feat(config): codegraph.json include to force gitignored first-party source into the index (#1063)

Adds an `include` list to the root `codegraph.json` that forces gitignored first-party source (second-VCS / SVN / Perforce dual-tracked repos) into the index — discovered directly off disk on the full index, incremental sync, and file-watching, on both git and non-git projects. Gitignore-style patterns, root-relative; explicit `exclude` still wins and built-in skips (node_modules, dist, .git) are never re-included. Complements `exclude` and `includeIgnored`.

Closes #1163.

Thanks @luoyxy for the contribution.

CHANGELOG.md

@@ -32,6 +32,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 - Anonymous usage telemetry now counts how often the context hook injected context, offered a hint, or stayed silent — fixed counter names only; the prompt's content is never stored or sent. This makes the hook's accuracy measurable instead of guessed. The counters record what actually happened, not what was attempted: a lookup that errors or comes back empty counts as a distinct silent outcome, never as delivered context (#1143, thanks @inth3shadows).
 - Metal shader files (`.metal`) are now indexed. Metal Shading Language is close enough to C++ that vertex/fragment/kernel functions, structs, type aliases, and the calls between them all land in the graph — so shader pipelines in Apple-platform projects show up in impact analysis and flow traces instead of being silently skipped. Metal's `[[buffer(0)]]`-style attribute annotations are handled so they can't corrupt what gets extracted. Thanks @FluxKo for the report. (#1121)
 - CodeGraph now indexes legacy **iBatis 2** SQL maps (`<sqlMap>`), not just MyBatis 3 `<mapper>` files. `<select>`/`<insert>`/`<update>`/`<delete>`, iBatis's `<statement>`/`<procedure>`, and `<sql>` fragments inside a `<sqlMap>` become searchable statement symbols — for both namespaced maps and the namespace-less `Map.statement` id style — and `<include>` references resolve to the fragment they pull in, so search, callers, and impact queries return results on iBatis codebases that previously produced no statement symbols at all. Thanks @ESPINS for the report and the reproduction. (#1182)
+- You can now force gitignored first-party source **into** the index with an `include` list in `codegraph.json`. The case this solves: a project tracked by a second VCS (SVN, Perforce, …) alongside Git, where some real source is committed to that VCS and deliberately listed in `.gitignore` so it never lands in Git — git never lists those files, so CodeGraph never indexed them, and neither `includeIgnored` (which only revives *embedded git repositories* inside a gitignored directory) nor `exclude` (its opposite) could help. Add a root `codegraph.json` with, e.g., `{ "include": ["Tools/", "Local/typescript/"] }` and CodeGraph discovers those files directly off disk — overriding `.gitignore` — and indexes them on the full index, incremental `sync`, and file-watching, on both git and non-git projects. Patterns are gitignore-style and matched against project-root-relative paths (a directory, a recursive `**` glob, or a single file). An explicit `exclude` still wins, and built-in skips like `node_modules`, `dist`, and `.git` are never re-included. This complements the existing `exclude` (its opposite — keep tracked files *out*) and `includeIgnored` (opt *in* to gitignored embedded repos).
 
 ### Fixes
 

README.md

@@ -686,6 +686,21 @@ watch:
 }
 ```
 
+Conversely, when real source is gitignored on purpose — a project under a second
+VCS (SVN, Perforce) that `.gitignore`s its own source so it stays out of Git —
+force it back in with `include` (the opposite of `exclude`; `includeIgnored`
+only revives embedded git repos, not plain source):
+
+```json
+{
+  "include": ["Tools/", "Local/typescript/"]
+}
+```
+
+CodeGraph discovers those files off disk, overriding `.gitignore`, on index,
+sync, and watch. An explicit `exclude` still wins, and built-in skips
+(`node_modules`, `dist`, `.git`) are never re-included.
+
 ### Custom file extensions
 
 If your project uses a non-standard extension for a [supported

__tests__/include-config.test.ts

@@ -0,0 +1,262 @@
+/**
+ * `codegraph.json` `include` — force first-party source INTO the index even when
+ * `.gitignore` would drop it.
+ *
+ * The whitelist `includeIgnored` never was: that one only revives *embedded git
+ * repos* inside ignored dirs (#622/#699), so pure source gitignored out of Git
+ * (the SVN+Git dual-VCS case — committed to SVN, `.gitignore`d so it never lands
+ * in Git) had no way in. Three layers under test:
+ *   1. Loader: parse/validate/cache, mirroring the `exclude` loader.
+ *   2. Behavior: `scanDirectory` adds included paths on BOTH the git
+ *      (`git ls-files`) and non-git (filesystem walk) enumeration paths.
