@optave/codegraph 3.9.1 → 3.9.3

package/src/domain/parser.ts

@@ -5,7 +5,7 @@ import type { Tree } from 'web-tree-sitter';
 import { Language, Parser, Query } from 'web-tree-sitter';
 import { debug, warn } from '../infrastructure/logger.js';
 import { getNative, getNativePackageVersion, loadNative } from '../infrastructure/native.js';
-import { toErrorMessage } from '../shared/errors.js';
+import { ParseError, toErrorMessage } from '../shared/errors.js';
 import type {
   EngineMode,
   ExtractorOutput,
@@ -188,7 +188,11 @@ async function doLoadLanguage(entry: LanguageRegistryEntry): Promise<void> {
       _queryCache.set(entry.id, new Query(lang, patterns.join('\n')));
     }
   } catch (e: unknown) {
-    if (entry.required) throw e;
+    if (entry.required)
+      throw new ParseError(`Required parser ${entry.id} failed to initialize`, {
+        file: entry.grammarFile,
+        cause: e as Error,
+      });
     warn(
       `${entry.id} parser failed to initialize: ${(e as Error).message}. ${entry.id} files will be skipped.`,
     );
@@ -776,7 +780,7 @@ export async function parseFileAuto(
   const { native } = resolveEngine(opts);
 
   if (native) {
-    const result = native.parseFile(filePath, source, !!opts.dataflow, opts.ast !== false);
+    const result = native.parseFile(filePath, source, true, true);
     if (!result) return null;
     const patched = patchNativeResult(result);
     // Always backfill typeMap for TS/TSX from WASM — native parser's type
@@ -874,7 +878,11 @@ export async function parseFilesAuto(
   if (!native) return parseFilesWasm(filePaths, rootDir);
 
   const result = new Map<string, ExtractorOutput>();
-  const nativeResults = native.parseFiles(filePaths, rootDir, !!opts.dataflow, opts.ast !== false);
+  // Always extract all analysis data (dataflow + AST nodes) during native parse.
+  // This eliminates the need for any downstream WASM re-parse or native standalone calls.
+  const nativeResults = native.parseFilesFull
+    ? native.parseFilesFull(filePaths, rootDir)
+    : native.parseFiles(filePaths, rootDir, true, true);
   const needsTypeMap: { filePath: string; relPath: string }[] = [];
   for (const r of nativeResults) {
     if (!r) continue;

package/src/domain/queries.ts

@@ -22,7 +22,7 @@ export {
   VALID_ROLES,
 } from '../shared/kinds.js';
 // ── Shared utilities ─────────────────────────────────────────────────────
-export { kindIcon, normalizeSymbol } from '../shared/normalize.js';
+export { kindIcon, normalizeSymbol, toSymbolRef } from '../shared/normalize.js';
 export { briefData } from './analysis/brief.js';
 export { contextData, explainData } from './analysis/context.js';
 export { fileDepsData, filePathData, fnDepsData, pathData } from './analysis/dependencies.js';

package/src/features/ast.ts

@@ -115,8 +115,8 @@ function tryNativeBulkInsert(
           receiver: n.receiver ?? '',
         })),
       });
-    } else if (symbols.calls || symbols._tree) {
-      return false; // needs JS fallback
+    } else if (symbols._tree) {
+      return false; // has WASM tree not yet processed — needs JS fallback
     }
   }
 

package/src/features/audit.ts

@@ -7,6 +7,7 @@ import { loadConfig } from '../infrastructure/config.js';
 import { debug } from '../infrastructure/logger.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { toErrorMessage } from '../shared/errors.js';
+import { toSymbolRef } from '../shared/normalize.js';
 import type { BetterSqlite3Database, CodegraphConfig } from '../types.js';
 import { RULE_DEFS } from './manifesto.js';
 
