@optave/codegraph 3.9.1 → 3.9.3

package/dist/domain/graph/builder/native-db-proxy.js

@@ -0,0 +1,91 @@
+/**
+ * NativeDbProxy — wraps a NativeDatabase (rusqlite via napi-rs) to satisfy the
+ * BetterSqlite3Database interface.  When the native addon is available, the
+ * build pipeline uses this proxy as `ctx.db` so that every stage operates on a
+ * single rusqlite connection — no dual-connection WAL corruption, no
+ * open/close/reopen dance.
+ *
+ * When native is unavailable, the pipeline falls back to real better-sqlite3.
+ */
+/** Sanitize params for napi-rs: better-sqlite3 treats `undefined` as NULL,
+ *  but serde_json cannot represent `undefined`. Replace with `null`. */
+function sanitize(params) {
+    return params.map((p) => (p === undefined ? null : p));
+}
+export class NativeDbProxy {
+    #ndb;
+    /** Advisory lock path — set by the pipeline so closeDb() can release it. */
+    __lockPath;
+    constructor(nativeDb) {
+        this.#ndb = nativeDb;
+    }
+    prepare(sql) {
+        const ndb = this.#ndb;
+        // Only INSERT statements need last_insert_rowid — skip the extra napi
+        // call for UPDATE/DELETE/other DML to halve per-statement overhead.
+        const isInsert = sql.trimStart().substring(0, 6).toUpperCase() === 'INSERT';
+        const stmt = {
+            all(...params) {
+                return ndb.queryAll(sql, sanitize(params));
+            },
+            get(...params) {
+                return (ndb.queryGet(sql, sanitize(params)) ?? undefined);
+            },
+            run(...params) {
+                ndb.queryAll(sql, sanitize(params));
+                if (isInsert) {
+                    const row = ndb.queryGet('SELECT last_insert_rowid() AS rid', []);
+                    return { changes: 0, lastInsertRowid: row?.rid ?? 0 };
+                }
+                return { changes: 0, lastInsertRowid: 0 };
+            },
+            iterate() {
+                throw new Error('iterate() is not supported via NativeDbProxy');
+            },
+            raw() {
+                return stmt; // no-op — .raw() is not used in the build pipeline
+            },
+        };
+        return stmt;
+    }
+    exec(sql) {
+        this.#ndb.exec(sql);
+        return this;
+    }
+    pragma(sql) {
+        return this.#ndb.pragma(sql);
+    }
+    close() {
+        // No-op: the pipeline manages the NativeDatabase lifecycle directly.
+        // closeDbPair() calls nativeDb.close() separately.
+    }
+    get open() {
+        return this.#ndb.isOpen;
+    }
+    get name() {
+        return this.#ndb.dbPath;
+    }
+    transaction(fn) {
+        const ndb = this.#ndb;
+        return ((...args) => {
+            // NOTE: nested transactions (savepoints) are not supported — ensure callers
+            // do not invoke a transaction() wrapper from within an existing transaction.
+            ndb.exec('BEGIN');
+            try {
+                const result = fn(...args);
+                ndb.exec('COMMIT');
+                return result;
+            }
+            catch (e) {
+                try {
+                    ndb.exec('ROLLBACK');
+                }
+                catch {
+                    // Ignore rollback errors — the original error is more important
+                }
+                throw e;
+            }
+        });
+    }
+}
+//# sourceMappingURL=native-db-proxy.js.map

package/dist/domain/graph/builder/native-db-proxy.js.map

@@ -0,0 +1 @@
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package/dist/domain/graph/builder/pipeline.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"pipeline.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/pipeline.ts"],"names":[],"mappings":"AAyBA,OAAO,KAAK,EAEV,cAAc,EACd,WAAW,EAGZ,MAAM,mBAAmB,CAAC;AAwvB3B;;;;GAIG;AACH,wBAAsB,UAAU,CAC9B,OAAO,EAAE,MAAM,EACf,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,WAAW,GAAG,SAAS,CAAC,CAiClC"}

package/dist/domain/graph/builder/pipeline.js

@@ -4,9 +4,10 @@
  * This is the heart of the builder refactor (ROADMAP 3.9): the monolithic buildGraph()
  * is decomposed into independently testable stages that communicate via PipelineContext.
