@optave/codegraph 3.7.0 → 3.8.0

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

@@ -15,15 +15,27 @@ import { readJournal, writeJournalHeader } from '../../journal.js';
 import { fileHash, fileStat, purgeFilesFromGraph, readFileSafe } from '../helpers.js';
 // ── Helpers ────────────────────────────────────────────────────────────
 function getChangedFiles(db, allFiles, rootDir, nativeDb) {
+    // Batched native path: single napi call for table check + all rows + max mtime
+    if (nativeDb?.getFileHashData) {
+        const data = nativeDb.getFileHashData();
+        if (!data.exists) {
+            return {
+                changed: allFiles.map((f) => ({ file: f })),
+                removed: [],
+                isFullBuild: true,
+            };
+        }
+        const existing = new Map(data.rows.map((r) => [r.file, r]));
+        const removed = detectRemovedFiles(existing, allFiles, rootDir);
+        const journalResult = tryJournalTier(db, existing, rootDir, removed, data.maxMtime);
+        if (journalResult)
+            return journalResult;
+        return mtimeAndHashTiers(existing, allFiles, rootDir, removed);
+    }
+    // WASM / fallback path
     let hasTable = false;
     try {
-        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)
+        db.prepare('SELECT 1 FROM file_hashes LIMIT 1').get();
         hasTable = true;
     }
     catch {
@@ -36,10 +48,7 @@ function getChangedFiles(db, allFiles, rootDir, nativeDb) {
             isFullBuild: true,
         };
     }
-    const sql = 'SELECT file, hash, mtime, size FROM file_hashes';
-    const rows = nativeDb
-        ? nativeDb.queryAll(sql, [])
-        : db.prepare(sql).all();
+    const rows = db.prepare('SELECT file, hash, mtime, size FROM file_hashes').all();
     const existing = new Map(rows.map((r) => [r.file, r]));
     const removed = detectRemovedFiles(existing, allFiles, rootDir);
     const journalResult = tryJournalTier(db, existing, rootDir, removed);
@@ -60,12 +69,13 @@ function detectRemovedFiles(existing, allFiles, rootDir) {
     }
     return removed;
 }
-function tryJournalTier(db, existing, rootDir, removed) {
+function tryJournalTier(db, existing, rootDir, removed, precomputedMaxMtime) {
     const journal = readJournal(rootDir);
     if (!journal.valid)
         return null;
-    const dbMtimes = db.prepare('SELECT MAX(mtime) as latest FROM file_hashes').get();
-    const latestDbMtime = dbMtimes?.latest || 0;
+    const latestDbMtime = precomputedMaxMtime ??
+        (db.prepare('SELECT MAX(mtime) as latest FROM file_hashes').get()?.latest ||
+            0);
     const hasJournalEntries = journal.changed.length > 0 || journal.removed.length > 0;
     if (!hasJournalEntries || journal.timestamp < latestDbMtime) {
         debug(`Tier 0: skipped (${hasJournalEntries ? 'timestamp stale' : 'no entries'}), falling to Tier 1`);
@@ -156,26 +166,39 @@ function mtimeAndHashTiers(existing, allFiles, rootDir, removed) {
 }
 async function runPendingAnalysis(ctx) {
     const { db, opts, engineOpts, allFiles, rootDir } = ctx;
-    const needsCfg = opts.cfg !== false &&
-        (() => {
-            try {
-                return (db.prepare('SELECT COUNT(*) as c FROM cfg_blocks').get()
-                    ?.c === 0);
-            }
-            catch {
-                return true;
-            }
-        })();
-    const needsDataflow = opts.dataflow !== false &&
-        (() => {
-            try {
-                return (db.prepare('SELECT COUNT(*) as c FROM dataflow').get()
-                    ?.c === 0);
-            }
-            catch {
-                return true;
-            }
-        })();
+    const useNative = ctx.engineName === 'native' && !!ctx.nativeDb?.checkPendingAnalysis;
+    let needsCfg;
+    let needsDataflow;
+    if (useNative) {
+        const counts = ctx.nativeDb.checkPendingAnalysis();
+        needsCfg = opts.cfg !== false && counts.cfgCount <= 0;
+        needsDataflow =
+            opts.dataflow !== false && counts.dataflowCount <= 0;
+    }
+    else {
+        needsCfg =
+            opts.cfg !== false &&
+                (() => {
+                    try {
+                        return (db.prepare('SELECT COUNT(*) as c FROM cfg_blocks').get()
+                            ?.c === 0);
+                    }
+                    catch {
+                        return true;
+                    }
+                })();
+        needsDataflow =
+            opts.dataflow !== false &&
+                (() => {
+                    try {
+                        return (db.prepare('SELECT COUNT(*) as c FROM dataflow').get()
+                            ?.c === 0);
+                    }
+                    catch {
+                        return true;
+                    }
+                })();
+    }
     if (!needsCfg && !needsDataflow)
         return false;
     info('No file changes. Running pending analysis pass...');
@@ -199,25 +222,47 @@ function healMetadata(ctx) {
     if (!metadataUpdates || metadataUpdates.length === 0)
         return;
     try {