+ *   3. Scope: `buildScopeIgnore` (the watcher's source of truth) treats an
+ *      included file — and the gitignored dirs leading to it — as not-ignored.
+ *
+ * Invariants: an explicit `exclude` still wins; built-in default-ignored dirs
+ * (`node_modules`, …) are never resurfaced; every loader failure mode degrades
+ * to the zero-config default (force nothing in), never a throw.
+ */
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import * as fs from 'node:fs';
+import * as path from 'node:path';
+import * as os from 'node:os';
+import { execFileSync } from 'node:child_process';
+import {
+  loadIncludePatterns,
+  loadExcludePatterns,
+  loadExtensionOverrides,
+  loadIncludeIgnoredPatterns,
+  clearProjectConfigCache,
+} from '../src/project-config';
+import { scanDirectory, buildScopeIgnore } from '../src/extraction';
+
+describe('include loader (codegraph.json)', () => {
+  let dir: string;
+  beforeEach(() => {
+    dir = fs.mkdtempSync(path.join(os.tmpdir(), 'cg-include-'));
+    clearProjectConfigCache();
+  });
+  afterEach(() => {
+    clearProjectConfigCache();
+    fs.rmSync(dir, { recursive: true, force: true });
+  });
+  const writeConfig = (obj: unknown) =>
+    fs.writeFileSync(
+      path.join(dir, 'codegraph.json'),
+      typeof obj === 'string' ? obj : JSON.stringify(obj)
+    );
+
+  it('returns an empty list when there is no codegraph.json (the default)', () => {
+    expect(loadIncludePatterns(dir)).toEqual([]);
+  });
+
+  it('loads a well-formed pattern array', () => {
+    writeConfig({ include: ['Tools/', 'Local/**'] });
+    expect(loadIncludePatterns(dir)).toEqual(['Tools/', 'Local/**']);
+  });
+
+  it('trims whitespace and drops blank / non-string entries', () => {
+    writeConfig({ include: ['  Tools/  ', '', '   ', 42, null, 'Local/'] });
+    expect(loadIncludePatterns(dir)).toEqual(['Tools/', 'Local/']);
+  });
+
+  it('ignores a non-array include value without throwing', () => {
+    writeConfig({ include: 'Tools/' });
+    expect(loadIncludePatterns(dir)).toEqual([]);
+  });
+
+  it('ignores malformed JSON without throwing', () => {
+    writeConfig('{ not: valid json ');
+    expect(loadIncludePatterns(dir)).toEqual([]);
+  });
+
+  it('coexists with extensions / includeIgnored / exclude in one file (shared single parse)', () => {
+    writeConfig({
+      extensions: { '.foo': 'typescript' },
+      includeIgnored: ['pkgs/'],
+      exclude: ['static/'],
+      include: ['Tools/'],
+    });
+    expect(loadExtensionOverrides(dir)).toEqual({ '.foo': 'typescript' });
+    expect(loadIncludeIgnoredPatterns(dir)).toEqual(['pkgs/']);
+    expect(loadExcludePatterns(dir)).toEqual(['static/']);
+    expect(loadIncludePatterns(dir)).toEqual(['Tools/']);
+  });
+
+  it('picks up a changed config (mtime-invalidated cache)', () => {
+    writeConfig({ include: ['Tools/'] });
+    expect(loadIncludePatterns(dir)).toEqual(['Tools/']);
+
+    writeConfig({ include: ['Local/'] });
+    const future = new Date(Date.now() + 2000);
+    fs.utimesSync(path.join(dir, 'codegraph.json'), future, future);
+
+    expect(loadIncludePatterns(dir)).toEqual(['Local/']);
+  });
+
+  it('drops the patterns again when the config file is removed', () => {
+    writeConfig({ include: ['Tools/'] });
+    expect(loadIncludePatterns(dir)).toEqual(['Tools/']);
+    fs.rmSync(path.join(dir, 'codegraph.json'));
+    expect(loadIncludePatterns(dir)).toEqual([]);
+  });
+});
+
+describe('include behavior — scanDirectory force-indexes gitignored source', () => {
+  let dir: string;
+  const mk = (rel: string, content = 'export const x = 1;\n') => {
+    const p = path.join(dir, rel);
+    fs.mkdirSync(path.dirname(p), { recursive: true });
+    fs.writeFileSync(p, content);
+  };
+  const writeConfig = (obj: unknown) =>
+    fs.writeFileSync(path.join(dir, 'codegraph.json'), JSON.stringify(obj));
+  const scan = () => scanDirectory(dir).map((f) => f.replace(/\\/g, '/'));
+
+  beforeEach(() => {
+    dir = fs.mkdtempSync(path.join(os.tmpdir(), 'cg-include-scan-'));
+    clearProjectConfigCache();
+  });
+  afterEach(() => {
+    clearProjectConfigCache();
+    fs.rmSync(dir, { recursive: true, force: true });
+  });
+
+  const gitInit = () => {
+    execFileSync('git', ['init', '-q'], { cwd: dir });
+    execFileSync('git', ['add', '-A'], { cwd: dir });
+    execFileSync('git', ['-c', 'user.email=a@b.c', '-c', 'user.name=t', 'commit', '-qm', 'x'], { cwd: dir });
+  };
+
+  it('indexes a .gitignored source dir when include opts it in (git path) — the core fix', () => {
+    mk('app/main.ts');
+    mk('Tools/gen.py', 'def gen():\n    return 1\n');
+    fs.writeFileSync(path.join(dir, '.gitignore'), 'Tools/\n'); // SVN-only source, kept out of Git
+    gitInit(); // Tools/ is gitignored → NOT tracked
+
+    // Sanity: without include the gitignored source is invisible.
