diff --git a/src/domain/graph/builder/helpers.ts b/src/domain/graph/builder/helpers.ts
index 15451b76..3d1be287 100644
--- a/src/domain/graph/builder/helpers.ts
+++ b/src/domain/graph/builder/helpers.ts
@@ -132,8 +132,7 @@ export function loadPathAliases(rootDir: string): PathAliases {
     try {
       const raw = fs
         .readFileSync(configPath, 'utf-8')
-        .replace(/\/\/.*$/gm, '')
-        .replace(/\/\*[\s\S]*?\*\//g, '')
+        .replace(/("(?:[^"\\]|\\.)*")|\/\*[\s\S]*?\*\/|\/\/.*$/gm, (_, str) => str ?? '')
         .replace(/,\s*([\]}])/g, '$1');
       const config = JSON.parse(raw) as {
         compilerOptions?: { baseUrl?: string; paths?: Record<string, string[]> };
diff --git a/src/domain/graph/builder/pipeline.ts b/src/domain/graph/builder/pipeline.ts
index 7418163b..47f54ffc 100644
--- a/src/domain/graph/builder/pipeline.ts
+++ b/src/domain/graph/builder/pipeline.ts
@@ -9,6 +9,7 @@ import { performance } from 'node:perf_hooks';
 import { closeDb, getBuildMeta, initSchema, MIGRATIONS, openDb } from '../../../db/index.js';
 import { detectWorkspaces, loadConfig } from '../../../infrastructure/config.js';
 import { info, warn } from '../../../infrastructure/logger.js';
+import { CODEGRAPH_VERSION } from '../../../shared/version.js';
 import type { BuildGraphOpts, BuildResult } from '../../../types.js';
 import { getActiveEngine } from '../../parser.js';
 import { setWorkspaces } from '../resolve.js';
@@ -57,6 +58,13 @@ function checkEngineSchemaMismatch(ctx: PipelineContext): void {
     );
     ctx.forceFullRebuild = true;
   }
+  const prevVersion = getBuildMeta(ctx.db, 'codegraph_version');
+  if (prevVersion && prevVersion !== CODEGRAPH_VERSION) {
+    info(
+      `Codegraph version changed (${prevVersion} → ${CODEGRAPH_VERSION}), promoting to full rebuild.`,
+    );
+    ctx.forceFullRebuild = true;
+  }
 }
 
 function loadAliases(ctx: PipelineContext): void {
diff --git a/src/domain/graph/builder/stages/finalize.ts b/src/domain/graph/builder/stages/finalize.ts
index f90b8b0a..3badf394 100644
--- a/src/domain/graph/builder/stages/finalize.ts
+++ b/src/domain/graph/builder/stages/finalize.ts
@@ -3,21 +3,14 @@
  *
  * WASM cleanup, stats logging, drift detection, build metadata, registry, journal.
  */
-import fs from 'node:fs';
 import path from 'node:path';
 import { performance } from 'node:perf_hooks';
 import { closeDb, getBuildMeta, setBuildMeta } from '../../../../db/index.js';
 import { debug, info, warn } from '../../../../infrastructure/logger.js';
+import { CODEGRAPH_VERSION } from '../../../../shared/version.js';
 import { writeJournalHeader } from '../../journal.js';
 import type { PipelineContext } from '../context.js';
 
-const __builderDir = path.dirname(new URL(import.meta.url).pathname.replace(/^\/([A-Z]:)/i, '$1'));
-const CODEGRAPH_VERSION = (
-  JSON.parse(
-    fs.readFileSync(path.join(__builderDir, '..', '..', '..', '..', '..', 'package.json'), 'utf-8'),
-  ) as { version: string }
-).version;
-
 export async function finalize(ctx: PipelineContext): Promise<void> {
   const { db, allSymbols, rootDir, isFullBuild, hasEmbeddings, config, opts, schemaVersion } = ctx;
 
diff --git a/src/shared/version.ts b/src/shared/version.ts
new file mode 100644
index 00000000..fe6f0a69
--- /dev/null
+++ b/src/shared/version.ts
@@ -0,0 +1,10 @@
+import fs from 'node:fs';
+import path from 'node:path';
+
+const __sharedDir = path.dirname(new URL(import.meta.url).pathname.replace(/^\/([A-Z]:)/i, '$1'));
+
+export const CODEGRAPH_VERSION: string = (
+  JSON.parse(fs.readFileSync(path.join(__sharedDir, '..', '..', 'package.json'), 'utf-8')) as {
+    version: string;
+  }
+).version;
diff --git a/tests/unit/builder.test.ts b/tests/unit/builder.test.ts
index 2d15c664..a7140e2a 100644
--- a/tests/unit/builder.test.ts
+++ b/tests/unit/builder.test.ts
@@ -200,6 +200,28 @@ describe('loadPathAliases', () => {
     fs.rmSync(dir, { recursive: true, force: true });
   });
 
+  it('preserves // inside string values (e.g. $schema URLs)', () => {
+    const dir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-jsonc-url-'));
+    fs.writeFileSync(
+      path.join(dir, 'tsconfig.json'),
+      `{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  // A comment
+  "compilerOptions": {
+    /* Language & Environment */
+    "baseUrl": "./src",
+    "paths": {
+      "@/*": ["*"]
+    }
+  }
+}`,
+    );
+    const aliases = loadPathAliases(dir);
+    expect(aliases.baseUrl).toContain('src');
+    expect(aliases.paths['@/*']).toBeDefined();
+    fs.rmSync(dir, { recursive: true, force: true });
+  });
+
   it('prefers tsconfig.json over jsconfig.json', () => {
     const dir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-both-'));
     fs.writeFileSync(