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>

CHANGELOG.md

@@ -40,6 +40,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Fixes
 
+- CodeGraph respects your `.gitignore` again when looking for nested git repositories. A directory you've gitignored — a `resource/` or `.repos/` folder of cloned reference projects, a large vendored data dir — is no longer walked into and indexed: version 1.0.0 started searching inside *every* gitignored directory for embedded git repos and pulling them all in, which could multiply a graph many times over and slow indexing to a crawl on a multi-gigabyte folder of clones, even though you'd explicitly excluded it. Indexing the repos inside a gitignored directory is now opt-in — add an `includeIgnored` list to a `codegraph.json` at your repo root, e.g. `{ "includeIgnored": ["packages/", "services/"] }`, to index the embedded repos under the directories you name. The "super-repo of independent clones" layout from 1.0.0 still works, just declared explicitly. Nested repos you *haven't* gitignored (untracked clones) are indexed as before, and a project without this layout is unaffected. (#970, #976, #622)
 - `codegraph index` and `codegraph init` no longer crawl during the "Resolving refs" phase on large projects — most painfully ones that mix a big front-end and back-end, where the phase could stretch to many minutes. A package or module imported across hundreds or thousands of files (`react`, a shared UI package, Python `logging` / `typing`) was being treated as if every one of those import statements might be its definition, so the resolver compared each import against all the others — work that grows with the *square* of how widely a package is imported, which is why it blew up only on big, import-heavy repos. Imports now resolve straight to the definitions they actually point at, so those redundant comparisons are gone (reference resolution is dramatically faster on large repos), and the graph no longer accumulates the meaningless import-to-import links the old fallback created. (#915)
 - MCP tool results no longer show up as oversized headings in Markdown-rendering clients (such as the Claude Code VSCode extension). Results used Markdown headings (`##`/`###`) for things like the status summary, each search hit, and every file section in an exploration, so a normal query filled the transcript with large-font lines — worst with `codegraph_search` and `codegraph_explore`, where the noise grew with the number of results. Section headers are now bold labels, which render at normal text size while keeping the same structure. Terminal/CLI output is unchanged. (#778)
 - An MCP server pointed at a very large repository (tens of thousands of files) no longer hangs on the first tool call after a fresh start. On startup CodeGraph reconciles its index against the current files on disk, and on a huge repo that reconcile could run for minutes while blocking the very first request — long enough that the background server was sometimes force-restarted mid-scan, so the first query never came back at all. The reconcile now yields as it runs (keeping the server responsive instead of pinning it), and the first tool call waits only briefly for it before answering and letting the rest finish in the background — so you get a fast first response and the index still catches up. Set `CODEGRAPH_CATCHUP_GATE_TIMEOUT_MS` to tune how long that first call waits (default 3000ms), or `=0` to always wait for the full reconcile. (#905)