@optave/codegraph 3.9.3 → 3.9.4

package/README.md

@@ -617,17 +617,17 @@ Codegraph also extracts symbols from common callback patterns: Commander `.comma
 
 Self-measured on every release via CI ([build benchmarks](generated/benchmarks/BUILD-BENCHMARKS.md) | [embedding benchmarks](generated/benchmarks/EMBEDDING-BENCHMARKS.md) | [query benchmarks](generated/benchmarks/QUERY-BENCHMARKS.md) | [incremental benchmarks](generated/benchmarks/INCREMENTAL-BENCHMARKS.md) | [resolution precision/recall](tests/benchmarks/resolution/)):
 
-*Last updated: v3.9.2 (2026-04-09)*
+*Last updated: v3.9.3 (2026-04-13)*
 
 | Metric | Native | WASM |
 |---|---|---|
-| Build speed | **15.7 ms/file** | **15 ms/file** |
-| Query time | **27ms** | **40ms** |
-| No-op rebuild | **9ms** | **20ms** |
-| 1-file rebuild | **558ms** | **624ms** |
-| Query: fn-deps | **2.3ms** | **2.4ms** |
-| Query: path | **2.5ms** | **2.4ms** |
-| ~50,000 files (est.) | **~785.0s build** | **~750.0s build** |
+| Build speed | **3.3 ms/file** | **15.9 ms/file** |
+| Query time | **30ms** | **42ms** |
+| No-op rebuild | **11ms** | **22ms** |
+| 1-file rebuild | **397ms** | **638ms** |
+| Query: fn-deps | **2.5ms** | **2.4ms** |
+| Query: path | **2.5ms** | **2.3ms** |
+| ~50,000 files (est.) | **~165.0s build** | **~795.0s build** |
 | Resolution precision | **90.7%** | — |
 | Resolution recall | **42.9%** | — |
 

package/dist/ast-analysis/visitor.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"visitor.d.ts","sourceRoot":"","sources":["../../src/ast-analysis/visitor.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAGH,OAAO,KAAK,EAEV,cAAc,EACd,OAAO,EAEP,WAAW,EACX,WAAW,EACZ,MAAM,aAAa,CAAC;AAqIrB;;;;;;;;;;;GAWG;AACH,wBAAgB,gBAAgB,CAC9B,QAAQ,EAAE,cAAc,EACxB,QAAQ,EAAE,OAAO,EAAE,EACnB,MAAM,EAAE,MAAM,EACd,OAAO,GAAE,WAAgB,GACxB,WAAW,CAgEb"}

package/dist/ast-analysis/visitor.js

@@ -10,6 +10,7 @@
  * The walker maintains shared context (nestingLevel, scopeStack, currentFunction)
  * so individual visitors don't need to track traversal state themselves.
  */
+import { debug } from '../infrastructure/logger.js';
 /** Merge each visitor's custom functionNodeTypes into the master set. */
 function mergeFunctionNodeTypes(visitors, base) {
     const merged = new Set(base);
@@ -82,6 +83,15 @@ function dispatchExitFunction(visitors, skipDepths, node, funcName, context, dep
         }
     }
 }
+/**
+ * Maximum AST depth before walk() bails out.  WASM-backed tree-sitter parsers
+ * have a smaller stack than native V8 (~64-256 KB).  Deep recursion in
+ * generated code, deeply nested object literals, or pathologically large
+ * switch statements can exhaust that stack, causing a V8 fatal error /
+ * segfault (#931).  500 levels is well beyond any realistic hand-written
+ * code while staying safely inside the WASM stack budget.
+ */
+const MAX_WALK_DEPTH = 500;
 /** Collect finish() results from all visitors into a name-keyed map. */
 function collectResults(visitors) {
     const results = {};
@@ -118,6 +128,10 @@ export function walkWithVisitors(rootNode, visitors, langId, options = {}) {
     function walk(node, depth) {
         if (!node)
             return;
+        if (depth > MAX_WALK_DEPTH) {
+            debug(`walkWithVisitors: AST depth limit (${MAX_WALK_DEPTH}) hit — subtree truncated`);
+            return;
+        }
         const type = node.type;
         const isFuncBoundary = allFuncTypes.has(type);
         let funcName = null;

package/dist/ast-analysis/visitor.js.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/context.d.ts

