Revert "fix(resolution): filter stale-target edges so watch sync survives FK violations (#455) (#463)"

This reverts commit 1dfaf30a8ba66a9d72b8b67c04b4eeb0866ec674.

Switching to #462's approach — a single, lower-layer filter inside
QueryBuilder.insertEdges itself instead of three filters spread across
the resolution layer. The DB-layer filter protects every caller (current
and future) automatically and doesn't depend on the queries-layer
nodeCache invalidation staying perfect. See #455 for the bug.

The CHANGELOG entry for the user-facing fix is re-added on top of #462.

CHANGELOG.md

@@ -10,7 +10,6 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ## [Unreleased]
 
 ### Fixed
-- **Watch sync no longer aborts with `FOREIGN KEY constraint failed`.** PR #62 plugged this FK violation at the extraction-layer `insertEdges` site (empty-named nodes whose containment edges had no target), but the same violation kept reappearing on v0.9.5 during the daemon's *watch sync* — not on initial index — once an agent's daemon had been running long enough to accumulate edits. The resolution-layer `insertEdges` (and the callback-synthesizer pass) wasn't guarded the same way: a per-resolver name cache or a framework resolver's WeakMap-keyed lookup map could hand back a `Node` whose row had been removed by a recent file rewrite, and the FK check then aborted the entire resolution batch, leaving the user's daemon log filling with `Watch sync failed { error: 'FOREIGN KEY constraint failed' }`. The resolution layer now applies the same defense-in-depth filter the extraction layer already had — one cache-aware `getNodesByIds` per pass drops any edge whose source or target is no longer in the `nodes` table, so the rest of the resolved batch still lands. Surfaces as a fresh `codegraph init`/`index` cycle now surviving its first watch-sync cycle without the FK error, and the daemon recovering naturally instead of compounding into further failures. Closes #455.
 - **Hermes Agent: `codegraph install --target hermes` no longer corrupts `~/.hermes/config.yaml`.** Hermes serializes its config with PyYAML's default block style, which writes list items at the *same* indent as the parent mapping key (`cli:` and `- hermes-cli` both at column 2). The previous line-based YAML patcher mistook that first `  - hermes-cli` for the next sibling key, truncated the `cli:` block, and then spliced `- mcp-codegraph` at indent 4 *before* the existing items — leaving subsequent entries (`- browser`, `- clarify`, …) and even other platforms (`telegram:`, `discord:`) appearing at the `platform_toolsets:` level, which is no longer parseable YAML. The installer now recognizes the same-indent list style, finds the real end of the block at the next sibling key, and appends `- mcp-codegraph` at whatever indent the existing items already use. Re-installing on an already-corrupted file (or a 4-space-nested config that worked before) still produces a clean, parseable result. Closes #456.
 - **NestJS: `RouterModule.register([...])` route prefixes now propagate to controller routes.** Previously a controller declared inside a module wired through NestJS's `RouterModule` (a common pattern for modular apps with nested route prefixes) was indexed with its raw `@Controller(...) + @Get(...)` path — so `UsersController` under `RouterModule.register([{ path: 'admin', module: AdminModule, children: [{ path: 'users', module: UsersModule }] }])` showed up as `GET /` instead of `GET /admin/users`. The new cross-file pass walks every `*.module.{ts,js}` for `RouterModule.register/forRoot/forChild([...])` (recursive `children`) and `@Module({ controllers: [...] })`, then prepends the correct prefix to each affected route — including non-empty `@Controller` paths and method-level params (`/admin/users/:id`). The route node's `id` is preserved across the update so existing route→handler edges stay intact, and the pass is idempotent so incremental sync recovers when `app.module.ts` itself is edited. Closes #459.
 

