feat(indexing): respect .gitignore when indexing

[torresmateo]

Closes #28.

Summary

• Aggregate patterns from every .gitignore under the indexed root and skip matching files during indexing.
• Hardcoded baseline (.git, node_modules, __pycache__, caches, binaries, fonts, media) still applies — .gitignore layers on top.
• New --include-ignored flag on libr add (and include_ignored arg on index_directory_to_library) opts out. The flag is persisted on the source entry and honored by libr index build on rebuild.
• The previously-duplicated _should_skip_file in cli.py and server.py now delegates to a shared librarian/sources/ignore.py. This file is the home for the new GitignoreMatcher (which uses pathspec's GitIgnoreSpec under the hood and rewrites nested patterns to be anchored under their containing directory).

Test plan

• make check clean (lint, format, mypy)
• make test-fast — 96 passed / 8 skipped
• 13 new unit tests in tests/test_gitignore.py covering: no-gitignore, root patterns, floating patterns at any depth, anchored patterns, nested-gitignore scoping, negation, out-of-root paths, the always-skip baseline, and the include-ignored path
• CLI smoke test: created a tree with build/ in .gitignore; libr add --dry-run shows 1 file, libr add --dry-run --include-ignored shows 2 files
• E2E smoke test on synthetic node_modules/ tree: SKIP node_modules/pkg/skip.md, KEEP src/readme.md

[sdserranog]

I sometimes look into node_modules to figure out a library's types or to debug a bug and see whether it's in my code or a dependency. Not sure if we can add an explicit flag to include a file or directory, even if it's on the list or in .gitignore, instead of --include-ignored.

[torresmateo]

This is a good point, I think having --include-ignore makes sense as a convenience shorthand. I'm thinking of these options for manually allowlisting specific files/directories:

• Have .librariantrack which overrides .gitignore on the specific directory
• Have --force-include <list of files/directories> to include.

In both cases pointing to a directory will recursively include files inside as if --include-igore was used. And for this we'll also remove the hardcoded default in these lines.

How does this sound?

[sdserranog]

That sounds great!