+    let files = scan();
+    expect(files).toContain('app/main.ts');
+    expect(files.some((f) => f.startsWith('Tools/'))).toBe(false);
+
+    // With include the gitignored source is forced in, app code still there.
+    writeConfig({ include: ['Tools/'] });
+    clearProjectConfigCache();
+    files = scan();
+    expect(files).toContain('app/main.ts');
+    expect(files).toContain('Tools/gen.py');
+  });
+
+  it('forces gitignored source in on the non-git filesystem-walk path too', () => {
+    mk('app/main.ts');
+    mk('Tools/gen.py', 'def gen():\n    return 1\n');
+    fs.writeFileSync(path.join(dir, '.gitignore'), 'Tools/\n');
+    // No git init → scanDirectory falls back to the filesystem walk (which still
+    // honours .gitignore), so Tools/ must be re-added by include.
+    writeConfig({ include: ['Tools/'] });
+    clearProjectConfigCache();
+    const files = scan();
+    expect(files).toContain('app/main.ts');
+    expect(files).toContain('Tools/gen.py');
+  });
+
+  it('supports a recursive ** glob and nested dirs', () => {
+    mk('src/a.ts');
+    mk('Local/ts/a.ts');
+    mk('Local/ts/nested/b.ts');
+    fs.writeFileSync(path.join(dir, '.gitignore'), 'Local/\n');
+    gitInit();
+    writeConfig({ include: ['Local/**'] });
+    clearProjectConfigCache();
+    const files = scan();
+    expect(files).toContain('Local/ts/a.ts');
+    expect(files).toContain('Local/ts/nested/b.ts');
+  });
+
+  it('lets an explicit exclude win over include', () => {
+    mk('Tools/keep.py', 'def k():\n    return 1\n');
+    mk('Tools/secret/drop.py', 'def d():\n    return 1\n');
+    fs.writeFileSync(path.join(dir, '.gitignore'), 'Tools/\n');
+    gitInit();
+    writeConfig({ include: ['Tools/'], exclude: ['Tools/secret/'] });
+    clearProjectConfigCache();
+    const files = scan();
+    expect(files).toContain('Tools/keep.py');
+    expect(files.some((f) => f.startsWith('Tools/secret/'))).toBe(false);
+  });
+
+  it('prunes an explicitly-excluded subtree under an included dir (a frontend own deps stay out)', () => {
+    // The real-world case: an SVN-committed frontend is force-included, but its
+    // own vendored deps live in a NON-default-named dir (`third_party/`) the
+    // built-in ignore list does not cover, so it is excluded explicitly. The
+    // whole subtree - nested files and all - must stay out, while sibling source
+    // stays in.
+    mk('Local/frontend/src/app.ts');
+    mk('Local/frontend/src/util.ts');
+    mk('Local/frontend/third_party/lib/a.ts');
+    mk('Local/frontend/third_party/lib/nested/b.ts');
+    fs.writeFileSync(path.join(dir, '.gitignore'), 'Local/\n');
+    gitInit();
+    writeConfig({ include: ['Local/frontend/'], exclude: ['Local/frontend/third_party/'] });
+    clearProjectConfigCache();
+    const files = scan();
+    expect(files).toContain('Local/frontend/src/app.ts');
+    expect(files).toContain('Local/frontend/src/util.ts');
+    expect(files.some((f) => f.startsWith('Local/frontend/third_party/'))).toBe(false);
+  });
+
+  it('never resurrects a built-in default-ignored dir (node_modules) via include', () => {
+    mk('src/a.ts');
+    mk('node_modules/pkg/index.js');
+    gitInit();
+    // Even explicitly opting node_modules in must not pull it into the graph.