  */
+import fs from 'node:fs';
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
-import { closeDbPair, getBuildMeta, initSchema, MIGRATIONS, openDb, setBuildMeta, } from '../../../db/index.js';
+import { acquireAdvisoryLock, closeDbPair, getBuildMeta, initSchema, MIGRATIONS, openDb, releaseAdvisoryLock, setBuildMeta, } from '../../../db/index.js';
 import { detectWorkspaces, loadConfig } from '../../../infrastructure/config.js';
 import { debug, info, warn } from '../../../infrastructure/logger.js';
 import { loadNative } from '../../../infrastructure/native.js';
@@ -17,6 +18,7 @@ import { getActiveEngine } from '../../parser.js';
 import { setWorkspaces } from '../resolve.js';
 import { PipelineContext } from './context.js';
 import { loadPathAliases } from './helpers.js';
+import { NativeDbProxy } from './native-db-proxy.js';
 import { buildEdges } from './stages/build-edges.js';
 import { buildStructure } from './stages/build-structure.js';
 // Pipeline stages
@@ -33,28 +35,11 @@ function initializeEngine(ctx) {
         engine: ctx.opts.engine || 'auto',
         dataflow: ctx.opts.dataflow !== false,
         ast: ctx.opts.ast !== false,
-        nativeDb: ctx.nativeDb,
-        // WAL checkpoint callbacks for dual-connection WAL guard (#696, #715).
-        // Feature modules (ast, cfg, complexity, dataflow) receive `db` as a
-        // parameter and cannot tolerate close/reopen (stale reference). Instead,
-        // checkpoint the WAL so native writes start with a clean slate.
-        // After native writes, resumeJsDb checkpoints through rusqlite so
-        // better-sqlite3 never reads WAL frames from a different SQLite library.
-        suspendJsDb: ctx.nativeDb
-            ? () => {
-                ctx.db.pragma('wal_checkpoint(TRUNCATE)');
-            }
-            : undefined,
-        resumeJsDb: ctx.nativeDb
-            ? () => {
-                try {
-                    ctx.nativeDb?.exec('PRAGMA wal_checkpoint(TRUNCATE)');
-                }
-                catch (e) {
-                    debug(`resumeJsDb: WAL checkpoint failed (nativeDb may already be closed): ${toErrorMessage(e)}`);
-                }
-            }
-            : undefined,
+        // nativeDb and WAL callbacks are set later when NativeDatabase is opened
+        // (deferred to skip overhead on no-op rebuilds).
+        nativeDb: undefined,
+        suspendJsDb: undefined,
+        resumeJsDb: undefined,
     };
     const { name: engineName, version: engineVersion } = getActiveEngine(ctx.engineOpts);
     ctx.engineName = engineName;
@@ -67,10 +52,10 @@ function checkEngineSchemaMismatch(ctx) {
     ctx.forceFullRebuild = false;
     if (!ctx.incremental)
         return;
-    // Route metadata reads through NativeDatabase only when using the native engine,
-    // to avoid dual-SQLite WAL conflicts (rusqlite + better-sqlite3 on same file).
-    const useNativeDb = ctx.engineName === 'native' && !!ctx.nativeDb;
-    const meta = (key) => useNativeDb ? ctx.nativeDb.getBuildMeta(key) : getBuildMeta(ctx.db, key);
+    // NativeDatabase is deferred until after change detection, so always use
+    // better-sqlite3 for metadata reads here. Reads are safe — WAL conflicts
+    // only arise from concurrent writes.