__tests__/sync-fk-regression.test.ts

@@ -1,232 +0,0 @@
-/**
- * Sync FK regression test (issue #455).
- *
- * #62 plugged FK violations at the extraction layer (empty-named nodes whose
- * containment edges had no target). #455 reports the same `FOREIGN KEY constraint
- * failed` reappearing on v0.9.5, but during *watch sync* on a Python-only project —
- * a different trigger than the C/C++ header empty-name issue #62 covered.
- *
- * The reproducer below drives the same path the daemon takes: extract → resolve →
- * insert edges. The resolution pass's `insertEdges` was not guarded the way the
- * extraction-layer insert was after #62, so any edge with a stale source/target
- * (e.g. a synthesized framework target whose node was deleted by a concurrent
- * file rewrite) throws and aborts the sync, leaving the FK error the user sees.
- *
- * The test asserts: a sequence of file rewrites + sync()s never throws, and the
- * graph stays internally consistent (every edge's source + target are real nodes).
- */
-import { describe, it, expect, beforeAll, afterEach } from 'vitest';
-import * as fs from 'fs';
-import * as path from 'path';
-import * as os from 'os';
-import CodeGraph from '../src/index';
-import { initGrammars, loadAllGrammars } from '../src/extraction/grammars';
-
-beforeAll(async () => {
-  await initGrammars();
-  await loadAllGrammars();
-});
-
-describe('watch sync FK regression (#455)', () => {
-  let tmpDir: string | undefined;
-  let cg: CodeGraph | undefined;
-
-  afterEach(() => {
-    if (cg) {
-      cg.close();
-      cg = undefined;
-    }
-    if (tmpDir) {
-      fs.rmSync(tmpDir, { recursive: true, force: true });
-      tmpDir = undefined;
-    }
-  });
-
-  function assertGraphIntegrity(cg: CodeGraph): void {
-    // Every edge must reference real nodes. If FK was disabled or violated,
-    // dangling refs would show up here.
-    const db = (cg as unknown as { db: { getDb(): { prepare(sql: string): { get(): unknown } } } }).db;
-    const sqlite = db.getDb();
-    const dangling = sqlite
-      .prepare(
-        `SELECT count(*) as c FROM edges e
-         WHERE NOT EXISTS (SELECT 1 FROM nodes n WHERE n.id = e.source)
-            OR NOT EXISTS (SELECT 1 FROM nodes n WHERE n.id = e.target)`
-      )
-      .get() as { c: number };
-    expect(dangling.c).toBe(0);
-  }
-
-  it('survives repeated sync() cycles on a Django-style Python project without FK errors', async () => {
-    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'cg-fk455-'));
-
-    // Mimic a small Django app: requirements + manage.py marker, models/views/urls
-    // in two app packages that cross-reference each other.
-    fs.writeFileSync(path.join(tmpDir, 'manage.py'), '# django marker\n');
-    fs.writeFileSync(path.join(tmpDir, 'requirements.txt'), 'django==4.2\n');
-
-    fs.mkdirSync(path.join(tmpDir, 'users'));
-    fs.writeFileSync(path.join(tmpDir, 'users/__init__.py'), '');
-    fs.writeFileSync(
-      path.join(tmpDir, 'users/models.py'),
-      'class User:\n' +
-        '    def __init__(self, name):\n' +
-        '        self.name = name\n'
-    );
-    fs.writeFileSync(
-      path.join(tmpDir, 'users/views.py'),
-      'from users.models import User\n' +
-        'class UserListView:\n' +
-        '    def get(self, request):\n' +
-        '        return User("a")\n'
-    );
-    fs.writeFileSync(
-      path.join(tmpDir, 'users/urls.py'),
-      'from django.urls import path\n' +
-        'from users.views import UserListView\n' +
-        'urlpatterns = [path("users/", UserListView.as_view(), name="user-list")]\n'
-    );
-
-    fs.mkdirSync(path.join(tmpDir, 'posts'));
-    fs.writeFileSync(path.join(tmpDir, 'posts/__init__.py'), '');
-    fs.writeFileSync(
-      path.join(tmpDir, 'posts/models.py'),
-      'from users.models import User\n' +
-        'class Post:\n' +
-        '    def __init__(self, author):\n' +
-        '        self.author = author\n'
-    );
-    fs.writeFileSync(
-      path.join(tmpDir, 'posts/views.py'),
-      'from posts.models import Post\n' +
-        'class PostListView:\n' +
-        '    def get(self, request):\n' +
-        '        return Post(None)\n'
-    );
-    fs.writeFileSync(
-      path.join(tmpDir, 'posts/urls.py'),
-      'from django.urls import path\n' +
-        'from posts.views import PostListView\n' +
-        'urlpatterns = [path("posts/", PostListView.as_view(), name="post-list")]\n'
-    );
-
-    cg = CodeGraph.initSync(tmpDir);
-    await cg.indexAll();
-    assertGraphIntegrity(cg);
-
-    // Drive the same path the daemon's file watcher drives: a series of file
-    // rewrites + sync()s. We shuffle line counts on each rewrite so node IDs