@@ -38,6 +38,21 @@ export declare class PipelineContext {
     barrelOnlyFiles: Set<string>;
     nodesByName: Map<string, NodeRow[]>;
     nodesByNameAndFile: Map<string, NodeRow[]>;
+    /**
+     * Edges from reverse-dep files to changed files, saved before purge so they
+     * can be reconnected to new node IDs after insertNodes (#932, #933).
+     * Eliminates the need to reparse reverse-dep files entirely.
+     */
+    savedReverseDepEdges: Array<{
+        sourceId: number;
+        tgtName: string;
+        tgtKind: string;
+        tgtFile: string;
+        tgtLine: number;
+        edgeKind: string;
+        confidence: number;
+        dynamic: number;
+    }>;
     hasEmbeddings: boolean;
     lineCountMap: Map<string, number>;
     timing: {

package/dist/domain/graph/builder/context.d.ts.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/context.js

@@ -37,6 +37,13 @@ export class PipelineContext {
     // ── Node lookup (set by insertNodes / buildEdges stages) ───────────
     nodesByName;
     nodesByNameAndFile;
+    // ── Reverse-dep edge reconnection (set by detectChanges) ───────────
+    /**
+     * Edges from reverse-dep files to changed files, saved before purge so they
+     * can be reconnected to new node IDs after insertNodes (#932, #933).
+     * Eliminates the need to reparse reverse-dep files entirely.
+     */
+    savedReverseDepEdges = [];
     // ── Misc state ─────────────────────────────────────────────────────
     hasEmbeddings = false;
     lineCountMap;

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

@@ -1 +1 @@
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+{"version":3,"file":"context.js","sourceRoot":"","sources":["../../../../src/domain/graph/builder/context.ts"],"names":[],"mappings":"AAoBA,MAAM,OAAO,eAAe;IAC1B,sEAAsE;IACtE,OAAO,CAAU;IACjB,EAAE,CAAyB;IAC3B,MAAM,CAAU;IAChB,MAAM,CAAmB;IACzB,IAAI,CAAkB;IACtB,UAAU,CAAc;IACxB,UAAU,CAAqB;IAC/B,aAAa,CAAiB;IAC9B,OAAO,CAAe;IACtB,WAAW,CAAW;IACtB,gBAAgB,GAAY,KAAK,CAAC;IAClC,aAAa,CAAU;IACvB,QAAQ,CAAkB;IAC1B,kFAAkF;IAClF,eAAe,GAAY,KAAK,CAAC;IACjC,gGAAgG;IAChG,gBAAgB,GAAY,KAAK,CAAC;IAElC,sEAAsE;IACtE,QAAQ,CAAY;IACpB,cAAc,CAAe;IAE7B,sEAAsE;IACtE,WAAW,CAAW;IACtB,YAAY,CAAiB;IAC7B,eAAe,CAAoB;IACnC,OAAO,CAAY;IACnB,SAAS,GAAY,KAAK,CAAC;IAE3B,sEAAsE;IACtE,UAAU,CAAgC;IAC1C,WAAW,CAAgC;IAC3C,YAAY,CAAiB;IAE7B,sEAAsE;IACtE,aAAa,CAA8B;IAC3C,WAAW,CAA0B;IACrC,eAAe,CAAe;IAE9B,sEAAsE;IACtE,WAAW,CAA0B;IACrC,kBAAkB,CAA0B;IAE5C,sEAAsE;IACtE;;;;OAIG;IACH,oBAAoB,GASf,EAAE,CAAC;IAER,sEAAsE;IACtE,aAAa,GAAY,KAAK,CAAC;IAC/B,YAAY,CAAuB;IAEnC,sEAAsE;IACtE,MAAM,GAcF,EAAE,CAAC;IACP,UAAU,CAAU;CACrB"}

package/dist/domain/graph/builder/pipeline.d.ts.map

@@ -1 +1 @@
-{"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"}
+{"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;AA0wB3B;;;;GAIG;AACH,wBAAsB,UAAU,CAC9B,OAAO,EAAE,MAAM,EACf,IAAI,GAAE,cAAmB,GACxB,OAAO,CAAC,WAAW,GAAG,SAAS,CAAC,CA8DlC"}

