Skills indexing scans into dependency directories (.venv, __pycache__, etc.)

[Oceanswave]

When indexing skills, loadSkillsFromDirInternal currently only skips node_modules. It misses other common dependency and build directories.

Impact:

• Slow indexing on projects (especially those with Python venvs)
• Unnecessary scanning of .venv, __pycache__, .git, dist, and build folders
• File handle leaks when recursing into large dependency trees

Proposed fix:
Add a SKIP_DIRS set to exclude these common directories alongside node_modules.

[Oceanswave]

A PR is ready for this #1071