@@ -317,7 +318,7 @@ function enrichSymbol(
          WHERE e.source_id = ? AND e.kind = 'calls'`,
         )
         .all(nodeId) as SymbolRef[]
-    ).map((c) => ({ name: c.name, kind: c.kind, file: c.file, line: c.line }));
+    ).map(toSymbolRef);
 
     callers = (
       db
@@ -327,7 +328,7 @@ function enrichSymbol(
          WHERE e.target_id = ? AND e.kind = 'calls'`,
         )
         .all(nodeId) as SymbolRef[]
-    ).map((c) => ({ name: c.name, kind: c.kind, file: c.file, line: c.line }));
+    ).map(toSymbolRef);
     if (noTests) callers = callers.filter((c) => !isTestFile(c.file));
 
     const testCallerRows = db

package/src/features/boundaries.ts

@@ -1,5 +1,5 @@
-import { debug } from '../infrastructure/logger.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
+import { BoundaryError } from '../shared/errors.js';
 import type { BetterSqlite3Database } from '../types.js';
 
 // ─── Glob-to-Regex ───────────────────────────────────────────────────
@@ -269,8 +269,7 @@ export function evaluateBoundaries(
 
   const { valid, errors } = validateBoundaryConfig(boundaryConfig);
   if (!valid) {
-    debug(`boundary config validation failed: ${errors.join('; ')}`);
-    return { violations: [], violationCount: 0 };
+    throw new BoundaryError(`Invalid boundary configuration: ${errors.join('; ')}`);
   }
 
   const modules = resolveModules(boundaryConfig);
@@ -297,8 +296,7 @@ export function evaluateBoundaries(
       )
       .all() as Array<{ source: string; target: string }>;
   } catch (err) {
-    debug(`boundary edge query failed: ${(err as Error).message}`);
-    return { violations: [], violationCount: 0 };
+    throw new BoundaryError('Boundary evaluation failed', { cause: err as Error });
   }
 
   if (opts.noTests) {

package/src/features/branch-compare.ts

@@ -9,6 +9,7 @@ import { debug } from '../infrastructure/logger.js';
 import { getNative, isNativeAvailable } from '../infrastructure/native.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
 import { toErrorMessage } from '../shared/errors.js';
+import { toSymbolRef } from '../shared/normalize.js';
 import type { EngineMode, NativeDatabase } from '../types.js';
 
 // ─── Git Helpers ────────────────────────────────────────────────────────
@@ -255,9 +256,7 @@ function loadCallersFromDb(
             if (!visited.has(c.id) && (!noTests || !isTestFile(c.file))) {
               visited.add(c.id);
               nextFrontier.push(c.id);
-              allCallers.add(
-                JSON.stringify({ name: c.name, kind: c.kind, file: c.file, line: c.line }),
-              );
+              allCallers.add(JSON.stringify(toSymbolRef(c)));
             }
           }
         }

package/src/features/cfg.ts

@@ -369,7 +369,7 @@ export async function buildCFGData(
   db: BetterSqlite3Database,
   fileSymbols: Map<string, FileSymbols>,
   rootDir: string,
-  _engineOpts?: {
+  engineOpts?: {
     nativeDb?: { bulkInsertCfg?(entries: Array<Record<string, unknown>>): number };
     suspendJsDb?: () => void;
     resumeJsDb?: () => void;
@@ -379,11 +379,56 @@ export async function buildCFGData(
   // skip WASM parser init, tree parsing, and JS visitor entirely — just persist.
   const allNative = allCfgNative(fileSymbols);
 
-  // NOTE: nativeDb.bulkInsertCfg is intentionally NOT used here.
-  // The CFG path requires delete-before-insert (deleteCfgForNode) which creates
-  // a dual-connection WAL conflict when deletes go through JS (better-sqlite3)
-  // and inserts go through native (rusqlite). The JS-only persistNativeFileCfg
-  // path below handles both on a single connection safely.
+  // ── Native bulk-insert fast path ──────────────────────────────────────
+  // The Rust bulkInsertCfg handles delete-before-insert atomically on a
+  // single rusqlite connection, so there is no dual-connection WAL conflict.
+  const nativeDb = engineOpts?.nativeDb;
+  if (allNative && nativeDb?.bulkInsertCfg) {
+    const entries: Array<Record<string, unknown>> = [];
+    for (const [relPath, symbols] of fileSymbols) {
+      const ext = path.extname(relPath).toLowerCase();
+      if (!CFG_EXTENSIONS.has(ext)) continue;
+
+      for (const def of symbols.definitions) {
+        if (def.kind !== 'function' && def.kind !== 'method') continue;
+        if (!def.line) continue;
+
+        const nodeId = getFunctionNodeId(db, def.name, relPath, def.line);
+        if (!nodeId) continue;
+
+        const cfg = def.cfg as { blocks?: CfgBuildBlock[]; edges?: CfgBuildEdge[] } | undefined;
+        if (!cfg?.blocks?.length) continue;
+
+        entries.push({
+          nodeId,
+          blocks: cfg.blocks.map((b) => ({
+            index: b.index,
+            blockType: b.type,
+            startLine: b.startLine ?? undefined,
+            endLine: b.endLine ?? undefined,
+            label: b.label ?? undefined,
+          })),
+          edges: (cfg.edges || []).map((e) => ({
+            sourceIndex: e.sourceIndex,
+            targetIndex: e.targetIndex,
+            kind: e.kind,
+          })),
+        });
+      }
+    }
+
+    if (entries.length > 0) {
+      let inserted = 0;
+      try {
+        engineOpts?.suspendJsDb?.();
+        inserted = nativeDb.bulkInsertCfg(entries);
+      } finally {
+        engineOpts?.resumeJsDb?.();
+      }
+      info(`CFG (native bulk): ${inserted} functions analyzed`);
+    }
+    return;
+  }
 
