Please make ALWAYS_SKIP_DIRS configurable by user

[zeronewb]

What problem does this solve?

Rignt now codebase-memory-mcp excluding part of repo blindly, for example:
"nixl/src/plugins/obj","nixl/test/gtest/unit/obj" from https://github.com/ai-dynamo/nixl

Proposed solution

Make it configurable like .gitignore

Alternatives considered

Compiling by hand and replacing skip list not very fun.

Confirmations

• I searched existing issues and this is not a duplicate.

[DeusData]

Thanks for raising this, @zeronewb 🙏 It's a fair point. Today .cbmignore (gitignore syntax) lets you add excludes, but it can't un skip a directory the built in list drops, which is exactly your case. That also overlaps with #497.

The clean design is to make the skip list an overridable default (a config key plus .cbmignore negation like !obj/) rather than a hardcoded constant. We'll treat #500 and #497 together as making the ignore and skip layer fully user controllable. Appreciate the report!

[mvanhorn]

Implemented in #543

[DeusData]

Cross-linking #403 as a concrete use case for the deferred config-key half here: there, the IDE install directory gets auto-indexed as a root, so the user override needs to be settable globally (in ~/.config/codebase-memory-mcp/config.json) and consulted during auto-index root selection, not just during the subdirectory walk. The .cbmignore !negation work in #543 covers the in-walk half but not root selection.