fix: skip files ignored by gitignore

[zerone0x]

Summary

• load the project .gitignore with pathspec and merge nested rules
• wrap the directory walker with a gitignore-aware matcher so we skip ignored files
• add regression coverage to ensure ignored files stay out of the index while negations still work

Fixes #62

Testing

• uv run pytest tests/test_e2e.py::test_session_respects_gitignore
• uv run pytest tests/test_e2e.py::test_session_happy_path