[BUG] LSP goToDefinition drops definitions in git-ignored dependency folders (deps/, .venv, node_modules): reopen of #72594

Preflight Checklist

• [x] I have searched existing issues. This is the bug from #72594 and #76371, which a maintainer confirmed and said a fix was being looked at. Both were then auto-closed as stale, so I am opening a new issue as the bot asked.
• [x] This is a single bug report
• [x] I am using the latest version of Claude Code available to me (2.1.280)

What's Wrong?

The LSP tool drops every goToDefinition, goToImplementation, findReferences and workspaceSymbol location whose path git check-ignore reports as ignored. For dependencies installed inside the project, the definition is always in an ignored folder: Elixir deps/, Python .venv/, JS node_modules/. Go-to-definition into a library therefore always reports:

No definition found. This may occur if the cursor is not on a symbol, or if the definition is in an external library not indexed by the LSP server.

The language server did return the location, so the hint points the wrong way. hover on the same position works, because it carries no URI, which makes this look like a language server bug.

Filtering ignored paths makes sense for findReferences and workspaceSymbol, where hits inside dependencies are noise. For goToDefinition and goToImplementation, the ignored location is usually the only correct answer.

What Should Happen?

goToDefinition and goToImplementation should return definitions in ignored paths. Alternatively, a setting could turn the filter off, or the tool could say that N results were hidden because they are git-ignored.

Steps to Reproduce

Elixir project with /deps/ in .gitignore, using the Dexter LSP plugin (dexter-lsp, Dexter 0.7.2):

1. Run the LSP tool goToDefinition on Ecto.Multi.new() or Phoenix.PubSub.broadcast(...) in lib/.
2. Result: "No definition found."
3. hover at the same position returns the function's docs.
4. workspaceSymbol with query Ecto.Multi.new returns "No symbols found in workspace."

Driving dexter lsp directly over stdio at the same positions returns the locations:

textDocument/definition => [{"uri":"file:///.../deps/ecto/lib/ecto/multi.ex","range":{"start":{"line":177,"character":0},...}}]
workspace/symbol        => Ecto.Multi.new/0 file:///.../deps/ecto/lib/ecto/multi.ex

Controls in the same session:

• Enum.group_by resolves, because the Elixir stdlib is in /nix/store, outside the repo, where git check-ignore does not apply.
• Definitions in lib/ resolve.

Where it happens

In the 2.1.280 bundle, after sendRequest, the tool runs this when the operation is findReferences, goToDefinition, goToImplementation or workspaceSymbol:

if (F && Array.isArray(F) && (n.operation==="findReferences" || n.operation==="goToDefinition" || n.operation==="goToImplementation" || n.operation==="workspaceSymbol"))
  // ... $p(locations, cwd) runs `git check-ignore <paths...>` in batches of 50
  // and removes every location whose path is printed

No setting or environment variable guards it, so users have no workaround short of un-ignoring their dependency folders.

Is this a regression?

Yes. According to the maintainer comment on #72594, it started in 2.1.47 with the fix for #26051.

Claude Code Version

2.1.280 (Claude Code)

Operating System

macOS 26.6, arm64

Additional Information

Related: #72594 (.venv, confirmed and reproduced by a maintainer), #76371 (same filter hides .claude/worktrees/), #26051 (the original request to filter references).

~/ws/                  <- git repo, launch directory
  .gitignore           <- "/*/"  (sibling clones are not content of this repo)
  service/             <- separate git clone, Maven project