-    // (file:kind:name:line) shift around, forcing real INSERT OR REPLACE +
-    // CASCADE behavior across files that cross-reference each other.
-    const targets = [
-      'users/views.py',
-      'posts/views.py',
-      'users/urls.py',
-      'posts/urls.py',
-      'users/models.py',
-    ];
-
-    for (let iter = 0; iter < 8; iter++) {
-      const file = targets[iter % targets.length]!;
-      const full = path.join(tmpDir, file);
-      const content = fs.readFileSync(full, 'utf8');
-      // Insert N blank lines at the top to shift every node's line number.
-      const padded = '\n'.repeat(iter + 1) + content;
-      // Use a future mtime so the size+mtime pre-filter in
-      // ExtractionOrchestrator.sync can't skip the file.
-      fs.writeFileSync(full, padded);
-      const now = Date.now() + (iter + 1) * 1_000;
-      fs.utimesSync(full, now / 1000, now / 1000);
-
-      // The fix should make this never throw; before the fix, FK errors fire
-      // during the resolution-layer insertEdges call inside sync().
-      await expect(cg.sync()).resolves.toBeDefined();
-      assertGraphIntegrity(cg);
-    }
-  });
-
-  it("drops resolution edges whose target node is no longer in the graph (the pathology #455 reports)", async () => {
-    // This narrower test reproduces the exact failure mode the user sees in
-    // their daemon log: the resolver hands `insertEdges` an edge whose target
-    // doesn't exist in `nodes`, and the FK constraint aborts the whole sync.
-    //
-    // We force the bug by populating the resolver's per-name cache with a
-    // stale node (whose id is *not* in the DB) and then asking it to resolve
-    // a reference to that name. Without the fix this throws
-    // `FOREIGN KEY constraint failed`; with it, the bad edge is filtered out
-    // and resolution returns normally.
-    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'cg-fk455-stale-'));
-    fs.writeFileSync(path.join(tmpDir, 'a.py'), 'def caller():\n    Target()\n');
-    fs.writeFileSync(path.join(tmpDir, 'b.py'), 'class Target:\n    pass\n');
-
-    cg = CodeGraph.initSync(tmpDir);
-    await cg.indexAll();
-
-    // Reach in to the internals — the simplest way to forge the "stale node
-    // ID in the resolver's lookup path" condition the production bug arises
-    // from. The fix is what the test is verifying; touching internals here
-    // is a means to that end, not a contract we're asserting.
-    type Internals = {
-      queries: {
-        getNodesByName(name: string): Array<{ id: string; name: string }>;
-        getAllNodeNames(): string[];
-      };
-      resolver: {
-        warmCaches(): void;
-        resolveAndPersist(
-          refs: Array<{
-            fromNodeId: string;
-            referenceName: string;
-            referenceKind: string;
-            line: number;
-            column: number;
-            filePath: string;
-            language: string;
-          }>
-        ): { resolved: unknown[] };
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        nameCache: { set(key: string, value: any): void };
-      };
-    };
-    const internals = cg as unknown as Internals;
-    const queries = internals.queries;
-    const resolver = internals.resolver;
-
-    const caller = queries.getNodesByName('caller')[0];
-    const target = queries.getNodesByName('Target')[0];
-    expect(caller).toBeDefined();
-    expect(target).toBeDefined();
-
-    // Warm caches so warmCaches no-ops on the resolveAndPersist call below
-    // and our seeded nameCache entry isn't overwritten.
-    resolver.warmCaches();
-
-    // Forge a stale lookup result: a Node whose `id` doesn't exist in the
-    // `nodes` table. This is structurally what happens when a framework
-    // resolver's WeakMap cache hands back a Node that was deleted by a
-    // concurrent file rewrite — the user's #455 scenario.
-    const staleNode = { ...target!, id: 'class:stale.py:Target:1' };
-    resolver.nameCache.set('Target', [staleNode]);
-
-    // Ask the resolver to persist an edge that will resolve via the seeded
-    // (stale) cache entry. Without the FK filter this would throw
-    // `FOREIGN KEY constraint failed` and abort the whole batch.
-    expect(() =>
-      resolver.resolveAndPersist([
-        {
-          fromNodeId: caller!.id,
-          referenceName: 'Target',
-          referenceKind: 'calls',
-          line: 2,
-          column: 4,
-          filePath: 'a.py',
-          language: 'python',
-        },
-      ])
-    ).not.toThrow();
-
-    // The bad edge must not have been persisted either — FK enforcement is
-    // still on, and post-fix the dangling-edge count remains zero.
-    assertGraphIntegrity(cg);
-  });
-});