+    writeConfig({ include: ['node_modules/'] });
+    clearProjectConfigCache();
+    const files = scan();
+    expect(files).toContain('src/a.ts');
+    expect(files.some((f) => f.startsWith('node_modules/'))).toBe(false);
+  });
+
+  it('is a no-op with no include config (gitignored source stays out)', () => {
+    mk('app/main.ts');
+    mk('Tools/gen.py', 'def gen():\n    return 1\n');
+    fs.writeFileSync(path.join(dir, '.gitignore'), 'Tools/\n');
+    gitInit();
+    const files = scan();
+    expect(files).toContain('app/main.ts');
+    expect(files.some((f) => f.startsWith('Tools/'))).toBe(false);
+  });
+});
+
+describe('include scope — buildScopeIgnore keeps included paths watchable', () => {
+  let dir: string;
+  beforeEach(() => {
+    dir = fs.mkdtempSync(path.join(os.tmpdir(), 'cg-include-scope-'));
+    clearProjectConfigCache();
+    execFileSync('git', ['init', '-q'], { cwd: dir });
+    fs.writeFileSync(path.join(dir, '.gitignore'), 'Tools/\nOther/\n');
+    fs.writeFileSync(path.join(dir, 'codegraph.json'), JSON.stringify({ include: ['Tools/'] }));
+  });
+  afterEach(() => {
+    clearProjectConfigCache();
+    fs.rmSync(dir, { recursive: true, force: true });
+  });
+
+  it('does not ignore an included file, nor the gitignored dir leading to it', () => {
+    const scope = buildScopeIgnore(dir);
+    // The included file and its (gitignored) directory are watchable.
+    expect(scope.ignores('Tools/gen.py')).toBe(false);
+    expect(scope.ignores('Tools/')).toBe(false);
+    // A different gitignored dir that was NOT opted in stays ignored.
+    expect(scope.ignores('Other/')).toBe(true);
+    expect(scope.ignores('Other/x.py')).toBe(true);
+  });
+
+  it('still ignores everything when no include is configured', () => {
+    fs.writeFileSync(path.join(dir, 'codegraph.json'), JSON.stringify({}));
+    clearProjectConfigCache();
+    const scope = buildScopeIgnore(dir);
+    expect(scope.ignores('Tools/gen.py')).toBe(true);
+    expect(scope.ignores('Tools/')).toBe(true);
+  });
+});

site/src/content/docs/getting-started/configuration.md

@@ -1,9 +1,9 @@
 ---
 title: Configuration
-description: CodeGraph is zero-config by default, with one optional codegraph.json for custom extensions, excluding tracked directories, and indexing nested git repositories.
+description: CodeGraph is zero-config by default, with one optional codegraph.json for custom extensions, excluding tracked directories, indexing gitignored source, and indexing nested git repositories.
 ---
 
-Next to none — CodeGraph is **zero-config by default**, with nothing to write or keep in sync to get started. Language support is automatic from the file extension; there's nothing to wire up per language. The one optional file, `codegraph.json`, covers [custom file extensions](#custom-file-extensions), [excluding tracked directories](#excluding-a-tracked-directory), and [indexing nested git repositories](#indexing-nested-git-repositories).
+Next to none — CodeGraph is **zero-config by default**, with nothing to write or keep in sync to get started. Language support is automatic from the file extension; there's nothing to wire up per language. The one optional file, `codegraph.json`, covers [custom file extensions](#custom-file-extensions), [excluding tracked directories](#excluding-a-tracked-directory), [indexing gitignored source](#indexing-gitignored-source-a-second-vcs), and [indexing nested git repositories](#indexing-nested-git-repositories).
 
 ## What it skips out of the box
 
@@ -31,6 +31,28 @@ Each entry is a gitignore-style pattern, matched against project-root-relative p
 
 Re-index (`codegraph index`) after adding or changing `exclude`.
 
+## Indexing gitignored source (a second VCS)
+
+`.gitignore` keeps files out of the index — which is usually what you want, but not when the gitignored files are real first-party source. The case this exists for: a project tracked by **SVN, Perforce, or another VCS alongside Git**, where some source is committed to that VCS and deliberately listed in `.gitignore` so it never lands in Git. That source is still yours and you want it in the graph, but git never lists it, so CodeGraph never sees it. (`includeIgnored` doesn't help — it only revives *embedded git repositories* inside a gitignored directory, not plain source.)