-        const healHash = db.prepare('INSERT OR REPLACE INTO file_hashes (file, hash, mtime, size) VALUES (?, ?, ?, ?)');
-        const healTx = db.transaction(() => {
-            for (const item of metadataUpdates) {
-                const mtime = item.stat ? Math.floor(item.stat.mtime) : 0;
-                const size = item.stat ? item.stat.size : 0;
-                healHash.run(item.relPath, item.hash, mtime, size);
-            }
-        });
-        healTx();
+        if (ctx.engineName === 'native' && ctx.nativeDb?.healFileMetadata) {
+            const entries = metadataUpdates.map((item) => ({
+                file: item.relPath,
+                hash: item.hash,
+                mtime: item.stat ? Math.floor(item.stat.mtime) : 0,
+                size: item.stat ? item.stat.size : 0,
+            }));
+            ctx.nativeDb.healFileMetadata(entries);
+        }
+        else {
+            const healHash = db.prepare('INSERT OR REPLACE INTO file_hashes (file, hash, mtime, size) VALUES (?, ?, ?, ?)');
+            const healTx = db.transaction(() => {
+                for (const item of metadataUpdates) {
+                    const mtime = item.stat ? Math.floor(item.stat.mtime) : 0;
+                    const size = item.stat ? item.stat.size : 0;
+                    healHash.run(item.relPath, item.hash, mtime, size);
+                }
+            });
+            healTx();
+        }
         debug(`Self-healed mtime/size for ${metadataUpdates.length} files`);
     }
     catch {
         /* ignore heal errors */
     }
 }
-function findReverseDependencies(db, changedRelPaths, rootDir) {
+function findReverseDependencies(db, changedRelPaths, rootDir, nativeDb) {
     const reverseDeps = new Set();
     if (changedRelPaths.size === 0)
         return reverseDeps;
+    if (nativeDb?.findReverseDependencies) {
+        const changedArray = [...changedRelPaths];
+        const nativeResults = nativeDb.findReverseDependencies(changedArray);
+        for (const dep of nativeResults) {
+            const absPath = path.join(rootDir, dep);
+            if (fs.existsSync(absPath)) {
+                reverseDeps.add(dep);
+            }
+        }
+        return reverseDeps;
+    }
     const findReverseDepsStmt = db.prepare(`
     SELECT DISTINCT n_src.file FROM edges e
     JOIN nodes n_src ON e.source_id = n_src.id
@@ -264,7 +309,10 @@ function purgeAndAddReverseDeps(ctx, changePaths, reverseDeps) {
         ctx.parseChanges.push({ file: absPath, relPath, _reverseDepOnly: true });
     }
 }
-function detectHasEmbeddings(db) {
+function detectHasEmbeddings(db, nativeDb) {
+    if (nativeDb?.hasEmbeddings) {
+        return nativeDb.hasEmbeddings();
+    }
     try {
         db.prepare('SELECT 1 FROM embeddings LIMIT 1').get();
         return true;
@@ -275,19 +323,19 @@ function detectHasEmbeddings(db) {
 }
 function handleScopedBuild(ctx) {
     const { db, rootDir, opts } = ctx;
-    ctx.hasEmbeddings = detectHasEmbeddings(db);
+    ctx.hasEmbeddings = detectHasEmbeddings(db, ctx.nativeDb);
     const changePaths = ctx.parseChanges.map((item) => item.relPath || normalizePath(path.relative(rootDir, item.file)));
     let reverseDeps = new Set();
     if (!opts.noReverseDeps) {
         const changedRelPaths = new Set([...changePaths, ...ctx.removed]);
-        reverseDeps = findReverseDependencies(db, changedRelPaths, rootDir);
+        reverseDeps = findReverseDependencies(db, changedRelPaths, rootDir, ctx.nativeDb);
     }
     purgeAndAddReverseDeps(ctx, changePaths, reverseDeps);
     info(`Scoped rebuild: ${changePaths.length} changed, ${ctx.removed.length} removed, ${reverseDeps.size} reverse-deps`);
 }
 function handleFullBuild(ctx) {
     const { db } = ctx;
-    const hasEmbeddings = detectHasEmbeddings(db);
+    const hasEmbeddings = detectHasEmbeddings(db, ctx.nativeDb);
     ctx.hasEmbeddings = hasEmbeddings;
     const deletions = 'PRAGMA foreign_keys = OFF; DELETE FROM cfg_edges; DELETE FROM cfg_blocks; DELETE FROM node_metrics; DELETE FROM edges; DELETE FROM function_complexity; DELETE FROM dataflow; DELETE FROM ast_nodes; DELETE FROM nodes; PRAGMA foreign_keys = ON;';
     db.exec(hasEmbeddings
@@ -296,7 +344,7 @@ function handleFullBuild(ctx) {
 }
 function handleIncrementalBuild(ctx) {
     const { db, rootDir, opts } = ctx;
-    ctx.hasEmbeddings = detectHasEmbeddings(db);
+    ctx.hasEmbeddings = detectHasEmbeddings(db, ctx.nativeDb);
     let reverseDeps = new Set();
     if (!opts.noReverseDeps) {
         const changedRelPaths = new Set();
@@ -306,7 +354,7 @@ function handleIncrementalBuild(ctx) {
         for (const relPath of ctx.removed) {
             changedRelPaths.add(relPath);
         }
-        reverseDeps = findReverseDependencies(db, changedRelPaths, rootDir);
+        reverseDeps = findReverseDependencies(db, changedRelPaths, rootDir, ctx.nativeDb);
     }
     info(`Incremental: ${ctx.parseChanges.length} changed, ${ctx.removed.length} removed${reverseDeps.size > 0 ? `, ${reverseDeps.size} reverse-deps` : ''}`);
     if (ctx.parseChanges.length > 0)

