Sub-repos / nested workspaces can't be indexed when parent .gitignore excludes them

[cdel1]

Summary

When contextplus is rooted at a workspace whose .gitignore excludes the
sub-trees containing the actual source (e.g. monorepos with git-managed
sub-repos under repos/ or packages/, or any layout using nested git
repos / git submodules / local symlinks), those sub-trees are invisible
to the indexer. There's no way to override this short of editing the
parent .gitignore.

Repro

workspace/
├── .gitignore            # contains:  repos/
├── docs/                 # indexed
└── repos/
    ├── lib-a/            # own git repo — NOT indexed
    │   └── src/...
    └── lib-b/            # own git repo — NOT indexed
        └── src/...

bunx contextplus /path/to/workspace indexes only docs/. The
embeddings-cache.json contains zero entries from repos/lib-a/ or
repos/lib-b/, even though each sub-repo has its own .gitignore that
would happily include its src/.

Cause

src/core/walker.ts:

• L44 — loadIgnoreRules reads .gitignore only at rootDir. Nested
  .gitignore files (per-repo, per-package) are never loaded, so the
  ignore matcher uses only the parent's rules.
• L63 — entry.name.startsWith(".") skips every dotfile/dir
  unconditionally, including any nested .git markers that might
  otherwise signal "this is a sub-repo, treat its own ignore rules".
• No mechanism for multiple roots, include-overrides, or submodule
  awareness in WalkOptions.

Why the obvious workarounds don't work

• Un-ignore the sub-trees in the parent .gitignore — changes the
  parent repo's git behavior (sub-repo contents start showing up in
  git status, gitlinks vs. embedded trees confusion, etc.). Also
  exposes build artifacts that the sub-repos correctly ignore but the
  parent doesn't know about.
• Run a separate contextplus per sub-repo — works, but defeats
  cross-repo tools (get_blast_radius, semantic_navigate,
  get_feature_hub) at the workspace level. You can't ask "where is
  X used across all my packages" from one place.

Suggested resolutions (any one would solve it)

1. Walk nested .gitignore files. When recursing into a directory,
   load its .gitignore (if any) and merge with the inherited rules.
   This is what ripgrep does and matches user mental model.
2. Treat nested .git as a sub-repo boundary: when walkRecursive
   sees .git/ in a subdirectory, swap to that subdirectory's ignore
   rules instead of inheriting the parent's. (Closer to native git
   submodule semantics.)
3. Add an include / extraRoots option to WalkOptions — an
   allow-list of paths that bypass parent ignore rules. Easiest to ship,
   most explicit, doesn't change defaults.

Happy to send a PR for option (1) or (3) if you have a preference.

Environment

• contextplus 1.0.8
• Node via bun (bunx contextplus)
• macOS 25.1.0

[cdel1]

PR ready: #39