+    const meta = (key) => getBuildMeta(ctx.db, key);
     const prevEngine = meta('engine');
     if (prevEngine && prevEngine !== ctx.engineName) {
         info(`Engine changed (${prevEngine} → ${ctx.engineName}), promoting to full rebuild.`);
@@ -107,36 +92,44 @@ function loadAliases(ctx) {
 function setupPipeline(ctx) {
     ctx.rootDir = path.resolve(ctx.rootDir);
     ctx.dbPath = path.join(ctx.rootDir, '.codegraph', 'graph.db');
-    ctx.db = openDb(ctx.dbPath);
-    // Use NativeDatabase for schema init when native engine is available (Phase 6.13).
-    // better-sqlite3 (ctx.db) is still always opened — needed for queries and stages
-    // that haven't been migrated to rusqlite yet.
-    // Skip native DB entirely when user explicitly requested --engine wasm.
+    // Detect whether native engine is available.
     const enginePref = ctx.opts.engine || 'auto';
     const native = enginePref !== 'wasm' ? loadNative() : null;
-    if (native?.NativeDatabase) {
+    ctx.nativeAvailable = !!native?.NativeDatabase;
+    // When native is available, use a NativeDbProxy backed by a single rusqlite
+    // connection. This eliminates the dual-connection WAL corruption problem.
+    // The Rust orchestrator handles the full pipeline; the proxy is used for any
+    // JS post-processing (e.g. structure fallback on large builds).
+    if (ctx.nativeAvailable && native?.NativeDatabase) {
         try {
+            const dir = path.dirname(ctx.dbPath);
+            if (!fs.existsSync(dir))
+                fs.mkdirSync(dir, { recursive: true });
+            acquireAdvisoryLock(ctx.dbPath);
             ctx.nativeDb = native.NativeDatabase.openReadWrite(ctx.dbPath);
             ctx.nativeDb.initSchema();
-            // Checkpoint WAL through rusqlite so better-sqlite3 sees a clean DB
-            // with no cross-library WAL frames (#715, #717).
-            ctx.nativeDb.exec('PRAGMA wal_checkpoint(TRUNCATE)');
+            const proxy = new NativeDbProxy(ctx.nativeDb);
+            proxy.__lockPath = `${ctx.dbPath}.lock`;
+            ctx.db = proxy;
+            ctx.nativeFirstProxy = true;
         }
         catch (err) {
-            warn(`NativeDatabase setup failed, falling back to JS: ${toErrorMessage(err)}`);
+            warn(`NativeDatabase setup failed, falling back to better-sqlite3: ${toErrorMessage(err)}`);
             try {
                 ctx.nativeDb?.close();
             }
-            catch (e) {
-                debug(`setupNativeDb: close failed during fallback: ${toErrorMessage(e)}`);
+            catch {
+                /* ignore */
             }
             ctx.nativeDb = undefined;
+            ctx.nativeFirstProxy = false;
+            releaseAdvisoryLock(`${ctx.dbPath}.lock`);
+            ctx.db = openDb(ctx.dbPath);
+            initSchema(ctx.db);
         }
-        // Always run JS initSchema so better-sqlite3 sees the schema —
-        // nativeDb is closed during pipeline stages and reopened for analyses.
-        initSchema(ctx.db);
     }
     else {
+        ctx.db = openDb(ctx.dbPath);
         initSchema(ctx.db);
     }
     ctx.config = loadConfig(ctx.rootDir);
@@ -230,11 +223,12 @@ function refreshJsDb(ctx) {
 // ── Native orchestrator helpers ───────────────────────────────────────
 /** Determine whether the native orchestrator should be skipped. Returns a reason string, or null if it should run. */
 function shouldSkipNativeOrchestrator(ctx) {
-    if (process.env.CODEGRAPH_FORCE_JS_PIPELINE === '1')
-        return 'CODEGRAPH_FORCE_JS_PIPELINE=1';
     if (ctx.forceFullRebuild)
         return 'forceFullRebuild';
-    const orchestratorBuggy = !!ctx.engineVersion && semverCompare(ctx.engineVersion, '3.10.0') < 0;
+    // v3.9.0 addon had buggy incremental purge (wrong SQL on analysis tables,
+    // scoped removal over-detection). Fixed in v3.9.1 by PR #865. Gate on
+    // < 3.9.1 so v3.9.1+ uses the fast Rust orchestrator path.
