@optave/codegraph 3.9.2 → 3.9.3

package/README.md

@@ -544,6 +544,35 @@ The graph stays current without re-parsing your entire codebase. Three-tier chan
 
 **Result:** change one file in a 3,000-file project and the rebuild completes in under a second. Put it in a commit hook, a file watcher, or let your AI agent trigger it.
 
+#### What incremental rebuilds refresh — and what they don't
+
+Incremental builds re-parse changed files and rebuild their edges, structure metrics, and role classifications. But some data is **only fully refreshed on a full rebuild:**
+
+| Data | Incremental | Full rebuild |
+|------|:-----------:|:------------:|
+| Symbols & edges for changed files | Yes | Yes |
+| Reverse-dependency cascade (importers of changed files) | Yes | Yes |
+| AST nodes, complexity, CFG, dataflow for changed files | Yes | Yes |
+| Directory-level cohesion metrics | Partial (skipped for ≤5 files) | Yes |
+| Advisory checks (orphaned embeddings, stale embeddings, unused exports) | Skipped | Yes |
+| Build metadata persistence | Skipped for ≤3 files | Yes |
+| Incremental drift detection | Skipped | Yes |
+
+**When to run a full rebuild:**
+
+```bash
+codegraph build --no-incremental   # Force full rebuild
+```
+
+- **After large refactors** (renames, moves, deleted files) — the reverse-dependency cascade handles most cases, but a full rebuild ensures nothing is stale
+- **If you suspect stale analysis data** — complexity or dataflow results for files you didn't directly edit won't update incrementally
+- **Periodically** — if you rely heavily on `complexity`, `dataflow`, `roles --role dead`, or `communities` queries, run a full rebuild weekly or after major merges
+- **After upgrading codegraph** — engine, schema, or version changes trigger an automatic full rebuild, but if you skip versions you may want to force one
+
+Codegraph auto-detects and forces a full rebuild when the engine, schema version, or codegraph version changes between builds. For everything else, incremental is the safe default — a full rebuild is a correctness guarantee, not a frequent necessity.
+
+> **Detailed guide:** See [docs/guides/incremental-builds.md](docs/guides/incremental-builds.md) for a complete breakdown of what each build mode refreshes and recommended rebuild schedules.
+
 ### Dual Engine
 
 Codegraph ships with two parsing engines:
@@ -588,22 +617,76 @@ 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: v3.9.1 (2026-04-06)*
+*Last updated: v3.9.2 (2026-04-09)*
 
 | Metric | Native | WASM |
 |---|---|---|
-| Build speed | **10.2 ms/file** | **13.7 ms/file** |
-| Query time | **23ms** | **36ms** |
-| No-op rebuild | **17ms** | **15ms** |
-| 1-file rebuild | **767ms** | **639ms** |
-| Query: fn-deps | **2.2ms** | **2.2ms** |
-| Query: path | **2.2ms** | **2.2ms** |
-| ~50,000 files (est.) | **~510.0s build** | **~685.0s build** |
-| Resolution precision | **100.0%** | — |
-| Resolution recall | **71.1%** | — |
+| 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** |
+| Resolution precision | **90.7%** | — |
+| Resolution recall | **42.9%** | — |
 
 Metrics are normalized per file for cross-version comparability. Times above are for a full initial build — incremental rebuilds only re-parse changed files.
 