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

@@ -66,9 +66,15 @@ function checkEngineSchemaMismatch(ctx) {
         info(`Schema version changed (${prevSchema} → ${ctx.schemaVersion}), promoting to full rebuild.`);
         ctx.forceFullRebuild = true;
     }
+    // When the native engine is active, the Rust addon's version (ctx.engineVersion)
+    // is written into codegraph_version by setBuildMeta after a native orchestrator
+    // build. The check must compare against the same version, otherwise JS and Rust
+    // fight over which version to record — causing every incremental build to be
+    // promoted to a full rebuild when npm and crate versions diverge.
+    const effectiveVersion = ctx.engineName === 'native' && ctx.engineVersion ? ctx.engineVersion : CODEGRAPH_VERSION;
     const prevVersion = meta('codegraph_version');
-    if (prevVersion && prevVersion !== CODEGRAPH_VERSION) {
-        info(`Codegraph version changed (${prevVersion} → ${CODEGRAPH_VERSION}), promoting to full rebuild.`);
+    if (prevVersion && prevVersion !== effectiveVersion) {
+        info(`Codegraph version changed (${prevVersion} → ${effectiveVersion}), promoting to full rebuild.`);
         ctx.forceFullRebuild = true;
     }
 }
@@ -96,42 +102,16 @@ function setupPipeline(ctx) {
     const enginePref = ctx.opts.engine || 'auto';
     const native = enginePref !== 'wasm' ? loadNative() : null;
     ctx.nativeAvailable = !!native?.NativeDatabase;
-    // When native is available, use a NativeDbProxy backed by a single rusqlite
-    // connection. This eliminates the dual-connection WAL corruption problem.
-    // The Rust orchestrator handles the full pipeline; the proxy is used for any
-    // JS post-processing (e.g. structure fallback on large builds).
-    if (ctx.nativeAvailable && native?.NativeDatabase) {
-        try {
-            const dir = path.dirname(ctx.dbPath);
-            if (!fs.existsSync(dir))
-                fs.mkdirSync(dir, { recursive: true });
-            acquireAdvisoryLock(ctx.dbPath);
-            ctx.nativeDb = native.NativeDatabase.openReadWrite(ctx.dbPath);
-            ctx.nativeDb.initSchema();
-            const proxy = new NativeDbProxy(ctx.nativeDb);
-            proxy.__lockPath = `${ctx.dbPath}.lock`;
-            ctx.db = proxy;
-            ctx.nativeFirstProxy = true;
-        }
-        catch (err) {
-            warn(`NativeDatabase setup failed, falling back to better-sqlite3: ${toErrorMessage(err)}`);
-            try {
-                ctx.nativeDb?.close();
-            }
-            catch {
-                /* ignore */
-            }
-            ctx.nativeDb = undefined;
-            ctx.nativeFirstProxy = false;
-            releaseAdvisoryLock(`${ctx.dbPath}.lock`);
-            ctx.db = openDb(ctx.dbPath);
-            initSchema(ctx.db);
-        }
-    }
-    else {
-        ctx.db = openDb(ctx.dbPath);
-        initSchema(ctx.db);
-    }
+    // Always use better-sqlite3 for setup — it's cheap (~4ms) and only needed
+    // for metadata reads (schema mismatch check). NativeDatabase.openReadWrite
+    // is deferred to tryNativeOrchestrator, saving ~60ms on incremental builds
+    // where the Rust orchestrator handles the full pipeline, and avoiding the
+    // cost entirely on no-op builds that exit before reaching the orchestrator.
+    const dir = path.dirname(ctx.dbPath);
+    if (!fs.existsSync(dir))
+        fs.mkdirSync(dir, { recursive: true });
+    ctx.db = openDb(ctx.dbPath);
+    initSchema(ctx.db);
     ctx.config = loadConfig(ctx.rootDir);
     ctx.incremental =