+    const orchestratorBuggy = !!ctx.engineVersion && semverCompare(ctx.engineVersion, '3.9.1') < 0;
     if (orchestratorBuggy)
         return `buggy addon ${ctx.engineVersion}`;
     if (ctx.engineName !== 'native')
@@ -366,7 +360,11 @@ async function runPostNativeStructure(ctx, allFileSymbols, isFullBuild, changedF
     }
     return performance.now() - structureStart;
 }
-/** Run AST/complexity/CFG/dataflow analysis after native orchestrator. */
+/**
+ * JS fallback for AST/complexity/CFG/dataflow analysis after native orchestrator.
+ * Used when the Rust addon doesn't include analysis persistence (older addon
+ * version) or when analysis failed on the Rust side.
+ */
 async function runPostNativeAnalysis(ctx, allFileSymbols, changedFiles) {
     const timing = { astMs: 0, complexityMs: 0, cfgMs: 0, dataflowMs: 0 };
     // Scope analysis fileSymbols to changed files only
@@ -396,8 +394,16 @@ async function runPostNativeAnalysis(ctx, allFileSymbols, changedFiles) {
                 ctx.engineOpts.nativeDb = undefined;
         }
     }
+    // Flush JS WAL pages once so Rust can see them, then no-op callbacks.
+    // Previously each feature called wal_checkpoint(TRUNCATE) individually
+    // (~68ms each × 3-4 features). One FULL checkpoint suffices.
+    if (ctx.nativeDb && ctx.engineOpts) {
+        ctx.db.pragma('wal_checkpoint(FULL)');
+        ctx.engineOpts.suspendJsDb = () => { };
+        ctx.engineOpts.resumeJsDb = () => { };
+    }
     try {
-        const { runAnalyses: runAnalysesFn } = await import('../../../ast-analysis/engine.js');
+        const { runAnalyses: runAnalysesFn } = (await import('../../../ast-analysis/engine.js'));
         const result = await runAnalysesFn(ctx.db, analysisFileSymbols, ctx.rootDir, ctx.opts, ctx.engineOpts);
         timing.astMs = result.astMs ?? 0;
         timing.complexityMs = result.complexityMs ?? 0;
@@ -407,7 +413,9 @@ async function runPostNativeAnalysis(ctx, allFileSymbols, changedFiles) {
     catch (err) {
         warn(`Analysis phases failed after native build: ${toErrorMessage(err)}`);
     }
-    // Close nativeDb after analyses
+    // Close nativeDb after analyses — TRUNCATE checkpoint flushes all Rust
+    // WAL writes so JS and external readers can see them. Runs once after
+    // all analysis features complete (not per-feature).
     if (ctx.nativeDb) {
         try {
             ctx.nativeDb.exec('PRAGMA wal_checkpoint(TRUNCATE)');
@@ -422,8 +430,11 @@ async function runPostNativeAnalysis(ctx, allFileSymbols, changedFiles) {
             /* ignore close errors */
         }
         ctx.nativeDb = undefined;
-        if (ctx.engineOpts)
+        if (ctx.engineOpts) {
             ctx.engineOpts.nativeDb = undefined;
+            ctx.engineOpts.suspendJsDb = undefined;
+            ctx.engineOpts.resumeJsDb = undefined;
+        }
     }
     return timing;
 }
@@ -453,6 +464,28 @@ async function tryNativeOrchestrator(ctx) {
         debug(`Skipping native orchestrator: ${skipReason}`);
         return undefined;
     }
+    // In native-first mode, nativeDb is already open from setupPipeline.
+    // Otherwise, open it on demand (deferred to skip overhead on no-op rebuilds).
