A Git super-repo whose `.gitignore` excludes its child repositories indexed
~nothing at the parent: CodeGraph respects `.gitignore` by default (#970,
#1065), so the excluded children were skipped and `codegraph init` printed
"Done" with 0 nodes — even though `init` inside each child worked fine. The
empty index was silent and unexplained.
`init`/`index` now detect the gitignored child repos they skipped when an
index comes up empty of symbols, name them, and — in an interactive terminal
— offer to index them (writing an `includeIgnored` entry to codegraph.json and
re-indexing on the spot); non-interactive runs print the exact codegraph.json
snippet to add. Gated on nodesCreated === 0, so a project that deliberately
keeps gitignored reference clones out of a working index is never nagged.
- extraction: findUnindexedIgnoredRepos — the inverse of discoverEmbeddedRepoRoots
(bounded, skips default-ignored dirs, respects existing includeIgnored)
- project-config: addIncludeIgnoredPatterns — create/merge codegraph.json,
idempotent, refuses to clobber malformed JSON
- cli: wire the detect-name-offer flow into both `init` and `index`
- tests: +13 covering detection, config writing, and the no-nag gate
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
#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>