         ctx.opts.incremental !== false && ctx.config.build && ctx.config.build.incremental !== false;
@@ -464,15 +444,26 @@ async function tryNativeOrchestrator(ctx) {
         debug(`Skipping native orchestrator: ${skipReason}`);
         return undefined;
     }
-    // In native-first mode, nativeDb is already open from setupPipeline.
-    // Otherwise, open it on demand (deferred to skip overhead on no-op rebuilds).
+    // Open NativeDatabase on demand — deferred from setupPipeline to skip the
+    // ~60ms cost on no-op/early-exit builds. Close the better-sqlite3 connection
+    // first to avoid dual-connection WAL corruption.
     if (!ctx.nativeDb && ctx.nativeAvailable) {
         const native = loadNative();
         if (native?.NativeDatabase) {
             try {
+                // Close better-sqlite3 before opening rusqlite to avoid WAL conflicts.
+                // Uses raw close() instead of closeDb() intentionally — the advisory lock
+                // is kept and transferred to the NativeDbProxy below, not released here.
+                ctx.db.close();
+                acquireAdvisoryLock(ctx.dbPath);
                 ctx.nativeDb = native.NativeDatabase.openReadWrite(ctx.dbPath);
                 ctx.nativeDb.initSchema();
-                ctx.nativeDb.exec('PRAGMA wal_checkpoint(TRUNCATE)');
+                // Replace ctx.db with a NativeDbProxy so post-native JS fallback
+                // (structure, analysis) can use it without reopening better-sqlite3.
+                const proxy = new NativeDbProxy(ctx.nativeDb);
+                proxy.__lockPath = `${ctx.dbPath}.lock`;
+                ctx.db = proxy;
+                ctx.nativeFirstProxy = true;
             }
             catch (err) {
                 warn(`NativeDatabase setup failed, falling back to JS: ${toErrorMessage(err)}`);
@@ -483,6 +474,10 @@ async function tryNativeOrchestrator(ctx) {
                     debug(`tryNativeOrchestrator: close failed during fallback: ${toErrorMessage(e)}`);
                 }
                 ctx.nativeDb = undefined;
+                ctx.nativeFirstProxy = false; // defensive: reset in case future refactors move the assignment above throwing lines
+                releaseAdvisoryLock(`${ctx.dbPath}.lock`);
+                // Reopen better-sqlite3 for JS pipeline fallback
+                ctx.db = openDb(ctx.dbPath);
             }
         }
     }
@@ -503,14 +498,18 @@ async function tryNativeOrchestrator(ctx) {
     }
     const p = result.phases;
     // Sync build_meta so JS-side version/engine checks work on next build.
+    // Use the Rust addon version as codegraph_version when the native
+    // orchestrator performed the build — the Rust side's check_version_mismatch
+    // compares this value against CARGO_PKG_VERSION.  Writing the JS
+    // CODEGRAPH_VERSION here would create a permanent mismatch whenever the
+    // npm package version diverges from the Rust crate version, forcing every
+    // subsequent native build to be a full rebuild (no incremental).
     setBuildMeta(ctx.db, {
         engine: ctx.engineName,
         engine_version: ctx.engineVersion || '',
-        codegraph_version: CODEGRAPH_VERSION,
+        codegraph_version: ctx.engineVersion || CODEGRAPH_VERSION,
         schema_version: String(ctx.schemaVersion),
         built_at: new Date().toISOString(),
-        node_count: String(result.nodeCount ?? 0),
-        edge_count: String(result.edgeCount ?? 0),
     });
     info(`Native build orchestrator completed: ${result.nodeCount ?? 0} nodes, ${result.edgeCount ?? 0} edges, ${result.fileCount ?? 0} files`);
