From ee949262995fcbff01128d87b4cdb69b2beb6ce1 Mon Sep 17 00:00:00 2001
From: Seungjae Jay Lee <mixxer@me.com>
Date: Fri, 30 Oct 2026 13:12:02 -0400
Subject: [PATCH] fix(status): detect changes to included gitignored source

---
 CHANGELOG.md                                  |  1 +
 .../included-ignored-source-status.test.ts    | 52 +++++++++++++++++++
 src/extraction/index.ts                       |  7 +++
 3 files changed, 60 insertions(+)
 create mode 100644 __tests__/included-ignored-source-status.test.ts

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 32df517fb..a2e5ccfcf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Fixes
 
+- `codegraph status` now reports added, changed and deleted source files explicitly included despite Git ignoring them, including edits that preserve file size and modification time, instead of incorrectly reporting no pending changes.
 - In TypeScript, an awaited call with type arguments like `await fetchApi<User>("/me")` or `await api.get<T>(url)` now links to the function it calls. Before, the call was dropped, so typed fetch wrappers looked like they had no callers. (#2586)
 - In JavaScript and TypeScript, a call or `new` in a parameter's default value, like `function renderWithNote(note = buildNote())`, a destructured `{ size = defaultSize() }` or `constructor(private svc = new Service())`, now counts as the function's own call. Before, it was dropped, so `buildNote` was missing that caller and impact on it came back incomplete. Re-index JavaScript and TypeScript projects after upgrading. Thanks @inth3shadows for the report and the pull request. (#2588)
 - In React, a component rendered at module scope, in a top-level constant or inside a test's `it(…)` callback, like `createRoot(el).render(<App />)` or `render(<Card />)`, now counts as rendered there, so an app's entry reaches its root component and a component's tests show among its callers. (#2587)
diff --git a/__tests__/included-ignored-source-status.test.ts b/__tests__/included-ignored-source-status.test.ts
new file mode 100644
index 000000000..e4dade6e7
--- /dev/null
+++ b/__tests__/included-ignored-source-status.test.ts
@@ -0,0 +1,52 @@
+import { afterEach, beforeEach, describe, expect, it } from 'vitest';
+import * as fs from 'node:fs';
+import * as os from 'node:os';
+import * as path from 'node:path';
+import { execFileSync } from 'node:child_process';
+import { CodeGraph } from '../src';
+
+describe('Explicitly included gitignored source status', () => {
+  let dir: string;
+  let cg: CodeGraph | undefined;
+  const write = (rel: string, source: string) => {
+    const file = path.join(dir, rel);
+    fs.mkdirSync(path.dirname(file), { recursive: true });
+    fs.writeFileSync(file, source);
+  };
+  beforeEach(() => {
+    dir = fs.mkdtempSync(path.join(os.tmpdir(), 'cg-included-status-'));
+  });
+  afterEach(() => {
+    cg?.destroy();
+    cg = undefined;
+    fs.rmSync(dir, { recursive: true, force: true });
+  });
+
+  it('reports included additions, edits with preserved metadata, and deletions', async () => {
+    write('local/Device.java', 'package p; public class Device { public void run() {} }');
+    write('local/excluded/Noise.java', 'public class Noise {}');
+    write('.gitignore', 'local/\n');
+    write('codegraph.json', JSON.stringify({ include: ['local/'], exclude: ['local/excluded/'] }));
+    execFileSync('git', ['init', '-q'], { cwd: dir });
+    execFileSync('git', ['add', '-A'], { cwd: dir });
+    execFileSync('git', ['-c', 'user.name=t', '-c', 'user.email=a@b.c', 'commit', '-qm', 'base'], { cwd: dir });
+    cg = await CodeGraph.init(dir, { index: true });
+    expect(cg.getNodesByName('Device')).toHaveLength(1);
+    expect(cg.getNodesByName('Noise')).toHaveLength(0);
+    expect(cg.getChangedFiles()).toEqual({ added: [], modified: [], removed: [] });
+
+    const file = path.join(dir, 'local/Device.java');
+    const originalStat = fs.statSync(file);
+    // Git never reports this ignored file, and metadata cannot prove it unchanged.
+    write('local/Device.java', 'package p; public class Device { public void end() {} }');
+    fs.utimesSync(file, originalStat.atime, originalStat.mtime);
+    expect(fs.statSync(file).size).toBe(originalStat.size);
+    expect(cg.getChangedFiles().modified).toEqual(['local/Device.java']);
+
+    write('local/New.java', 'package p; public class New {}');
+    write('local/excluded/NewNoise.java', 'public class NewNoise {}');
+    expect(cg.getChangedFiles().added).toEqual(['local/New.java']);
+    fs.rmSync(file);
+    expect(cg.getChangedFiles().removed).toEqual(['local/Device.java']);
+  });
+});
diff --git a/src/extraction/index.ts b/src/extraction/index.ts
index 55f927c15..e9bed435a 100644
--- a/src/extraction/index.ts
+++ b/src/extraction/index.ts
@@ -4137,6 +4137,13 @@ export class ExtractionOrchestrator {
       // have been recreated locally; a previously indexed dirty path may have
       // vanished from git status after restore. Classify current disk vs DB once.
       const candidates = new Set([...gitChanges.deleted, ...gitChanges.modified, ...gitChanges.added, ...dirtyPaths!]);
+      const include = loadIncludeMatcher(this.rootDir);
+      if (include) {
+        for (const file of collectIncludedFilesForRoot(this.rootDir)) candidates.add(file);
+        for (const file of this.queries.getAllFiles()) {
+          if (include.ignores(file.path)) candidates.add(file.path);
+        }
+      }
       const scope = this.scopedSyncMatcher();
       const overrides = loadExtensionOverrides(this.rootDir);
       for (const filePath of candidates) {