,wBAAsB,aAAa,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA6DvE"}

package/dist/domain/graph/builder/stages/detect-changes.js

@@ -14,10 +14,16 @@ import { parseFilesAuto } from '../../../parser.js';
 import { readJournal, writeJournalHeader } from '../../journal.js';
 import { fileHash, fileStat, purgeFilesFromGraph, readFileSafe } from '../helpers.js';
 // ── Helpers ────────────────────────────────────────────────────────────
-function getChangedFiles(db, allFiles, rootDir) {
+function getChangedFiles(db, allFiles, rootDir, nativeDb) {
     let hasTable = false;
     try {
-        db.prepare('SELECT 1 FROM file_hashes LIMIT 1').get();
+        if (nativeDb) {
+            nativeDb.queryGet('SELECT 1 FROM file_hashes LIMIT 1', []);
+        }
+        else {
+            db.prepare('SELECT 1 FROM file_hashes LIMIT 1').get();
+        }
+        // Query succeeded → table exists (result may be undefined if table is empty)
         hasTable = true;
     }
     catch {
@@ -30,7 +36,11 @@ function getChangedFiles(db, allFiles, rootDir) {
             isFullBuild: true,
         };
     }
-    const existing = new Map(db.prepare('SELECT file, hash, mtime, size FROM file_hashes').all().map((r) => [r.file, r]));
+    const sql = 'SELECT file, hash, mtime, size FROM file_hashes';
+    const rows = nativeDb
+        ? nativeDb.queryAll(sql, [])
+        : db.prepare(sql).all();
+    const existing = new Map(rows.map((r) => [r.file, r]));
     const removed = detectRemovedFiles(existing, allFiles, rootDir);
     const journalResult = tryJournalTier(db, existing, rootDir, removed);
     if (journalResult)
@@ -228,19 +238,31 @@ function findReverseDependencies(db, changedRelPaths, rootDir) {
 }
 function purgeAndAddReverseDeps(ctx, changePaths, reverseDeps) {
     const { db, rootDir } = ctx;
-    if (changePaths.length > 0 || ctx.removed.length > 0) {
-        purgeFilesFromGraph(db, [...ctx.removed, ...changePaths], { purgeHashes: false });
-    }
-    if (reverseDeps.size > 0) {
-        const deleteOutgoingEdgesForFile = db.prepare('DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE file = ?)');
-        for (const relPath of reverseDeps) {
-            deleteOutgoingEdgesForFile.run(relPath);
+    const hasPurge = changePaths.length > 0 || ctx.removed.length > 0;
+    const hasReverseDeps = reverseDeps.size > 0;
+    const reverseDepList = hasReverseDeps ? [...reverseDeps] : [];
+    if (hasPurge || hasReverseDeps) {
+        const filesToPurge = hasPurge ? [...ctx.removed, ...changePaths] : [];
+        // Prefer NativeDatabase: purge + reverse-dep edge deletion in one transaction (#670)
+        if (ctx.engineName === 'native' && ctx.nativeDb?.purgeFilesData) {
+            ctx.nativeDb.purgeFilesData(filesToPurge, false, hasReverseDeps ? reverseDepList : undefined);
         }
-        for (const relPath of reverseDeps) {
-            const absPath = path.join(rootDir, relPath);
-            ctx.parseChanges.push({ file: absPath, relPath, _reverseDepOnly: true });
+        else {
+            if (hasPurge) {
+                purgeFilesFromGraph(db, filesToPurge, { purgeHashes: false });
+            }
+            if (hasReverseDeps) {
+                const deleteOutgoingEdgesForFile = db.prepare('DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE file = ?)');
+                for (const relPath of reverseDepList) {
+                    deleteOutgoingEdgesForFile.run(relPath);
+                }
+            }
         }
     }
+    for (const relPath of reverseDeps) {
+        const absPath = path.join(rootDir, relPath);
+        ctx.parseChanges.push({ file: absPath, relPath, _reverseDepOnly: true });
+    }
 }
 function detectHasEmbeddings(db) {
     try {
@@ -301,7 +323,7 @@ export async function detectChanges(ctx) {
         return;
     }
     const increResult = incremental && !forceFullRebuild
-        ? getChangedFiles(db, allFiles, rootDir)
+        ? getChangedFiles(db, allFiles, rootDir, ctx.engineName === 'native' ? ctx.nativeDb : undefined)
         : {
             changed: allFiles.map((f) => ({ file: f })),
             removed: [],

package/dist/domain/graph/builder/stages/detect-changes.js.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/stages/finalize.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"finalize.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/finalize.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAErD,wBAAsB,QAAQ,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAqLlE"}
+{"version":3,"file":"finalize.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/finalize.ts"],"names":[],"mappings":"AAiBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA2KrD,wBAAsB,QAAQ,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAsElE"}