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

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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":"AAiBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA2KrD,wBAAsB,QAAQ,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAsElE"}
+{"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;AAiMrD,wBAAsB,QAAQ,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA8ElE"}

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

@@ -94,7 +94,25 @@ function persistBuildMetadata(ctx, nodeCount, actualEdgeCount, buildNow) {
  * Run advisory checks on full builds: orphaned embeddings, stale embeddings,
  * and unused exports. Informational only — does not affect correctness.
  */
-function runAdvisoryChecks(db, hasEmbeddings, buildNow) {
+function runAdvisoryChecks(ctx, hasEmbeddings, buildNow) {
+    // Batched native path: single napi call for all 3 advisory checks
+    if (ctx.engineName === 'native' && ctx.nativeDb?.runAdvisoryChecks) {
+        const result = ctx.nativeDb.runAdvisoryChecks(hasEmbeddings);
+        if (result.orphanedEmbeddings > 0) {
+            warn(`${result.orphanedEmbeddings} embeddings are orphaned (nodes changed). Run "codegraph embed" to refresh.`);
+        }
+        if (result.embedBuiltAt) {
+            const embedTime = new Date(result.embedBuiltAt).getTime();
+            if (!Number.isNaN(embedTime) && embedTime < buildNow.getTime()) {
+                warn('Embeddings were built before the last graph rebuild. Run "codegraph embed" to update.');
+            }
+        }
+        if (result.unusedExports > 0) {
+            warn(`${result.unusedExports} exported symbol${result.unusedExports > 1 ? 's have' : ' has'} zero cross-file consumers. Run "codegraph exports <file> --unused" to inspect.`);
+        }
+        return;
+    }
+    const { db } = ctx;
     // Orphaned embeddings warning
     if (hasEmbeddings) {
         try {
@@ -151,9 +169,18 @@ export async function finalize(ctx) {
     // 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;
+    const useNative = ctx.engineName === 'native' && !!ctx.nativeDb?.getFinalizeCounts;
+    let nodeCount;
+    let actualEdgeCount;
+    if (useNative) {
+        const counts = ctx.nativeDb.getFinalizeCounts();
+        nodeCount = counts.nodeCount;
+        actualEdgeCount = counts.edgeCount;
+    }
+    else {
+        nodeCount = ctx.db.prepare('SELECT COUNT(*) as c FROM nodes').get().c;
+        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);
@@ -164,7 +191,7 @@ export async function finalize(ctx) {
         debug('Finalize: skipping advisory queries (orphaned/stale embeddings, unused exports) for incremental build');
     }
     else {
-        runAdvisoryChecks(ctx.db, hasEmbeddings, buildNow);
+        runAdvisoryChecks(ctx, hasEmbeddings, buildNow);
     }
     // Intentionally measured before closeDb / writeJournalHeader / auto-registration:
     // for the deferred-close path the close is async (setImmediate), and for full

