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>
A worktree of a submodule points its `.git` into
`.git/modules/<module>/worktrees/<name>`, but `classifyGitDir` only matched
the top-level `.git/worktrees/` shape — so submodule worktrees fell through
to "embedded" and every symbol they shared with the real submodule checkout
got indexed twice (one report: ~28% of the index was duplicates, inflating
both query results and the DB). Broaden the worktree detector to allow the
optional `modules/<module>` segment. The submodule's own checkout
(`.git/modules/<module>`, no `worktrees/`) is unaffected and stays indexed as
distinct code.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
When the indexed root is a directory an enclosing git repo ignores,
`git ls-files --directory` collapses the whole cwd to a single literal
`./` entry. That sentinel reached the `ignore` matcher, which rejects it
("path should be a `path.relative()`d string, but got "./""), aborting
buildScopeIgnore — the one ignore-building call in FileWatcher.start().
So the MCP daemon's startWatching() threw, was caught as "Failed to open
project", and auto-sync never started: the index silently went stale
until a manual `codegraph sync` (CODEGRAPH_NO_DAEMON=1 was the only
workaround).
Filter the `./`/`.` self-entry wherever we consume `--directory` output
(listIgnoredDirs + the untracked-dir loop in discoverEmbeddedRepoRoots).
Semantically correct, not just a crash guard: `./` means "the whole cwd",
never a nested repo to recurse into.
Not platform-specific (reported on Codex/Windows, reproduced on macOS):
the trigger is git state, not the OS.
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
A git worktree nested in a project (e.g. Claude Code's gitignored
`.claude/worktrees/<name>/`) was swept into the index as an embedded repo: its
`.git` is a FILE pointing into the host repo's `.git/worktrees/`, and embedded-
repo discovery treated any `.git` (file or directory) as a distinct repo to
index. Each worktree then duplicated the entire graph — one report went from
~1,850 files to 24,533, with search/explore flooded by stale copies.
classifyGitDir() now distinguishes:
- `.git` directory -> embedded clone, index (#193/#514/#622, unchanged)
- `.git` file → worktrees/ -> worktree, skip (#848)
- `.git` file → modules/ -> submodule, index (unchanged)
Applied at both embedded-repo entry points: findNestedGitRepos discovery (which
also covers the sync/change-detection path) and the untracked-subdir recursion
in collectGitFiles.
Verified: the reproduction drops from 6 files / betaHelper×3 to 3 files / ×1,
with a genuine embedded clone and submodules still indexed. Regression test added.
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
A workspace holding several independent git repos failed two ways:
- Enumeration: a super-repo whose .gitignore hides its child repos
(/packages/) indexed 0 of their files — git never lists ignored dirs,
and the #193 embedded-repo recursion only fired for UNTRACKED dirs.
Gitignored embedded repos are now discovered (ignored-dirs listing +
bounded .git search) and enumerated by their own git ls-files.
- Change detection: git status in the parent says nothing about embedded
repos (untracked OR ignored), so codegraph sync missed every child
change. Status now recurses per embedded repo.
ScopeIgnore is the new single source of truth for indexer + watcher
scope: parent rules for ordinary paths, the child repo's own rules for
paths inside it, built-in defaults uniformly on full paths (a git repo
inside node_modules is an npm git-dependency, not project code), and
ancestors of embedded roots are never pruned (the Linux per-directory
watcher must descend to reach them).
Non-git workspace roots already worked via the per-directory gitignore
walk — locked in by test.
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>