package/dist/domain/graph/builder/stages/finalize.js

@@ -6,14 +6,12 @@
 import { tmpdir } from 'node:os';
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { closeDb, closeDbDeferred, getBuildMeta, setBuildMeta } from '../../../../db/index.js';
+import { closeDbPair, closeDbPairDeferred, getBuildMeta, setBuildMeta, } from '../../../../db/index.js';
 import { debug, info, warn } from '../../../../infrastructure/logger.js';
 import { CODEGRAPH_VERSION } from '../../../../shared/version.js';
 import { writeJournalHeader } from '../../journal.js';
-export async function finalize(ctx) {
-    const { db, allSymbols, rootDir, isFullBuild, hasEmbeddings, config, opts, schemaVersion } = ctx;
-    const t0 = performance.now();
-    // Release cached WASM trees
+/** Release cached WASM parse trees to free memory. */
+function releaseWasmTrees(allSymbols) {
     for (const [, symbols] of allSymbols) {
         const tree = symbols._tree;
         if (tree && typeof tree.delete === 'function') {
@@ -27,91 +25,109 @@ export async function finalize(ctx) {
         symbols._tree = undefined;
         symbols._langId = undefined;
     }
-    // Capture a single wall-clock timestamp for the current build — used for
-    // both the stale-embeddings comparison and the persisted built_at metadata.
-    const buildNow = new Date();
-    const nodeCount = db.prepare('SELECT COUNT(*) as c FROM nodes').get().c;
-    const actualEdgeCount = db.prepare('SELECT COUNT(*) as c FROM edges').get().c;
-    info(`Graph built: ${nodeCount} nodes, ${actualEdgeCount} edges`);
-    info(`Stored in ${ctx.dbPath}`);
-    // Incremental drift detection — skip for small incremental changes where
-    // count fluctuation is expected (reverse-dep edge churn).
-    if (!isFullBuild && allSymbols.size > 3) {
-        const prevNodes = getBuildMeta(db, 'node_count');
-        const prevEdges = getBuildMeta(db, 'edge_count');
-        if (prevNodes && prevEdges) {
-            const prevN = Number(prevNodes);
-            const prevE = Number(prevEdges);
-            if (prevN > 0) {
-                const nodeDrift = Math.abs(nodeCount - prevN) / prevN;
-                const edgeDrift = prevE > 0 ? Math.abs(actualEdgeCount - prevE) / prevE : 0;
-                const driftThreshold = config.build?.driftThreshold ?? 0.2;
-                if (nodeDrift > driftThreshold || edgeDrift > driftThreshold) {
-                    warn(`Incremental build diverged significantly from previous counts (nodes: ${prevN}\u2192${nodeCount} [${(nodeDrift * 100).toFixed(1)}%], edges: ${prevE}\u2192${actualEdgeCount} [${(edgeDrift * 100).toFixed(1)}%], threshold: ${(driftThreshold * 100).toFixed(0)}%). Consider rebuilding with --no-incremental.`);
-                }
-            }
-        }
+}
+/**
+ * Detect significant drift between current and previous node/edge counts.
+ * Skipped for small incremental changes where count fluctuation is expected.
+ */
+function detectIncrementalDrift(ctx, nodeCount, actualEdgeCount) {
+    const { db, allSymbols, config } = ctx;
+    const useNativeDb = ctx.engineName === 'native' && !!ctx.nativeDb;
+    if (ctx.isFullBuild || allSymbols.size <= 3)
+        return;
+    const prevNodes = useNativeDb
+        ? ctx.nativeDb.getBuildMeta('node_count')
+        : getBuildMeta(db, 'node_count');
+    const prevEdges = useNativeDb
+        ? ctx.nativeDb.getBuildMeta('edge_count')
+        : getBuildMeta(db, 'edge_count');
+    if (!prevNodes || !prevEdges)
+        return;
+    const prevN = Number(prevNodes);
+    const prevE = Number(prevEdges);
+    if (prevN <= 0)
+        return;
+    const nodeDrift = Math.abs(nodeCount - prevN) / prevN;
+    const edgeDrift = prevE > 0 ? Math.abs(actualEdgeCount - prevE) / prevE : 0;
+    const driftThreshold = config.build?.driftThreshold ?? 0.2;
+    if (nodeDrift > driftThreshold || edgeDrift > driftThreshold) {
+        warn(`Incremental build diverged significantly from previous counts (nodes: ${prevN}\u2192${nodeCount} [${(nodeDrift * 100).toFixed(1)}%], edges: ${prevE}\u2192${actualEdgeCount} [${(edgeDrift * 100).toFixed(1)}%], threshold: ${(driftThreshold * 100).toFixed(0)}%). Consider rebuilding with --no-incremental.`);
     }
-    // For small incremental builds, skip persisting build metadata — the
-    // engine/version/schema haven't changed (would have triggered a full rebuild),
-    // built_at is only used by stale-embeddings check (skipped for incremental),
-    // and counts are only used by drift detection (skipped for ≤3 files).
-    // This avoids a transaction commit + WAL fsync (~15-30ms).