+    if (!ctx.nativeDb && ctx.nativeAvailable) {
+        const native = loadNative();
+        if (native?.NativeDatabase) {
+            try {
+                ctx.nativeDb = native.NativeDatabase.openReadWrite(ctx.dbPath);
+                ctx.nativeDb.initSchema();
+                ctx.nativeDb.exec('PRAGMA wal_checkpoint(TRUNCATE)');
+            }
+            catch (err) {
+                warn(`NativeDatabase setup failed, falling back to JS: ${toErrorMessage(err)}`);
+                try {
+                    ctx.nativeDb?.close();
+                }
+                catch (e) {
+                    debug(`tryNativeOrchestrator: close failed during fallback: ${toErrorMessage(e)}`);
+                }
+                ctx.nativeDb = undefined;
+            }
+        }
+    }
     if (!ctx.nativeDb?.buildGraph)
         return undefined;
     const resultJson = ctx.nativeDb.buildGraph(ctx.rootDir, JSON.stringify(ctx.config), JSON.stringify(ctx.aliases), JSON.stringify(ctx.opts));
@@ -481,30 +514,42 @@ async function tryNativeOrchestrator(ctx) {
     });
     info(`Native build orchestrator completed: ${result.nodeCount ?? 0} nodes, ${result.edgeCount ?? 0} edges, ${result.fileCount ?? 0} files`);
     // ── Post-native structure + analysis ──────────────────────────────
-    let analysisTiming = { astMs: 0, complexityMs: 0, cfgMs: 0, dataflowMs: 0 };
+    let analysisTiming = {
+        astMs: +(p.astMs ?? 0),
+        complexityMs: +(p.complexityMs ?? 0),
+        cfgMs: +(p.cfgMs ?? 0),
+        dataflowMs: +(p.dataflowMs ?? 0),
+    };
     let structurePatchMs = 0;
-    const needsAnalysis = ctx.opts.ast !== false ||
-        ctx.opts.complexity !== false ||
-        ctx.opts.cfg !== false ||
-        ctx.opts.dataflow !== false;
     // Skip JS structure when the Rust pipeline's small-incremental fast path
     // already handled it. For full builds and large incrementals where Rust
     // skipped structure, we must run the JS fallback.
     const needsStructure = !result.structureHandled;
-    if (needsAnalysis || needsStructure) {
-        if (!handoffWalAfterNativeBuild(ctx)) {
+    // When the Rust addon doesn't include analysis persistence (older addon
+    // version or analysis failed), fall back to JS-side analysis.
+    const needsAnalysisFallback = !result.analysisComplete &&
+        (ctx.opts.ast !== false ||
+            ctx.opts.complexity !== false ||
+            ctx.opts.cfg !== false ||
+            ctx.opts.dataflow !== false);
+    if (needsStructure || needsAnalysisFallback) {
+        // When analysis fallback is needed, handoff to better-sqlite3 — the
+        // analysis engine uses the suspend/resume WAL pattern that requires a
+        // real better-sqlite3 connection, not the NativeDbProxy.
+        if (needsAnalysisFallback && ctx.nativeFirstProxy) {
+            closeNativeDb(ctx, 'pre-analysis-fallback');
+            ctx.db = openDb(ctx.dbPath);
+            ctx.nativeFirstProxy = false;
+        }
+        else if (!ctx.nativeFirstProxy && !handoffWalAfterNativeBuild(ctx)) {
             // DB reopen failed — return partial result
             return formatNativeTimingResult(p, 0, analysisTiming);
         }
-        // When structure was handled by Rust, we only need changed files for
-        // analysis — no need to load the entire graph from DB. When structure
-        // was NOT handled, we need all files to build the complete directory tree.
-        const scopeFiles = needsStructure ? undefined : result.changedFiles;
-        const fileSymbols = reconstructFileSymbolsFromDb(ctx, scopeFiles);
+        const fileSymbols = reconstructFileSymbolsFromDb(ctx);
         if (needsStructure) {
             structurePatchMs = await runPostNativeStructure(ctx, fileSymbols, !!result.isFullBuild, result.structureScope ?? result.changedFiles);
         }
-        if (needsAnalysis) {
+        if (needsAnalysisFallback) {
             analysisTiming = await runPostNativeAnalysis(ctx, fileSymbols, result.changedFiles);
         }
     }
@@ -513,24 +558,33 @@ async function tryNativeOrchestrator(ctx) {
 }
 // ── Pipeline stages execution ───────────────────────────────────────────
 async function runPipelineStages(ctx) {
-    // Prevent dual-connection WAL corruption during pipeline stages: when both
-    // better-sqlite3 (ctx.db) and rusqlite (ctx.nativeDb) are open to the same
-    // WAL-mode file, native writes corrupt the DB. Close nativeDb so stages
-    // use JS fallback paths. Reopened before runAnalyses for feature modules
-    // that use suspendJsDb/resumeJsDb WAL checkpoint pattern (#696).
