includeIgnored in codegraph.json does not revive embedded git repos on init/index (v1.4.1)

[joaofbcastro]

Summary

codegraph.json's includeIgnored (introduced in v1.1.1 per #970/#980) no longer opts gitignored embedded git repos back into the index. codegraph init/codegraph index report the repos as excluded and print the exact config the user already has as the "fix," in a loop.

Environment

• CodeGraph: 1.4.1 (npm install, @colbymchenry/codegraph)
• OS: macOS (Darwin arm64)
• Project shape: a meta-repo whose root .gitignore excludes /repos/, which contains 3 independently-git-tracked projects (repos/a/, repos/b/, repos/c/), each with its own .git and its own .codegraph/ index.

Repro

.gitignore at root:

/repos/

codegraph.json at root:

{
  "includeIgnored": ["repos/a/", "repos/b/", "repos/c/"]
}

Run:

codegraph init

Actual

▲  No files found to index
▲  Your .gitignore excludes 3 nested git repositories here, so they were not indexed: repos/a, repos/b, repos/c.
●  If they're your code, add them to codegraph.json and re-index:
●    { "includeIgnored": ["repos/a/", "repos/b/", "repos/c/"] }

The suggested config is byte-for-byte identical to what's already in codegraph.json — confirmed the file is present, valid JSON, correctly parsed via python3 -m json.tool, and unmodified across codegraph uninit && codegraph init, codegraph index -f, with and without trailing slashes.

Expected

Per issue #970 (comment from @colbymchenry, 2026-06-XX): includeIgnored is documented and was originally shipped specifically to opt embedded git repos in a gitignored directory back into the index:

If you ever do want nested repos under a gitignored dir indexed, that's now an explicit opt-in via codegraph.json:
{ "includeIgnored": ["some/dir/"] }

The README (Configuration section) still documents the same contract today: "includeIgnored only revives embedded git repos, not plain source."

With the config above, codegraph init should discover and index the 3 nested repos as part of the root project.

Workaround found

Swapping the key from includeIgnored to include (documented as being for plain gitignored source, explicitly not for embedded git repos) does work — it finds and indexes all files in the nested repos:

{
  "include": ["repos/a/", "repos/b/", "repos/c/"]
}

This indexed 1105 files / 18k nodes successfully. So the file-discovery path for include correctly walks into gitignored embedded repos, but the dedicated includeIgnored path (whatever gates specifically on nested-.git detection) appears to no longer trigger — looks like a regression introduced somewhere after v1.1.1, possibly during the work that added include in #1163/PR #1063, since both features touch the same ignore/discovery logic.

Impact

Anyone relying on includeIgnored to index a "folder of repos" workspace root (the documented, supported use case per #514/#837) currently gets zero files indexed at the root, with no error beyond the exclusion notice — the suggested fix in the CLI's own message doesn't fix it. include is a viable workaround once you know to look for it, but it's a different, undocumented-for-this-purpose knob.

[colbymchenry]

Fixed in #1318 (merged to main, ships in the next release). Your workaround observation pinpointed it: the include walk matches per-file, but includeIgnored gated on nested-repo discovery — and that gate tested your patterns against the parent ignored directory only. With .gitignore: /repos/, git reports a single ignored entry repos/, which "repos/a/" (the exact spelling codegraph init's hint told you to use!) can never match. Hence the loop: correct config, zero effect, same suggestion again.

Now:

• Both spellings work. "includeIgnored": ["repos/a/", "repos/b/", "repos/c/"] opts in exactly those repos; "includeIgnored": ["repos/"] opts in every repo under the directory. Your exact meta-repo layout is a pinned regression test, including the partial case (opting in only repos/a/ leaves repos/b/ out and still hinted).
• The hint stops nagging about repos that are already configured.
• The watcher's discovery shares the fixed path, so auto-sync scope matches the index.

You can switch back from the include workaround to includeIgnored after upgrading (codegraph uninit && codegraph init, or index -f) — includeIgnored keeps the "only revive embedded repos, not plain gitignored source" contract the README documents, which include doesn't.