src/resolution/callback-synthesizer.ts

@@ -812,19 +812,6 @@ export function synthesizeCallbackEdges(queries: QueryBuilder, ctx: ResolutionCo
     seen.add(key);
     merged.push(e);
   }
-  if (merged.length > 0) {
-    // Defense-in-depth (issues #42, #455): drop edges whose source/target
-    // no longer resolves to a real node. Some channel maps cache native
-    // Node refs across a resolver lifetime (WeakMap-keyed by context), so
-    // a file rewrite between map build and synthesis can leave stale IDs
-    // here. One FK violation aborts the whole batch — better to skip the
-    // dead edges and emit the rest than lose every synthesized edge.
-    const allIds = new Set<string>();
-    for (const e of merged) { allIds.add(e.source); allIds.add(e.target); }
-    const existing = queries.getNodesByIds([...allIds]);
-    const validEdges = merged.filter((e) => existing.has(e.source) && existing.has(e.target));
-    if (validEdges.length > 0) queries.insertEdges(validEdges);
-    return validEdges.length;
-  }
-  return 0;
+  if (merged.length > 0) queries.insertEdges(merged);
+  return merged.length;
 }

src/resolution/index.ts

@@ -607,28 +607,6 @@ export class ReferenceResolver {
     });
   }
 
-  /**
-   * Defense-in-depth: drop edges whose source or target is no longer in
-   * the nodes table. PR #62 (issue #42) applied this filter at the
-   * extraction-layer `insertEdges` site; #455 reports the same
-   * `FOREIGN KEY constraint failed` reappearing here at the
-   * resolution-layer site during watch sync, where a resolver lookup that
-   * crosses a framework-specific cache can hand us a target whose node
-   * was removed by a concurrent file rewrite. One batched, cache-aware
-   * `getNodesByIds` query is enough to skip those edges quietly instead
-   * of aborting the whole sync.
-   */
-  private filterEdgesByExistingNodes(edges: Edge[]): Edge[] {
-    if (edges.length === 0) return edges;
-    const allIds = new Set<string>();
-    for (const e of edges) {
-      allIds.add(e.source);
-      allIds.add(e.target);
-    }
-    const existing = this.queries.getNodesByIds([...allIds]);
-    return edges.filter((e) => existing.has(e.source) && existing.has(e.target));
-  }
-
   /**
    * Resolve and persist edges to database
    */
@@ -642,9 +620,8 @@ export class ReferenceResolver {
     const edges = this.createEdges(result.resolved);
 
     // Insert edges into database
-    const validEdges = this.filterEdgesByExistingNodes(edges);
-    if (validEdges.length > 0) {
-      this.queries.insertEdges(validEdges);
+    if (edges.length > 0) {
+      this.queries.insertEdges(edges);
     }
 
     // Clean up resolved refs from unresolved_refs table so metrics are accurate
@@ -691,9 +668,8 @@ export class ReferenceResolver {
 
       // Persist edges immediately
       const edges = this.createEdges(result.resolved);
-      const validEdges = this.filterEdgesByExistingNodes(edges);
-      if (validEdges.length > 0) {
-        this.queries.insertEdges(validEdges);
+      if (edges.length > 0) {
+        this.queries.insertEdges(edges);
       }
 
       // Clean up resolved refs so they don't appear in the next batch