   const extToLang = buildExtToLangMap();
   let parsers: unknown = null;

package/src/features/complexity.ts

@@ -545,6 +545,10 @@ function collectNativeBulkRows(
   const rows: Array<Record<string, unknown>> = [];
 
   for (const [relPath, symbols] of fileSymbols) {
+    const ext = path.extname(relPath).toLowerCase();
+    const langId = symbols._langId || '';
+    const langSupported = COMPLEXITY_EXTENSIONS.has(ext) || COMPLEXITY_RULES.has(langId);
+
     for (const def of symbols.definitions) {
       if (def.kind !== 'function' && def.kind !== 'method') continue;
       if (!def.line) continue;
@@ -554,6 +558,9 @@ function collectNativeBulkRows(
       // of the native bulk-insert path for every TypeScript codebase (#846).
       if (!def.complexity) {
         if (def.name.includes('.') || !def.endLine || def.endLine <= def.line) continue;
+        // Languages without complexity rules will never have data — skip them
+        // rather than bailing out of the entire native bulk path.
+        if (!langSupported) continue;
         return null; // genuine function body missing complexity — needs JS fallback
       }
       const nodeId = getFunctionNodeId(db, def.name, relPath, def.line);

package/src/features/flow.ts

@@ -8,6 +8,7 @@
 import { openReadonlyOrFail } from '../db/index.js';
 import { CORE_SYMBOL_KINDS, findMatchingNodes } from '../domain/queries.js';
 import { isTestFile } from '../infrastructure/test-filter.js';
+import { toSymbolRef } from '../shared/normalize.js';
 import { paginateResult } from '../shared/paginate.js';
 import { FRAMEWORK_ENTRY_PREFIXES } from './structure.js';
 
@@ -175,7 +176,7 @@ function bfsCallees(
 
         visited.add(c.id);
         nextFrontier.push(c.id);
-        const nodeInfo: NodeInfo = { name: c.name, kind: c.kind, file: c.file, line: c.line };
+        const nodeInfo: NodeInfo = toSymbolRef(c);
         levelNodes.push(nodeInfo);
         nodeDepths.set(c.id, d);
         idToNode.set(c.id, nodeInfo);

package/src/features/manifesto.ts

@@ -5,6 +5,7 @@ import { loadConfig } from '../infrastructure/config.js';
 import { debug } from '../infrastructure/logger.js';
 import { paginateResult } from '../shared/paginate.js';
 import type { BetterSqlite3Database, CodegraphConfig, ThresholdRule } from '../types.js';
+import type { BoundaryViolation } from './boundaries.js';
 import { evaluateBoundaries } from './boundaries.js';
 
 // ─── Rule Definitions ─────────────────────────────────────────────────
@@ -416,7 +417,20 @@ function evaluateBoundaryRules(
     return;
   }
 