-    const hadNativeDb = !!ctx.nativeDb;
+    // ── WASM / fallback dual-connection mode ─────────────────────────────
+    // NativeDatabase is deferred — not opened during setup. collectFiles and
+    // detectChanges only need better-sqlite3. If no files changed, we exit
+    // early without ever opening the native connection, saving ~5ms.
+    // If nativeDb was opened by tryNativeOrchestrator (which fell through),
+    // suspend it now to avoid dual-connection WAL corruption during stages.
     if (ctx.db && ctx.nativeDb) {
         suspendNativeDb(ctx, 'pre-collect');
+        // When nativeFirstProxy is true, ctx.db is a NativeDbProxy wrapping the
+        // now-closed NativeDatabase. Replace it with a real better-sqlite3
+        // connection so the JS pipeline stages can operate normally.
+        if (ctx.nativeFirstProxy) {
+            ctx.db = openDb(ctx.dbPath);
+            ctx.nativeFirstProxy = false;
+        }
     }
     await collectFiles(ctx);
     await detectChanges(ctx);
     if (ctx.earlyExit)
         return;
     await parseFiles(ctx);
-    // Temporarily reopen nativeDb for insertNodes — it uses the WAL checkpoint
-    // guard internally (same pattern as feature modules). Closed again before
-    // resolveImports/buildEdges which don't yet have the guard (#709).
-    if (hadNativeDb && ctx.engineName === 'native') {
+    // For small incremental builds (≤smallFilesThreshold files), skip the nativeDb open/close
+    // cycle for insertNodes — the WAL checkpoint + connection churn (~5-10ms)
+    // exceeds the napi bulk-insert savings on a handful of files. The JS
+    // fallback path inside insertNodes handles this case efficiently.
+    const smallIncremental = !ctx.isFullBuild && ctx.allSymbols.size <= ctx.config.build.smallFilesThreshold;
+    if (ctx.nativeAvailable && ctx.engineName === 'native' && !smallIncremental) {
         reopenNativeDb(ctx, 'insertNodes');
     }
     await insertNodes(ctx);
@@ -542,23 +596,38 @@ async function runPipelineStages(ctx) {
     await resolveImports(ctx);
     await buildEdges(ctx);
     await buildStructure(ctx);
-    // Reopen nativeDb for feature modules (ast, cfg, complexity, dataflow)
-    // which use suspendJsDb/resumeJsDb WAL checkpoint before native writes.
-    if (hadNativeDb) {
+    // Reopen nativeDb for feature modules (ast, cfg, complexity, dataflow).
+    // Skip for small incremental builds — same rationale as insertNodes above.
+    //
+    // Perf: do ONE upfront FULL checkpoint to flush JS WAL pages so Rust
+    // can see the latest rows, then make suspendJsDb/resumeJsDb no-ops.
+    // Previously each feature called wal_checkpoint(TRUNCATE) individually
+    // (~68ms each × 3-4 features = ~200-270ms overhead on incremental builds).