+
+List those paths under `include` in `codegraph.json` to force them in:
+
+```json
+{
+  "include": ["Tools/", "Local/typescript/"]
+}
+```
+
+Each entry is a gitignore-style pattern, matched against project-root-relative paths (a directory like `"Tools/"`, a recursive `"Tools/**"` glob, or a single file all work). CodeGraph discovers the matching files directly off disk — overriding `.gitignore` — and indexes them everywhere it looks at files: the full index, incremental `sync`, and file-watching.
+
+A few things to know:
+
+- An explicit [`exclude`](#excluding-a-tracked-directory) still wins — listing the same path in both keeps it out.
+- Built-in skips like `node_modules`, `dist`, and `.git` are never re-included, even when an `include` pattern would match inside them.
+- This is the opposite of `exclude` (which keeps tracked files *out*); it's for source git itself never tracks.
+
+Re-index (`codegraph index`) after adding or changing `include`.
+
 ## Custom file extensions
 
 If your project uses a non-standard extension for a [supported language](/codegraph/reference/languages/) — say `.dota_lua` for Lua, or `.tpl` for PHP — those files are skipped by default, because the extension isn't one CodeGraph recognizes. Map them with an optional `codegraph.json` at your project root:

src/extraction/index.ts

@@ -21,7 +21,7 @@ import { QueryBuilder } from '../db/queries';
 import { extractFromSource } from './tree-sitter';
 import { ParseWorkerPool, resolveParsePoolSize } from './parse-pool';
 import { detectLanguage, isSourceFile, isLanguageSupported, isFileLevelOnlyLanguage, initGrammars, loadGrammarsForLanguages } from './grammars';
-import { loadExtensionOverrides, loadIncludeIgnoredPatterns, loadExcludePatterns } from '../project-config';
+import { loadExtensionOverrides, loadIncludeIgnoredPatterns, loadExcludePatterns, loadIncludePatterns } from '../project-config';
 import { isCodeGraphDataDir } from '../directory';
 import { logDebug, logWarn } from '../errors';
 import { validatePathWithinRoot, normalizePath } from '../utils';
@@ -330,6 +330,158 @@ function loadExcludeMatcher(rootDir: string): Ignore | null {
   return patterns.length > 0 ? ignore().add(patterns) : null;
 }
 
+/**
+ * Matcher for the project's `codegraph.json` `include` patterns — first-party
+ * source to force INTO the index even when `.gitignore` drops it (the general
+ * whitelist `includeIgnored` never was — that one only revives *embedded git
+ * repos*). The case it exists for: a project under a second VCS (SVN/Perforce)
+ * `.gitignore`s its own real source so it stays out of Git, yet we still want it
+ * indexed. Returns `null` when nothing is force-included (the zero-config
+ * default → no overhead, no extra walk). Built once per scan/sync/scope
+ * operation from the scan root.
+ */
+function loadIncludeMatcher(rootDir: string): Ignore | null {
+  const patterns = loadIncludePatterns(rootDir);
+  return patterns.length > 0 ? ignore().add(patterns) : null;
+}
+
+/** Glob metacharacters that end the static (literal) prefix of an `include` pattern. */
+const GLOB_META = /[*?[\]{}!]/;
+
+/**
+ * The static directory prefix of each `include` pattern — the literal leading
+ * path up to the first glob segment — trailing-slashed, used to (a) walk only
+ * the opted-in subtrees in `collectIncludedFiles` and (b) let `ScopeIgnore` keep
+ * the watcher descending toward them. `Tools/` stays `Tools/`; a recursive
+ * `Tools/**` glob yields `Tools/`; `src/local/file.ts` yields `src/local/` (the
+ * file's dir); a pattern that starts with a glob (like a leading `**`) yields
+ * `''`, meaning "no static root — walk the whole tree". Duplicates and roots
+ * nested under a broader root are collapsed so each subtree is walked once.
+ */
+function includeStaticRoots(patterns: string[]): string[] {
+  const roots = new Set<string>();
+  for (const pattern of patterns) {
+    let p = pattern.replace(/^\/+/, '');
+    const trailingSlash = p.endsWith('/');
+    if (trailingSlash) p = p.slice(0, -1);
+    const segs = p.split('/').filter(Boolean);
+    const lead: string[] = [];
+    for (const s of segs) {
+      if (GLOB_META.test(s)) break;
+      lead.push(s);
+    }
+    const hadWildcard = lead.length < segs.length;
+    // A wholly-literal pattern with no trailing slash names a file (or a dir we
+    // can't tell apart) — drop its last segment so we walk the containing dir
+    // and let the matcher pick the file. A trailing slash or a glob means the
+    // remaining `lead` is already the directory to walk.