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

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

@@ -1 +1 @@
-{"version":3,"file":"insert-nodes.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/insert-nodes.ts"],"names":[],"mappings":"AAmBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA8TrD,wBAAsB,WAAW,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAsDrE"}
+{"version":3,"file":"insert-nodes.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/insert-nodes.ts"],"names":[],"mappings":"AAmBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAyUrD,wBAAsB,WAAW,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAsDrE"}

package/dist/domain/graph/builder/stages/insert-nodes.js

@@ -14,12 +14,6 @@ import { bulkNodeIdsByFile } from '../../../../db/index.js';
 import { batchInsertEdges, batchInsertNodes, fileHash, fileStat, readFileSafe, } from '../helpers.js';
 // ── Native fast-path ─────────────────────────────────────────────────
 function tryNativeInsert(ctx) {
-    // Disabled: bulkInsertNodes corrupts the DB when both the JS (better-sqlite3)
-    // and Rust (rusqlite) connections are open to the same WAL-mode file.
-    // The native path was never operational before — it always crashed on null
-    // visibility serialisation. See #696 for the dual-connection fix.
-    if (ctx.db)
-        return false;
     // Use NativeDatabase persistent connection (Phase 6.15+).
     // Standalone napi functions were removed in 6.17 — falls through to JS if nativeDb unavailable.
     if (!ctx.nativeDb?.bulkInsertNodes)
@@ -100,7 +94,26 @@ function tryNativeInsert(ctx) {
         const size = item.stat ? item.stat.size : 0;
         fileHashes.push({ file: item.relPath, hash: item.hash, mtime, size });
     }
-    return ctx.nativeDb.bulkInsertNodes(batches, fileHashes, removed);
+    // WAL guard: same suspendJsDb/resumeJsDb pattern used by feature modules
+    // (ast, cfg, complexity, dataflow). Checkpoint JS side before native write,
+    // then checkpoint native side after, so neither library reads WAL frames
+    // written by the other (#696, #709, #715, #717).
+    let result;
+    try {
+        if (ctx.db) {
+            ctx.db.pragma('wal_checkpoint(TRUNCATE)');
+        }
+        result = ctx.nativeDb.bulkInsertNodes(batches, fileHashes, removed);
+    }
+    finally {
+        try {
+            ctx.nativeDb?.exec('PRAGMA wal_checkpoint(TRUNCATE)');
+        }
+        catch {
+            /* ignore — nativeDb may already be closed */
+        }
+    }
+    return result;
 }
 // ── JS fallback: Phase 1 ────────────────────────────────────────────
 function insertDefinitionsAndExports(db, allSymbols) {

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

@@ -1 +1 @@
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package/dist/domain/parser.d.ts

@@ -1,6 +1,6 @@
 import { Parser } from 'web-tree-sitter';
 import type { EngineMode, ExtractorOutput, LanguageRegistryEntry } from '../types.js';
-export { extractBashSymbols, extractCppSymbols, extractCSharpSymbols, extractCSymbols, extractDartSymbols, extractElixirSymbols, extractGoSymbols, extractHaskellSymbols, extractHCLSymbols, extractJavaSymbols, extractKotlinSymbols, extractLuaSymbols, extractOCamlSymbols, extractPHPSymbols, extractPythonSymbols, extractRubySymbols, extractRustSymbols, extractScalaSymbols, extractSwiftSymbols, extractSymbols, extractZigSymbols, } from '../extractors/index.js';
+export { extractBashSymbols, extractClojureSymbols, extractCppSymbols, extractCSharpSymbols, extractCSymbols, extractCudaSymbols, extractDartSymbols, extractElixirSymbols, extractErlangSymbols, extractFSharpSymbols, extractGleamSymbols, extractGoSymbols, extractGroovySymbols, extractHaskellSymbols, extractHCLSymbols, extractJavaSymbols, extractJuliaSymbols, extractKotlinSymbols, extractLuaSymbols, extractObjCSymbols, extractOCamlSymbols, extractPHPSymbols, extractPythonSymbols, extractRSymbols, extractRubySymbols, extractRustSymbols, extractScalaSymbols, extractSoliditySymbols, extractSwiftSymbols, extractSymbols, extractVerilogSymbols, extractZigSymbols, } from '../extractors/index.js';
 export type { LanguageRegistryEntry } from '../types.js';
 interface ParseEngineOpts {
     engine?: EngineMode;

package/dist/domain/parser.d.ts.map

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