+<details><summary>Per-language resolution precision/recall</summary>
+
+| Language | Precision | Recall | TP | FP | FN | Edges | Dynamic |
+|----------|----------:|-------:|---:|---:|---:|------:|--------:|
+| javascript | 100.0% | 66.7% | 12 | 0 | 6 | 18 | 14/28 |
+| typescript | 100.0% | 75.0% | 15 | 0 | 5 | 20 | — |
+| bash | 100.0% | 100.0% | 12 | 0 | 0 | 12 | 0/1 |
+| c | 100.0% | 100.0% | 9 | 0 | 0 | 9 | — |
+| clojure | 80.0% | 26.7% | 4 | 1 | 11 | 15 | — |
+| cpp | 100.0% | 57.1% | 8 | 0 | 6 | 14 | — |
+| csharp | 100.0% | 52.6% | 10 | 0 | 9 | 19 | — |
+| cuda | 50.0% | 33.3% | 4 | 4 | 8 | 12 | — |
+| dart | 0.0% | 0.0% | 0 | 0 | 18 | 18 | — |
+| elixir | 0.0% | 0.0% | 0 | 0 | 15 | 15 | — |
+| erlang | 100.0% | 100.0% | 12 | 0 | 0 | 12 | — |
+| fsharp | 0.0% | 0.0% | 0 | 9 | 12 | 12 | — |
+| gleam | 100.0% | 26.7% | 4 | 0 | 11 | 15 | — |
+| go | 100.0% | 69.2% | 9 | 0 | 4 | 13 | 13/14 |
+| groovy | 100.0% | 7.7% | 1 | 0 | 12 | 13 | — |
+| haskell | 100.0% | 33.3% | 4 | 0 | 8 | 12 | — |
+| hcl | 0.0% | 0.0% | 0 | 0 | 2 | 2 | — |
+| java | 100.0% | 52.9% | 9 | 0 | 8 | 17 | — |
+| julia | 0.0% | 0.0% | 0 | 0 | 15 | 15 | — |
+| kotlin | 92.3% | 63.2% | 12 | 1 | 7 | 19 | — |
+| lua | 100.0% | 15.4% | 2 | 0 | 11 | 13 | — |
+| objc | 0.0% | 0.0% | 0 | 1 | 12 | 12 | — |
+| ocaml | 100.0% | 8.3% | 1 | 0 | 11 | 12 | — |
+| php | 100.0% | 31.6% | 6 | 0 | 13 | 19 | — |
+| python | 100.0% | 60.0% | 9 | 0 | 6 | 15 | 15/15 |
+| r | 100.0% | 100.0% | 11 | 0 | 0 | 11 | — |
+| ruby | 100.0% | 100.0% | 11 | 0 | 0 | 11 | 11/11 |
+| rust | 100.0% | 35.7% | 5 | 0 | 9 | 14 | — |
+| scala | 100.0% | 71.4% | 5 | 0 | 2 | 7 | — |
+| solidity | 33.3% | 7.7% | 1 | 2 | 12 | 13 | — |
+| swift | 75.0% | 42.9% | 6 | 2 | 8 | 14 | 9/9 |
+| tsx | 100.0% | 100.0% | 13 | 0 | 0 | 13 | — |
+| verilog | 0.0% | 0.0% | 0 | 0 | 4 | 4 | — |
+| zig | 0.0% | 0.0% | 0 | 0 | 15 | 15 | — |
+
+**By resolution mode (all languages):**
+
+| Mode | Resolved | Expected | Recall |
+|------|--------:|---------:|-------:|
+| module-function | 16 | 106 | 15.1% |
+| receiver-typed | 17 | 104 | 16.3% |
+| static | 66 | 93 | 71.0% |
+| same-file | 48 | 86 | 55.8% |
+| interface-dispatched | 7 | 12 | 58.3% |
+| class-inheritance | 0 | 4 | 0.0% |
+| trait-dispatch | 0 | 2 | 0.0% |
+| package-function | 1 | 1 | 100.0% |
+
+</details>
+
 ### Lightweight Footprint
 
 <a href="https://www.npmjs.com/package/@optave/codegraph"><img src="https://img.shields.io/npm/unpacked-size/@optave/codegraph?style=flat-square&label=unpacked%20size" alt="npm unpacked size" /></a>

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

@@ -1 +1 @@
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package/dist/ast-analysis/engine.js