+    if (!hadWildcard && !trailingSlash && lead.length > 0) lead.pop();
+    if (lead.length === 0) {
+      roots.clear();
+      roots.add('');
+      return ['']; // a top-level glob forces a whole-tree walk; nothing narrower matters
+    }
+    roots.add(lead.join('/') + '/');
+  }
+  // Collapse roots nested under a broader one (e.g. drop `a/b/` if `a/` is present).
+  const all = [...roots];
+  return all.filter((r) => !all.some((other) => other !== r && r.startsWith(other)));
+}
+
+/**
+ * Actively discover the source files an `include` whitelist forces in. `git
+ * ls-files` never lists gitignored files, so a filtered filesystem walk of just
+ * the opted-in subtrees (`includeStaticRoots`) is the only way to find them.
+ * Returns project-root-relative, normalized source-file paths.
+ *
+ * A file is collected when it MATCHES `include`, is NOT hit by `exclude` (an
+ * explicit exclude always wins), is a recognized source file, and does not live
+ * under a built-in default-ignored dir (`node_modules`, `dist`, …), `.git`, or
+ * CodeGraph's data dir — those are never resurfaced, mirroring `ScopeIgnore`.
+ * `.gitignore` is deliberately NOT consulted: overriding it is the whole point.
+ */
+function collectIncludedFiles(
+  rootDir: string,
+  include: Ignore,
+  exclude: Ignore | null,
+  roots: string[],
+  overrides: Record<string, Language>,
+): Set<string> {
+  const out = new Set<string>();
+  const defaults = defaultsOnlyIgnore();
+  const visited = new Set<string>();
+
+  const consider = (abs: string, rel: string, isDir: boolean): void => {
+    if (isDir) {
+      if (defaults.ignores(rel + '/')) return; // never node_modules/dist/… via include
+      // An explicit `exclude` always wins over `include`; prune the whole subtree
+      // here so a large excluded dir (a committed frontend's own vendored deps,
+      // build output, …) is never walked — the per-file guard below still catches
+      // anything a directory pattern doesn't, so this is a pure efficiency win.
+      if (exclude && exclude.ignores(rel + '/')) return;
+      walk(abs);
+    } else {
+      if (defaults.ignores(rel)) return;
+      if (!include.ignores(rel)) return;
+      if (exclude && exclude.ignores(rel)) return;
+      if (!isSourceFile(rel, overrides)) return;
+      out.add(rel);
+    }
+  };
+
+  function walk(absDir: string): void {
+    let realDir: string;
+    try {
+      realDir = fs.realpathSync(absDir);
+    } catch {
+      return;
+    }
+    if (visited.has(realDir)) return; // symlink-cycle guard
+    visited.add(realDir);
+
+    let entries: fs.Dirent[];
+    try {
+      entries = fs.readdirSync(absDir, { withFileTypes: true });
+    } catch {
+      return;
+    }
+    for (const entry of entries) {
+      if (entry.name === '.git' || isCodeGraphDataDir(entry.name)) continue;
+      const abs = path.join(absDir, entry.name);
+      const rel = normalizePath(path.relative(rootDir, abs));
+      if (!rel || rel.startsWith('..')) continue;
+      if (entry.isSymbolicLink()) {
+        try {
+          const st = fs.statSync(fs.realpathSync(abs));
+          consider(abs, rel, st.isDirectory());
+        } catch {
+          // broken symlink — skip
+        }
+        continue;
+      }
+      consider(abs, rel, entry.isDirectory());
+    }
+  }
+
+  for (const root of roots) {
+    walk(root === '' ? rootDir : path.join(rootDir, root));
+  }
+  return out;
+}
+
+/**
+ * The included source files (`codegraph.json` `include`) for a scan root, or an
+ * empty set when nothing is force-included. Centralizes loading the matcher,
+ * roots, exclude, and overrides so both enumeration paths (git and filesystem
+ * walk) add the same files.
+ */
+function collectIncludedFilesForRoot(rootDir: string): Set<string> {
+  const include = loadIncludeMatcher(rootDir);
+  if (!include) return new Set();
+  const roots = includeStaticRoots(loadIncludePatterns(rootDir));
+  return collectIncludedFiles(rootDir, include, loadExcludeMatcher(rootDir), roots, loadExtensionOverrides(rootDir));
+}
+
 /**
  * `git ls-files --directory` collapses a wholly-untracked/ignored directory into
  * one entry — and when the command's own cwd is such a directory (the indexed
@@ -477,6 +629,17 @@ export class ScopeIgnore {
      * exclude applies even to tracked files and even inside embedded repos.