     // ── Post-native structure + analysis ──────────────────────────────
@@ -547,7 +546,7 @@ async function tryNativeOrchestrator(ctx) {
         }
         const fileSymbols = reconstructFileSymbolsFromDb(ctx);
         if (needsStructure) {
-            structurePatchMs = await runPostNativeStructure(ctx, fileSymbols, !!result.isFullBuild, result.structureScope ?? result.changedFiles);
+            structurePatchMs = await runPostNativeStructure(ctx, fileSymbols, !!result.isFullBuild, result.changedFiles);
         }
         if (needsAnalysisFallback) {
             analysisTiming = await runPostNativeAnalysis(ctx, fileSymbols, result.changedFiles);
@@ -618,6 +617,23 @@ async function runPipelineStages(ctx) {
         }
     }
     await runAnalyses(ctx);
+    // Release WASM trees deterministically on the success path — same cleanup
+    // as the error-path catch block.  Without this, trees stay allocated until
+    // GC collects ctx, holding WASM memory for the rest of the build (#931).
+    if (ctx.allSymbols?.size > 0) {
+        for (const [, symbols] of ctx.allSymbols) {
+            const tree = symbols._tree;
+            if (tree && typeof tree.delete === 'function') {
+                try {
+                    tree.delete();
+                }
+                catch {
+                    /* ignore cleanup errors */
+                }
+            }
+            symbols._tree = undefined;
+        }
+    }
     // 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).
@@ -658,13 +674,41 @@ export async function buildGraph(rootDir, opts = {}) {
         }
         catch (err) {
             warn(`Native build orchestrator failed, falling back to JS pipeline: ${toErrorMessage(err)}`);
-            // Fall through to JS pipeline
+            // The version gate in checkEngineSchemaMismatch was skipped because
+            // nativeAvailable was true. Now that we're falling back to the JS
+            // pipeline, perform the codegraph_version check here so a version
+            // bump still promotes to a full rebuild (#928).
+            if (ctx.incremental && !ctx.forceFullRebuild) {
+                const prevVersion = getBuildMeta(ctx.db, 'codegraph_version');
+                if (prevVersion && prevVersion !== CODEGRAPH_VERSION) {
+                    info(`Codegraph version changed (${prevVersion} → ${CODEGRAPH_VERSION}), promoting to full rebuild.`);
+                    ctx.forceFullRebuild = true;
+                }
+            }
         }
         await runPipelineStages(ctx);
     }
     catch (err) {
-        if (!ctx.earlyExit && ctx.db) {
-            closeDbPair({ db: ctx.db, nativeDb: ctx.nativeDb });
+        if (!ctx.earlyExit) {
+            // Release WASM trees before closing DB to prevent V8 crash during
+            // GC cleanup of orphaned WASM objects (#931).
+            if (ctx.allSymbols?.size > 0) {
+                for (const [, symbols] of ctx.allSymbols) {
+                    const tree = symbols._tree;
+                    if (tree && typeof tree.delete === 'function') {
+                        try {
+                            tree.delete();
+                        }
+                        catch {
+                            /* ignore cleanup errors */
+                        }
+                    }
+                    symbols._tree = undefined;
+                }
+            }
+            if (ctx.db) {
+                closeDbPair({ db: ctx.db, nativeDb: ctx.nativeDb });
+            }
         }
         throw err;
     }

