Fix nested directory include and exclude filters

[wanghanyu654321-cell]

Directory rules such as ./test/reference_data/ are currently compared to individual path components, so nested exclusions leak files into the wiki/RAG input and nested inclusions return no files. Match normalized slash-delimited directory paths instead, preserving directory boundaries and support for bare directory names.

Fixes #79. This changes directory selectors only; file glob matching in #430 and cached database invalidation in #495 are separate. Adds six regression cases covering include/exclude rules, forward/backslashes, nested children, and similarly named sibling directories.

Validation:

• Before the fix: six new cases fail; all six existing test_config.py cases pass.
• Windows: 74 tests pass (tests/backend, tests/unit/test_chat.py, tests/test_config.py).
• Linux: 21 filtering/wiki-structure tests pass in the built application image with networking disabled.
• Actual read_repo_file_tree and read_all_documents inclusion/exclusion checks fail on the base and pass after the fix; the Linux image also passes all four checks offline, without model calls.
• The repository Dockerfile builds successfully, including the Next.js build/type/lint step; Python sources compile. Ruff 0.8.6 lint and backend format checks pass.
• All applicable repository pre-commit hooks pass, including secret scanning.

Full-suite limitations: pytest tests -q gives 110 passed, 4 failed, 1 error after this change; the untouched base gives 104 passed with the same four failures and one error. These are the GitLab clone network test, three embedder factory tests requiring GOOGLE_API_KEY, and the streaming endpoint test's missing repo_url fixture. Additional mypy checking reports the same existing implicit-Optional error in get_embedder on both versions. No tests or check settings were weakened to address these.

AI assistance: this patch and regression tests were prepared with Codex on behalf of the account owner; the diff and the reported test outputs were reviewed by the agent.

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