+    if (ctx.nativeAvailable && !smallIncremental) {
         reopenNativeDb(ctx, 'analyses');
         if (ctx.nativeDb && ctx.engineOpts) {
+            ctx.db.pragma('wal_checkpoint(FULL)');
             ctx.engineOpts.nativeDb = ctx.nativeDb;
+            ctx.engineOpts.suspendJsDb = () => { };
+            ctx.engineOpts.resumeJsDb = () => { };
         }
         if (!ctx.nativeDb && ctx.engineOpts) {
             ctx.engineOpts.nativeDb = undefined;
+            ctx.engineOpts.suspendJsDb = undefined;
+            ctx.engineOpts.resumeJsDb = undefined;
         }
     }
     await runAnalyses(ctx);
-    // Keep nativeDb open through finalize so persistBuildMetadata, advisory
-    // checks, and count queries use the native path.  closeDbPair inside
-    // finalize handles both connections.  Refresh the JS db so it has a
-    // valid page cache in case finalize falls back to JS paths (#751).
+    // Flush Rust WAL writes (AST, complexity, CFG, dataflow) so the JS
+    // connection and any post-build readers can see them.  One TRUNCATE
+    // here replaces the N per-feature resumeJsDb checkpoints (#checkpoint-opt).
     if (ctx.nativeDb) {
+        try {
+            ctx.nativeDb.exec('PRAGMA wal_checkpoint(TRUNCATE)');
+        }
+        catch (e) {
+            debug(`post-analyses WAL checkpoint failed: ${toErrorMessage(e)}`);
+        }
         refreshJsDb(ctx);
     }
     await finalize(ctx);

package/dist/domain/graph/builder/pipeline.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"build-edges.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/build-edges.ts"],"names":[],"mappings":"AAsBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAguBrD,wBAAsB,UAAU,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA0FpE"}
+{"version":3,"file":"build-edges.d.ts","sourceRoot":"","sources":["../../../../../src/domain/graph/builder/stages/build-edges.ts"],"names":[],"mappings":"AAsBA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AA6uBrD,wBAAsB,UAAU,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CA0FpE"}

package/dist/domain/graph/builder/stages/build-edges.js

@@ -208,7 +208,7 @@ function buildCallEdgesNative(ctx, getNodeIdStmt, allEdgeRows, allNodes, native)
         if (!fileNodeRow)
             continue;
         const importedNames = buildImportedNamesForNative(ctx, relPath, symbols, rootDir);
-        const typeMap = symbols.typeMap instanceof Map
+        const typeMapRaw = symbols.typeMap instanceof Map
             ? [...symbols.typeMap.entries()].map(([name, entry]) => ({
                 name,
                 typeName: typeof entry === 'string' ? entry : entry.type,
@@ -217,6 +217,19 @@ function buildCallEdgesNative(ctx, getNodeIdStmt, allEdgeRows, allNodes, native)
             : Array.isArray(symbols.typeMap)
                 ? symbols.typeMap
                 : [];
+        // Deduplicate: keep highest-confidence entry per name (first-wins on tie),
+        // matching JS setTypeMapEntry semantics.  The Map branch is already
+        // deduped by setTypeMapEntry — this loop is only needed for the Array
+        // branch (pre-rebuilt native addon) but runs unconditionally as
+        // belt-and-suspenders since it's a cheap O(n) pass.
+        const typeMapDedup = new Map();
+        for (const entry of typeMapRaw) {
+            const existing = typeMapDedup.get(entry.name);
+            if (!existing || entry.confidence > existing.confidence) {
+                typeMapDedup.set(entry.name, entry);
+            }
+        }
+        const typeMap = [...typeMapDedup.values()];
         nativeFiles.push({
             file: relPath,
             fileNodeId: fileNodeRow.id,
@@ -461,7 +474,7 @@ function loadNodes(ctx) {
     const { db, fileSymbols, isFullBuild, batchResolved } = ctx;
     const nodeKindFilter = `kind IN ('function','method','class','interface','struct','type','module','enum','trait','record','constant')`;
     // Gate: only scope for small incremental on large codebases
-    if (!isFullBuild && fileSymbols.size <= 5) {
+    if (!isFullBuild && fileSymbols.size <= ctx.config.build.smallFilesThreshold) {
         const existingFileCount = db.prepare("SELECT COUNT(*) as c FROM nodes WHERE kind = 'file'").get().c;
         if (existingFileCount > 20) {
             // Collect relevant files: changed files + their import targets