@@ -481,6 +481,60 @@ async function delegateToBuildFunctions(db, fileSymbols, rootDir, opts, engineOp
         timing.dataflowMs += performance.now() - t0;
     }
 }
+// ─── Native full-analysis fast path ────────────────────────────────────
+/**
+ * Check whether all files already have complete analysis data from the native
+ * parse pass (parseFilesFull). When true, no WASM re-parse or JS visitor walk
+ * is needed — the engine can skip directly to DB persistence.
+ */
+function allNativeDataComplete(fileSymbols, opts) {
+    const doAst = opts.ast !== false;
+    const doComplexity = opts.complexity !== false;
+    const doCfg = opts.cfg !== false;
+    const doDataflow = opts.dataflow !== false;
+    for (const [relPath, symbols] of fileSymbols) {
+        // If any file has a WASM tree, it was parsed by WASM — not native full
+        if (symbols._tree)
+            return false;
+        const ext = path.extname(relPath).toLowerCase();
+        const langId = symbols._langId || '';
+        // AST nodes: native must have produced them
+        if (doAst &&
+            !Array.isArray(symbols.astNodes) &&
+            (WALK_EXTENSIONS.has(ext) || AST_TYPE_MAPS.has(langId))) {
+            debug(`allNativeDataComplete: ${relPath} missing astNodes`);
+            return false;
+        }
+        // Dataflow: native must have produced it
+        if (doDataflow &&
+            !symbols.dataflow &&
+            (DATAFLOW_EXTENSIONS.has(ext) || DATAFLOW_RULES.has(langId))) {
+            debug(`allNativeDataComplete: ${relPath} missing dataflow`);
+            return false;
+        }
+        const defs = symbols.definitions || [];
+        for (const def of defs) {
+            if (!hasFuncBody(def))
+                continue;
+            // Complexity: every function must already have it
+            if (doComplexity &&
+                !def.complexity &&
+                (COMPLEXITY_EXTENSIONS.has(ext) || COMPLEXITY_RULES.has(langId))) {
+                debug(`allNativeDataComplete: ${relPath}:${def.name} missing complexity`);
+                return false;
+            }
+            // CFG: every function must already have blocks
+            if (doCfg &&
+                def.cfg !== null &&
+                !Array.isArray(def.cfg?.blocks) &&
+                (CFG_EXTENSIONS.has(ext) || CFG_RULES.has(langId))) {
+                debug(`allNativeDataComplete: ${relPath}:${def.name} missing cfg blocks`);
+                return false;
+            }
+        }
+    }
+    return fileSymbols.size > 0;
+}
 // ─── Public API ──────────────────────────────────────────────────────────
 export async function runAnalyses(db, fileSymbols, rootDir, opts, engineOpts) {
     const timing = { astMs: 0, complexityMs: 0, cfgMs: 0, dataflowMs: 0 };
@@ -491,6 +545,16 @@ export async function runAnalyses(db, fileSymbols, rootDir, opts, engineOpts) {
     if (!doAst && !doComplexity && !doCfg && !doDataflow)
         return timing;
     const extToLang = buildExtToLangMap();
+    // Fast path: when all files were parsed by the native engine with full analysis
+    // (parseFilesFull), all data is already present — skip WASM re-parse and JS
+    // visitor walks entirely, go straight to DB persistence.
+    if (allNativeDataComplete(fileSymbols, opts)) {
+        debug('native full-analysis fast path: all data present, skipping WASM/visitor passes');
+        if (doComplexity && doCfg)
+            reconcileCfgCyclomatic(fileSymbols);
+        await delegateToBuildFunctions(db, fileSymbols, rootDir, opts, engineOpts, timing);
+        return timing;
+    }
     // Native analysis pass: try Rust standalone functions before WASM fallback.
     // This fills in complexity/CFG/dataflow for files that the native parse pipeline
     // missed, avoiding the need to parse with WASM + run JS visitors.

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package/dist/domain/analysis/diff-impact.d.ts

@@ -12,6 +12,18 @@ export declare function diffImpactData(customDbPath: string, opts?: {
     offset?: number;
     config?: any;
 }): ({
+    changedFiles: number;
+    newFiles: string[];
+    affectedFunctions: unknown[];
+    affectedFiles: string[];
+    historicallyCoupled: unknown[];
+    ownership: null;
+    boundaryViolations: import("../../features/boundaries.js").BoundaryViolation[];
+    boundaryViolationCount: number;
+    summary: null;
+} & {
+    _pagination?: import("../../shared/paginate.js").PaginationMeta;
+}) | ({
     changedFiles: number;
     newFiles: string[];
     affectedFunctions: {

package/dist/domain/analysis/diff-impact.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"diff-impact.d.ts","sourceRoot":"","sources":["../../../src/domain/analysis/diff-impact.ts"],"names":[],"mappings":"AA6PA;;;GAGG;AACH,wBAAgB,cAAc,CAC5B,YAAY,EAAE,MAAM,EACpB,IAAI,GAAE;IACJ,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,GAAG,CAAC;CACT;;;;;;;;;;;;;;;;;;;kBAhIuB,MAAM;gBAAM,MAAM;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqNhD"}
+{"version":3,"file":"diff-impact.d.ts","sourceRoot":"","sources":["../../../src/domain/analysis/diff-impact.ts"],"names":[],"mappings":"AA6PA;;;GAGG;AACH,wBAAgB,cAAc,CAC5B,YAAY,EAAE,MAAM,EACpB,IAAI,GAAE;IACJ,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,GAAG,CAAC;CACT;;;uBAyDyB,OAAO,EAAE;mBACb,MAAM,EAAE;yBACF,OAAO,EAAE;;;;aAInB,IAAI;;;;;;;;;;;;;;;;;;;;;;kBA/LE,MAAM;gBAAM,MAAM;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgPhD"}