      */
     private exclude: Ignore | null = null,
+    /**
+     * Project `codegraph.json` `include` patterns — first-party source forced
+     * INTO the index despite `.gitignore`. When a path matches, it is NOT
+     * ignored (so the watcher watches it), overriding `.gitignore`/`rootMatcher`
+     * — but never `exclude` (checked first) and never a built-in default-ignored
+     * dir. `includeRoots` are the static prefixes so a gitignored ANCESTOR
+     * directory of an included subtree still isn't pruned by the directory
+     * walker/watcher.
+     */
+    private include: Ignore | null = null,
+    private includeRoots: string[] = [],
   ) {
     // Longest root first so paths in nested embedded repos hit the innermost matcher.
     this.embedded = [...embedded].sort((a, b) => b.root.length - a.root.length);
@@ -487,6 +650,18 @@ export class ScopeIgnore {
     // path: it must drop git-TRACKED paths (which `.gitignore` can't) and apply
     // everywhere, including ancestors of embedded repos.
     if (this.exclude && this.exclude.ignores(rel)) return true;
+    // User `include`: force first-party source in despite `.gitignore`. Never
+    // resurfaces a built-in default-ignored dir (node_modules/dist/…), so an
+    // include pattern can't accidentally pull in dependency/build trees.
+    if (this.include && !this.defaults.ignores(rel)) {
+      if (rel.endsWith('/')) {
+        // A directory on (or leading to) an included subtree must stay walkable
+        // so the watcher/walker descends to reach the forced-in files.
+        if (this.includeRoots.some((r) => r.startsWith(rel) || rel.startsWith(r))) return false;
+      } else if (this.include.ignores(rel)) {
+        return false;
+      }
+    }
     for (const { root, matcher } of this.embedded) {
       if (rel.startsWith(root)) {
         const inner = rel.slice(root.length);
@@ -512,10 +687,13 @@ export class ScopeIgnore {
  */
 export function buildScopeIgnore(rootDir: string, embeddedRoots?: Iterable<string>): ScopeIgnore {
   const roots = embeddedRoots ? [...embeddedRoots] : discoverEmbeddedRepoRoots(rootDir);
+  const include = loadIncludeMatcher(rootDir);
   return new ScopeIgnore(
     buildDefaultIgnore(rootDir),
     roots.map((root) => ({ root, matcher: buildDefaultIgnore(path.join(rootDir, root)) })),
     loadExcludeMatcher(rootDir),
+    include,
+    include ? includeStaticRoots(loadIncludePatterns(rootDir)) : [],
   );
 }
 
@@ -807,7 +985,14 @@ function getGitVisibleFiles(rootDir: string): Set<string> | null {
     // not the parent's: the parent's .gitignore hides the child repo from git,
     // not from the index. (#514)
     const ig = buildScopeIgnore(rootDir, embeddedRoots);
-    return new Set([...files].filter((f) => !ig.ignores(f)));
+    const visible = new Set([...files].filter((f) => !ig.ignores(f)));
+    // Force-include first-party source the project whitelisted in
+    // `codegraph.json` `include`. These are gitignored, so `git ls-files` never
+    // listed them above — discover them directly off disk and add them. (The
+    // common SVN+Git dual-VCS case: source committed to SVN, gitignored out of
+    // Git, but still wanted in the graph.)
+    for (const f of collectIncludedFilesForRoot(rootDir)) visible.add(f);
+    return visible;
   } catch {
     return null;
   }
@@ -1114,6 +1299,20 @@ function scanDirectoryWalk(
   const exclude = loadExcludeMatcher(rootDir);
   if (exclude) baseMatchers.push({ dir: rootDir, ig: exclude });
   walk(rootDir, baseMatchers);
+
+  // Force-include first-party source whitelisted in `codegraph.json` `include`
+  // — the walk above honours `.gitignore`, so anything gitignored was dropped;
+  // add it back here (deduped). Mirrors the git path's union.
+  const included = collectIncludedFilesForRoot(rootDir);
+  if (included.size > 0) {
+    const seen = new Set(files);
+    for (const f of included) {
+      if (!seen.has(f)) {
+        files.push(f);
+        seen.add(f);
+      }
+    }
+  }
   return files;
 }
 

src/project-config.ts

@@ -53,6 +53,20 @@ export interface ProjectConfig {
    * and your `.gitignore`.
    */
   exclude?: string[];
+  /**
+   * Gitignore-style patterns for first-party source to force INTO the index even
+   * when `.gitignore` would drop it — the general whitelist `includeIgnored`
+   * never was (that one only revives *embedded git repos* inside ignored dirs).