-    if (isFullBuild || allSymbols.size > 5) {
-        try {
-            setBuildMeta(db, {
+}
+/**
+ * Persist build metadata (engine, version, counts, timestamp).
+ * Skipped for small incremental builds to avoid WAL fsync cost.
+ */
+function persistBuildMetadata(ctx, nodeCount, actualEdgeCount, buildNow) {
+    const useNativeDb = ctx.engineName === 'native' && !!ctx.nativeDb;
+    if (!ctx.isFullBuild && ctx.allSymbols.size <= 3)
+        return;
+    try {
+        if (useNativeDb) {
+            ctx.nativeDb.setBuildMeta(Object.entries({
                 engine: ctx.engineName,
                 engine_version: ctx.engineVersion || '',
                 codegraph_version: CODEGRAPH_VERSION,
-                schema_version: String(schemaVersion),
+                schema_version: String(ctx.schemaVersion),
+                built_at: buildNow.toISOString(),
+                node_count: String(nodeCount),
+                edge_count: String(actualEdgeCount),
+            }).map(([key, value]) => ({ key, value: String(value) })));
+        }
+        else {
+            setBuildMeta(ctx.db, {
+                engine: ctx.engineName,
+                engine_version: ctx.engineVersion || '',
+                codegraph_version: CODEGRAPH_VERSION,
+                schema_version: String(ctx.schemaVersion),
                 built_at: buildNow.toISOString(),
                 node_count: nodeCount,
                 edge_count: actualEdgeCount,
             });
         }
-        catch (err) {
-            warn(`Failed to write build metadata: ${err.message}`);
-        }
     }
-    // Skip expensive advisory queries for incremental builds — these are
-    // informational warnings that don't affect correctness and cost ~40-60ms.
-    if (!isFullBuild) {
-        debug('Finalize: skipping advisory queries (orphaned/stale embeddings, unused exports) for incremental build');
+    catch (err) {
+        warn(`Failed to write build metadata: ${err.message}`);
     }
-    else {
-        // Orphaned embeddings warning
-        if (hasEmbeddings) {
-            try {
-                const orphaned = db
-                    .prepare('SELECT COUNT(*) as c FROM embeddings WHERE node_id NOT IN (SELECT id FROM nodes)')
-                    .get().c;
-                if (orphaned > 0) {
-                    warn(`${orphaned} embeddings are orphaned (nodes changed). Run "codegraph embed" to refresh.`);
-                }
-            }
-            catch {
-                /* ignore - embeddings table may have been dropped */
+}
+/**
+ * Run advisory checks on full builds: orphaned embeddings, stale embeddings,
+ * and unused exports. Informational only — does not affect correctness.
+ */
+function runAdvisoryChecks(db, hasEmbeddings, buildNow) {
+    // Orphaned embeddings warning
+    if (hasEmbeddings) {
+        try {
+            const orphaned = db
+                .prepare('SELECT COUNT(*) as c FROM embeddings WHERE node_id NOT IN (SELECT id FROM nodes)')
+                .get().c;
+            if (orphaned > 0) {
+                warn(`${orphaned} embeddings are orphaned (nodes changed). Run "codegraph embed" to refresh.`);
             }
         }
-        // Stale embeddings warning (built before current graph rebuild)
-        if (hasEmbeddings) {
-            try {
-                const embedBuiltAt = db.prepare("SELECT value FROM embedding_meta WHERE key = 'built_at'").get()?.value;
-                if (embedBuiltAt) {
-                    const embedTime = new Date(embedBuiltAt).getTime();
-                    if (!Number.isNaN(embedTime) && embedTime < buildNow.getTime()) {
-                        warn('Embeddings were built before the last graph rebuild. Run "codegraph embed" to update.');
-                    }
+        catch {
+            /* ignore - embeddings table may have been dropped */
+        }
+    }
+    // Stale embeddings warning (built before current graph rebuild)
+    if (hasEmbeddings) {
+        try {
+            const embedBuiltAt = db.prepare("SELECT value FROM embedding_meta WHERE key = 'built_at'").get()?.value;
+            if (embedBuiltAt) {
+                const embedTime = new Date(embedBuiltAt).getTime();
+                if (!Number.isNaN(embedTime) && embedTime < buildNow.getTime()) {
+                    warn('Embeddings were built before the last graph rebuild. Run "codegraph embed" to update.');
                 }
             }
-            catch {
-                /* ignore - embedding_meta table may not exist */
-            }
         }
-        // Unused exports warning
-        try {