-  const result = evaluateBoundaries(db, boundaryConfig, { noTests: opts.noTests || false });
+  let result: { violations: BoundaryViolation[]; violationCount: number };
+  try {
+    result = evaluateBoundaries(db, boundaryConfig, { noTests: opts.noTests || false });
+  } catch (e: unknown) {
+    debug(`boundary check failed: ${(e as Error).message}`);
+    ruleResults.push({
+      name: 'boundaries',
+      level: 'graph',
+      status: 'warn',
+      thresholds: effectiveThresholds,
+      violationCount: 0,
+    });
+    return;
+  }
   const hasBoundaryViolations = result.violationCount > 0;
 
   if (!hasBoundaryViolations) {

package/src/infrastructure/config.ts

@@ -23,6 +23,7 @@ export const DEFAULTS = {
     incremental: true,
     dbPath: '.codegraph/graph.db',
     driftThreshold: 0.2,
+    smallFilesThreshold: 5,
   },
   query: {
     defaultDepth: 3,

package/src/infrastructure/update-check.ts

@@ -18,11 +18,11 @@ interface UpdateCache {
 
 /**
  * Minimal semver comparison. Returns -1, 0, or 1.
- * Only handles numeric x.y.z (no pre-release tags).
+ * Strips pre-release suffixes (e.g. "3.9.3-dev.6" → "3.9.3") before comparing.
  */
 export function semverCompare(a: string, b: string): -1 | 0 | 1 {
-  const pa = a.split('.').map(Number);
-  const pb = b.split('.').map(Number);
+  const pa = a.replace(/-.*$/, '').split('.').map(Number);
+  const pb = b.replace(/-.*$/, '').split('.').map(Number);
   for (let i = 0; i < 3; i++) {
     const na = pa[i] || 0;
     const nb = pb[i] || 0;

package/src/presentation/batch.ts

@@ -36,6 +36,7 @@ export function batchQuery(
   const { command: defaultCommand = 'where', ...rest } = opts;
   const isMulti =
     targets.length > 0 &&
+    targets[0] !== null &&
     typeof targets[0] === 'object' &&
     !!(targets[0] as MultiBatchTarget).command;
 

package/src/presentation/structure.ts

@@ -75,7 +75,7 @@ export function formatHotspots(data: HotspotsResult): string {
 
 interface ModuleBoundaryEntry {
   directory: string;
-  cohesion: number;
+  cohesion: number | null;
   fileCount: number;
   symbolCount: number;
   fanIn: number;
@@ -95,7 +95,7 @@ export function formatModuleBoundaries(data: ModuleBoundariesResult): string {
   const lines = [`\nModule boundaries (cohesion >= ${data.threshold}, ${data.count} modules):\n`];
   for (const m of data.modules) {
     lines.push(
-      `  ${m.directory}/  cohesion=${m.cohesion.toFixed(2)}  (${m.fileCount} files, ${m.symbolCount} symbols)`,
+      `  ${m.directory}/  cohesion=${m.cohesion !== null ? m.cohesion.toFixed(2) : 'n/a'}  (${m.fileCount} files, ${m.symbolCount} symbols)`,
     );
     lines.push(`    Incoming: ${m.fanIn} edges    Outgoing: ${m.fanOut} edges`);
     if (m.files.length > 0) {

package/src/shared/normalize.ts

@@ -19,6 +19,16 @@ export function getFileHash(db: DbHandle, file: string): string | null {
   return row ? row.hash : null;
 }
 
+/** Pick the 4-field symbol reference from any row that carries at least {name, kind, file, line}. */
+export function toSymbolRef(row: { name: string; kind: string; file: string; line: number }): {
+  name: string;
+  kind: string;
+  file: string;
+  line: number;
+} {
+  return { name: row.name, kind: row.kind, file: row.file, line: row.line };
+}
+
 export function kindIcon(kind: string): string {
   switch (kind) {
     case 'function':

package/src/types.ts

@@ -1085,6 +1085,7 @@ export interface CodegraphConfig {
     incremental: boolean;
     dbPath: string;
     driftThreshold: number;
+    smallFilesThreshold: number;
   };
 
   query: {
@@ -1873,6 +1874,7 @@ export type StmtCache<TRow = unknown> = WeakMap<BetterSqlite3Database, SqliteSta
 export interface NativeAddon {
   parseFile(filePath: string, source: string, dataflow: boolean, ast: boolean): unknown;
   parseFiles(files: string[], rootDir: string, dataflow: boolean, ast: boolean): unknown[];
+  parseFilesFull?(files: string[], rootDir: string): unknown[];
   resolveImport(fromFile: string, importSource: string, rootDir: string, aliases: unknown): string;
   resolveImports(
     items: Array<{ fromFile: string; importSource: string }>,