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;AA6uBrD,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;AA4yBrD,wBAAsB,UAAU,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC,CAqGpE"}

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

@@ -463,6 +463,57 @@ function buildClassHierarchyEdges(ctx, relPath, symbols, allEdgeRows) {
         }
     }
 }
+// ── Reverse-dep edge reconnection (#932, #933) ─────────────────────────
+/**
+ * Reconnect edges that were saved before changed-file purge.
+ *
+ * Each saved edge records: sourceId (still valid — reverse-dep nodes were not
+ * purged) and target attributes (name, kind, file, line).  The target node was
+ * deleted and re-inserted with a new ID by insertNodes.  We look up the new ID
+ * by (name, kind, file) and re-create the edge.
+ */
+function reconnectReverseDepEdges(ctx) {
+    const { db } = ctx;
+    const findNodeStmt = db.prepare('SELECT id FROM nodes WHERE name = ? AND kind = ? AND file = ? ORDER BY ABS(line - ?) LIMIT 1');
+    const reconnectedRows = [];
+    let dropped = 0;
+    for (const saved of ctx.savedReverseDepEdges) {
+        const newTarget = findNodeStmt.get(saved.tgtName, saved.tgtKind, saved.tgtFile, saved.tgtLine);
+        if (newTarget) {
+            reconnectedRows.push([
+                saved.sourceId,
+                newTarget.id,
+                saved.edgeKind,
+                saved.confidence,
+                saved.dynamic,
+            ]);
+        }
+        else {
+            // Target was removed or renamed in the changed file — edge is stale
+            dropped++;
+        }
+    }
+    if (reconnectedRows.length > 0) {
+        if (ctx.nativeDb?.bulkInsertEdges) {
+            const nativeEdges = reconnectedRows.map((r) => ({
+                sourceId: r[0],
+                targetId: r[1],
+                kind: r[2],
+                confidence: r[3],
+                dynamic: r[4],
+            }));
+            const ok = ctx.nativeDb.bulkInsertEdges(nativeEdges);
+            if (!ok) {
+                batchInsertEdges(db, reconnectedRows);
+            }
+        }
+        else {
+            batchInsertEdges(db, reconnectedRows);
+        }
+    }
+    debug(`Reconnected ${reconnectedRows.length} reverse-dep edges` +
+        (dropped > 0 ? ` (${dropped} dropped — targets removed/renamed)` : ''));
+}
 // ── Main entry point ────────────────────────────────────────────────────
 /**
  * For small incremental builds (≤5 changed files on a large codebase), scope
@@ -545,9 +596,10 @@ export async function buildEdges(ctx) {
                 deleteOutgoingEdges.run(relPath);
             }
         }
-        // Skip native import-edge path for small incremental builds (≤3 files):
-        // napi-rs marshaling overhead exceeds computation savings.
-        const useNativeImportEdges = native?.buildImportEdges && (ctx.isFullBuild || ctx.fileSymbols.size > 3);
+        // Skip native import-edge path for small incremental builds: napi-rs
+        // marshaling overhead (~13ms) exceeds Rust computation savings at this scale.
+        const useNativeImportEdges = native?.buildImportEdges &&
+            (ctx.isFullBuild || ctx.fileSymbols.size > ctx.config.build.smallFilesThreshold);
         if (useNativeImportEdges) {
             const beforeLen = allEdgeRows.length;
             buildImportEdgesNative(ctx, getNodeIdStmt, allEdgeRows, native);
@@ -567,9 +619,10 @@ export async function buildEdges(ctx) {
         else {
             buildImportEdges(ctx, getNodeIdStmt, allEdgeRows);
         }
-        // Skip native call-edge path for small incremental builds (≤3 files):
-        // napi-rs marshaling overhead for allNodes exceeds computation savings.
-        const useNativeCallEdges = native?.buildCallEdges && (ctx.isFullBuild || ctx.fileSymbols.size > 3);
+        // Skip native call-edge path for small incremental builds: napi-rs
+        // marshaling overhead for allNodes exceeds Rust computation savings.
+        const useNativeCallEdges = native?.buildCallEdges &&
+            (ctx.isFullBuild || ctx.fileSymbols.size > ctx.config.build.smallFilesThreshold);
         if (useNativeCallEdges) {
             buildCallEdgesNative(ctx, getNodeIdStmt, allEdgeRows, allNodesBefore, native);
         }
@@ -601,6 +654,14 @@ export async function buildEdges(ctx) {
             batchInsertEdges(ctx.db, allEdgeRows);
         }
     }
+    // Phase 3: Reconnect saved reverse-dep edges (#932, #933).
+    // When the WASM/JS path purged changed files, edges FROM reverse-dep files TO
+    // those files were deleted (target-side).  The reverse-dep files were NOT
+    // reparsed — instead we saved the edge topology before purge and now reconnect
+    // each edge to the new node IDs created by insertNodes.
+    if (ctx.savedReverseDepEdges.length > 0) {
+        reconnectReverseDepEdges(ctx);
+    }
     ctx.timing.edgesMs = performance.now() - t0;
 }
 //# sourceMappingURL=build-edges.js.map