-            const unusedCount = db
-                .prepare(`SELECT COUNT(*) as c FROM nodes
+        catch {
+            /* ignore - embedding_meta table may not exist */
+        }
+    }
+    // Unused exports warning
+    try {
+        const unusedCount = db
+            .prepare(`SELECT COUNT(*) as c FROM nodes
          WHERE exported = 1 AND kind != 'file'
            AND id NOT IN (
              SELECT DISTINCT e.target_id FROM edges e
@@ -119,26 +135,53 @@ export async function finalize(ctx) {
              JOIN nodes target ON e.target_id = target.id
              WHERE e.kind = 'calls' AND caller.file != target.file
            )`)
-                .get().c;
-            if (unusedCount > 0) {
-                warn(`${unusedCount} exported symbol${unusedCount > 1 ? 's have' : ' has'} zero cross-file consumers. Run "codegraph exports <file> --unused" to inspect.`);
-            }
-        }
-        catch {
-            /* exported column may not exist on older DBs */
+            .get().c;
+        if (unusedCount > 0) {
+            warn(`${unusedCount} exported symbol${unusedCount > 1 ? 's have' : ' has'} zero cross-file consumers. Run "codegraph exports <file> --unused" to inspect.`);
         }
     }
+    catch {
+        /* exported column may not exist on older DBs */
+    }
+}
+export async function finalize(ctx) {
+    const { allSymbols, rootDir, isFullBuild, hasEmbeddings, opts } = ctx;
+    const t0 = performance.now();
+    releaseWasmTrees(allSymbols);
+    // Capture a single wall-clock timestamp for the current build — used for
+    // both the stale-embeddings comparison and the persisted built_at metadata.
+    const buildNow = new Date();
+    const nodeCount = ctx.db.prepare('SELECT COUNT(*) as c FROM nodes').get().c;
+    const actualEdgeCount = ctx.db.prepare('SELECT COUNT(*) as c FROM edges').get()
+        .c;
+    info(`Graph built: ${nodeCount} nodes, ${actualEdgeCount} edges`);
+    info(`Stored in ${ctx.dbPath}`);
+    detectIncrementalDrift(ctx, nodeCount, actualEdgeCount);
+    persistBuildMetadata(ctx, nodeCount, actualEdgeCount, buildNow);
+    // Skip expensive advisory queries for incremental builds — these are
+    // informational warnings that don't affect correctness and cost ~40-60ms.
+    if (!isFullBuild) {
+        debug('Finalize: skipping advisory queries (orphaned/stale embeddings, unused exports) for incremental build');
+    }
+    else {
+        runAdvisoryChecks(ctx.db, hasEmbeddings, buildNow);
+    }
+    // Intentionally measured before closeDb / writeJournalHeader / auto-registration:
+    // for the deferred-close path the close is async (setImmediate), and for full
+    // builds the metric captures finalize logic only — DB close cost is tracked
+    // separately via timing.closeDbMs when available.
     ctx.timing.finalizeMs = performance.now() - t0;
-    // For small incremental builds, defer db.close() to the next event loop tick.
-    // The WAL checkpoint in db.close() costs ~250ms on Windows NTFS due to fsync.
-    // Deferring lets buildGraph() return immediately; the checkpoint runs after.
-    // Skip for temp directories (tests) — they rmSync immediately after build.
+    // Close NativeDatabase (fast, ~1ms) then better-sqlite3 (WAL checkpoint).
+    // For small incremental builds, defer the expensive WAL checkpoint to the
+    // next event loop tick. Skip for temp directories (tests) — they rmSync
+    // immediately after build.
+    const pair = { db: ctx.db, nativeDb: ctx.nativeDb };
     const isTempDir = path.resolve(rootDir).startsWith(path.resolve(tmpdir()));
     if (!isFullBuild && allSymbols.size <= 5 && !isTempDir) {
-        closeDbDeferred(db);
+        closeDbPairDeferred(pair);
     }
     else {
-        closeDb(db);
+        closeDbPair(pair);
     }
     // Write journal header after successful build
     writeJournalHeader(rootDir, Date.now());
@@ -146,7 +189,6 @@ export async function finalize(ctx) {
     // registered during the initial full build. The dynamic import + file I/O
     // costs ~100ms which dominates incremental finalize time.
     if (!opts.skipRegistry && isFullBuild) {
-        const { tmpdir } = await import('node:os');
         const tmpDir = path.resolve(tmpdir());
         const resolvedRoot = path.resolve(rootDir);
         if (resolvedRoot.startsWith(tmpDir)) {

package/dist/domain/graph/builder/stages/finalize.js.map

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package/dist/domain/graph/builder/stages/insert-nodes.d.ts.map

@@ -1 +1 @@
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