package/dist/domain/analysis/diff-impact.js

@@ -247,6 +247,25 @@ export function diffImpactData(customDbPath, opts = {}) {
             };
         }
         const affectedFunctions = findAffectedFunctions(db, changedRanges, noTests);
+        // Short-circuit: when no function-level changes detected, skip expensive
+        // lookups (BFS, co-change, ownership).  Boundary checks are preserved
+        // because they are file-scoped and can surface real violations even when
+        // no function bodies were touched (e.g. import or type-alias changes).
+        if (affectedFunctions.length === 0) {
+            const { boundaryViolations, boundaryViolationCount } = checkBoundaryViolations(db, changedRanges, noTests, { ...opts, config }, repoRoot);
+            const base = {
+                changedFiles: changedRanges.size,
+                newFiles: [...newFiles],
+                affectedFunctions: [],
+                affectedFiles: [],
+                historicallyCoupled: [],
+                ownership: null,
+                boundaryViolations,
+                boundaryViolationCount,
+                summary: null,
+            };
+            return paginateResult(base, 'affectedFunctions', { limit: opts.limit, offset: opts.offset });
+        }
         const includeImplementors = opts.includeImplementors !== false;
         const { functionResults, allAffected } = buildFunctionImpactResults(db, affectedFunctions, noTests, maxDepth, includeImplementors);
         const affectedFiles = new Set();
@@ -254,7 +273,7 @@ export function diffImpactData(customDbPath, opts = {}) {
             affectedFiles.add(key.split(':')[0]);
         const historicallyCoupled = lookupCoChanges(db, changedRanges, affectedFiles, noTests);
         const ownership = lookupOwnership(changedRanges, affectedFiles, repoRoot);
-        const { boundaryViolations, boundaryViolationCount } = checkBoundaryViolations(db, changedRanges, noTests, opts, repoRoot);
+        const { boundaryViolations, boundaryViolationCount } = checkBoundaryViolations(db, changedRanges, noTests, { ...opts, config }, repoRoot);
         const base = {
             changedFiles: changedRanges.size,
             newFiles: [...newFiles],

package/dist/domain/analysis/diff-impact.js.map

@@ -1 +1 @@
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package/dist/domain/graph/builder/native-db-proxy.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"native-db-proxy.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/native-db-proxy.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,qBAAqB,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAQhG,qBAAa,aAAc,YAAW,qBAAqB;;IAEzD,4EAA4E;IAC5E,UAAU,CAAC,EAAE,MAAM,CAAC;gBAER,QAAQ,EAAE,cAAc;IAIpC,OAAO,CAAC,IAAI,GAAG,OAAO,EAAE,GAAG,EAAE,MAAM,GAAG,eAAe,CAAC,IAAI,CAAC;IA0B3D,IAAI,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI;IAKvB,MAAM,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO;IAI5B,KAAK,IAAI,IAAI;IAKb,IAAI,IAAI,IAAI,OAAO,CAElB;IAED,IAAI,IAAI,IAAI,MAAM,CAEjB;IAED,WAAW,CAAC,CAAC,SAAS,CAAC,GAAG,IAAI,EAAE,GAAG,EAAE,KAAK,GAAG,EAC3C,EAAE,EAAE,CAAC,GACJ,CAAC,GAAG,IAAI,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,MAAM,CAAC,KAAK,OAAO,GAAG,CAAC,GAAG,KAAK,KAAK,UAAU,CAAC,CAAC,CAAC;CAoBhF"}
+{"version":3,"file":"native-db-proxy.d.ts","sourceRoot":"","sources":["../../../../src/domain/graph/builder/native-db-proxy.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,qBAAqB,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAQhG,qBAAa,aAAc,YAAW,qBAAqB;;IAEzD,4EAA4E;IAC5E,UAAU,CAAC,EAAE,MAAM,CAAC;gBAER,QAAQ,EAAE,cAAc;IAIpC,OAAO,CAAC,IAAI,GAAG,OAAO,EAAE,GAAG,EAAE,MAAM,GAAG,eAAe,CAAC,IAAI,CAAC;IAgC3D,IAAI,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI;IAKvB,MAAM,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO;IAI5B,KAAK,IAAI,IAAI;IAKb,IAAI,IAAI,IAAI,OAAO,CAElB;IAED,IAAI,IAAI,IAAI,MAAM,CAEjB;IAED,WAAW,CAAC,CAAC,SAAS,CAAC,GAAG,IAAI,EAAE,GAAG,EAAE,KAAK,GAAG,EAC3C,EAAE,EAAE,CAAC,GACJ,CAAC,GAAG,IAAI,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,MAAM,CAAC,KAAK,OAAO,GAAG,CAAC,GAAG,KAAK,KAAK,UAAU,CAAC,CAAC,CAAC;CAoBhF"}

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

@@ -21,6 +21,9 @@ export class NativeDbProxy {
     }
     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));
@@ -30,10 +33,11 @@ export class NativeDbProxy {
             },
             run(...params) {
                 ndb.queryAll(sql, sanitize(params));
-                // Retrieve last_insert_rowid via SQLite scalar function so callers
-                // that depend on it (e.g. CFG block edge mapping) get correct values.
-                const row = ndb.queryGet('SELECT last_insert_rowid() AS rid', []);
-                return { changes: 0, lastInsertRowid: row?.rid ?? 0 };
+                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');

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

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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"}