fix(extraction): respect .gitignore by default for embedded-repo discovery (#970, #976) (#980)

#514 (v1.0.0) began walking into gitignored directories to discover and
index the git repos nested inside them. That broke users who rely on
.gitignore to exclude a directory: a gitignored folder of cloned
reference repos blew graphs up (one report went 10k to 500k edges, #976)
and stalled indexing on multi-gigabyte trees of clones (#970).

Respect .gitignore by default again. Discovering embedded repos inside a
gitignored directory is now opt-in via codegraph.json:

    { "includeIgnored": ["packages/", "services/"] }

The single choke point findIgnoredEmbeddedRepos now returns nothing
unless a gitignored dir matches the project's includeIgnored patterns,
and the matcher is threaded from the scan root through the full-index,
incremental-sync, and watcher-scope paths. Downstream ScopeIgnore and the
watcher are unchanged: they key off the discovered embedded roots, so
gating discovery fixes the indexer, sync, and watcher together. Untracked
embedded repos (#193) stay indexed by default.

This restores the super-repo-of-clones behavior (#622, #699) for the
people who want it, while making the default match what every other tool
(and CodeGraph's own git ls-files foundation) does: .gitignore excludes.

project-config.ts now parses codegraph.json once (loadParsedConfig) and
exposes loadIncludeIgnoredPatterns alongside the existing extension map.

Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

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

@@ -1,9 +1,9 @@
 ---
 title: Configuration
-description: CodeGraph is zero-config by default, with one optional file for mapping custom extensions.
+description: CodeGraph is zero-config by default, with one optional codegraph.json for custom extensions 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 is for mapping [custom file extensions](#custom-file-extensions).
+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) and [indexing nested git repositories](#indexing-nested-git-repositories).
 
 ## What it skips out of the box
 
@@ -34,6 +34,28 @@ Each value is a supported language id. The mappings merge on top of the built-in
 
 A typo'd language or a malformed file is warned about and skipped — it never breaks indexing — and a project with no `codegraph.json` behaves exactly as before. Re-index (`codegraph index`) after adding or changing mappings.
 
+## Indexing nested git repositories
+
+CodeGraph respects your `.gitignore`, so a directory you've gitignored stays out of the graph — **including any git repositories nested inside it.** If you keep cloned reference projects, vendored copies, or a folder of unrelated repos in a gitignored directory (a `resource/`, `.repos/`, or `examples/` dir), CodeGraph leaves it untouched: it won't walk in, discover the embedded repos, or index them.
+
+If instead you run a **"super-repo" of independent clones** — a workspace whose own `.gitignore` lists its child repos to keep `git status` quiet, where you genuinely want every child indexed into one graph — opt those directories back in with `includeIgnored`:
+
+```json
+{
+  "includeIgnored": ["packages/", "services/"]
+}
+```
+
+Each entry is a gitignore-style pattern naming a gitignored directory whose nested git repositories should be indexed anyway. CodeGraph descends into the directories you list and indexes each embedded repo by its own `git ls-files`, so every child repo's own `.gitignore` is still honored. Directories you don't list stay excluded.
+
+A few things to know:
+
+- **Untracked** nested repositories (ones you haven't gitignored) are indexed automatically — `includeIgnored` is only for the ones your `.gitignore` excludes.
+- Built-in skips like `node_modules` are never re-included, even inside an opted-in directory.
+- A project without this layout needs no `codegraph.json` at all.
+
+Re-index (`codegraph index`) after adding or changing `includeIgnored`.
+
 ## Where data lives
 
 Per-project data lives in a `.codegraph/` directory at your project root, containing the SQLite database (`codegraph.db`). Nothing leaves your machine.