Default "build" skip hides tracked first-party source, and explore returns unrelated matches instead of saying so #2462

Version: 1.6.2, Windows 11, Claude Code

Our repo (.NET) has a root build/ folder that's real, tracked source: about 86 C# files across several small tool projects (release notes builder, packaging, validators). Their actual build output lives in bin/ and obj/, which are already gitignored. Because build is on the default skip list, none of it was indexed.

That on its own would be easy to spot, but explore didn't tell us anything was missing. A query naming symbols that only exist under build/:

codegraph_explore "ReleaseNotesBuilder Program Main ChangelogParser PersistentData Entry AddFeatures"

returned Main from an unrelated Program.cs elsewhere in the repo plus a C++ Parser class, with no hint that most of the names matched nothing. We only figured it out after querying by file path, which gave "No indexed file uniquely matches". The agent was a few steps into reading the wrong code by then.

Workaround: !/build/ in the root .gitignore, then a full codegraph index. With the negation in .git/info/exclude, codegraph sync reported "Already up to date" and found nothing new; only a full index picked the folder up. include in codegraph.json isn't an option, since the docs say it never resurfaces built-in skipped dirs.

Suggestions:

1. Don't apply the build skip to a folder that contains tracked project/source files whose output is gitignored, or at least report skipped default dirs with tracked source in init/status, so people know to opt in. fix(extraction): preserve Java packages named build (#1642) #1998 did the first part for JVM packages named build; the same trap exists for .NET and others.
2. Extend the fix(explore): explain empty results with bounded lexical diagnostics (#1904) #2026 miss diagnostics to partial misses: when identifier-like query words match nothing, say so even if other results are returned.
3. Have sync notice newly un-ignored paths after an ignore-file change, or say that a full index is needed.