+   * The case this exists for: a project under a second VCS (SVN, Perforce, …)
+   * deliberately `.gitignore`s its own real source so it never lands in Git, yet
+   * that source must still be indexed. Matched against project-root-relative
+   * paths, so `"Tools/"`, a recursive `"Tools/**"` glob, or `"Local/typescript"`
+   * all work.
+   * Built-in default-ignored dirs (`node_modules`, `dist`, …), `.git`, and
+   * CodeGraph's own data dir are never resurfaced; an explicit `exclude` still
+   * wins. Absent/empty (the default) forces nothing in.
+   */
+  include?: string[];
 }
 
 /** Parsed, validated view of a project's `codegraph.json`. */
@@ -60,6 +74,7 @@ interface ParsedConfig {
   extensions: Record<string, Language>;
   includeIgnored: string[];
   exclude: string[];
+  include: string[];
 }
 
 interface CacheEntry {
@@ -81,6 +96,7 @@ const EMPTY_CONFIG: ParsedConfig = Object.freeze({
   extensions: EMPTY_EXTENSIONS,
   includeIgnored: Object.freeze([]) as unknown as string[],
   exclude: Object.freeze([]) as unknown as string[],
+  include: Object.freeze([]) as unknown as string[],
 });
 
 /**
@@ -132,10 +148,16 @@ function parseConfig(file: string): ParsedConfig {
   const extensions = extractExtensions(parsed, file);
   const includeIgnored = extractIncludeIgnored(parsed, file);
   const exclude = extractExclude(parsed, file);
-  if (extensions === EMPTY_EXTENSIONS && includeIgnored.length === 0 && exclude.length === 0) {
+  const include = extractInclude(parsed, file);
+  if (
+    extensions === EMPTY_EXTENSIONS &&
+    includeIgnored.length === 0 &&
+    exclude.length === 0 &&
+    include.length === 0
+  ) {
     return EMPTY_CONFIG;
   }
-  return { extensions, includeIgnored, exclude };
+  return { extensions, includeIgnored, exclude, include };
 }
 
 /**
@@ -214,6 +236,34 @@ function extractExclude(parsed: object, file: string): string[] {
   return out;
 }
 
+/**
+ * Validate the `include` patterns: an array of non-empty gitignore-style strings
+ * naming first-party source to force INTO the index despite `.gitignore` — the
+ * whitelist for SVN/Perforce-only source a project gitignores out of Git (the
+ * general case `includeIgnored` never covered). A non-array value or a
+ * non-string/blank entry warns-and-skips; never throws. Patterns are kept
+ * verbatim (trimmed) so they match exactly as a `.gitignore` line would, against
+ * project-root-relative paths.
+ */
+function extractInclude(parsed: object, file: string): string[] {
+  const raw = (parsed as ProjectConfig).include;
+  if (raw === undefined) return [];
+  if (!Array.isArray(raw)) {
+    logWarn(`Ignoring "include" in ${PROJECT_CONFIG_FILENAME}: must be an array of gitignore-style patterns`, { file });
+    return [];
+  }
+
+  const out: string[] = [];
+  for (const entry of raw) {
+    if (typeof entry !== 'string' || !entry.trim()) {
+      logWarn(`Ignoring an "include" entry in ${PROJECT_CONFIG_FILENAME}: every pattern must be a non-empty string`, { file });
+      continue;
+    }
+    out.push(entry.trim());
+  }
+  return out;
+}
+
 /**
  * Load the parsed `codegraph.json` for a project, mtime-cached. A missing or
  * malformed file yields the zero-config default. One `stat` (and at most one
@@ -275,6 +325,19 @@ export function loadExcludePatterns(rootDir: string): string[] {
   return loadParsedConfig(rootDir).exclude;
 }
 
+/**
+ * Load the validated `include` patterns for a project, mtime-cached.
+ *
+ * These name first-party source to force INTO the index even when `.gitignore`
+ * would drop it — the whitelist for SVN/Perforce-only source a project
+ * gitignores out of Git. An empty result — the zero-config default — forces
+ * nothing in. Built-in default-ignored dirs, `.git`, and CodeGraph's data dir
+ * are never resurfaced, and an explicit `exclude` still wins.
+ */
+export function loadIncludePatterns(rootDir: string): string[] {
+  return loadParsedConfig(rootDir).include;
+}
+
 /** Test/maintenance hook: forget cached config (e.g. after rewriting it in a test). */
 export function clearProjectConfigCache(): void {
   cache.clear();