fix: correctly merge conflicting paths when files (instead of dirs) are being linked

[rickeylev]

When a file (instead of directory) was duplicated, it was incorrectly be treated as
a directory. The conflicting path was turned into a directory and all the files
were made child paths of it. In practice, this usually worked out OK still because
the conflicting file was an __init__.py file for a pkgutil-style namespace package,
which effectively converted it to an implicit namespace package.

I think this was introduced by #3448,
but am not 100% sure.

To fix, first check for exact path equality when merging conflicting paths. If the
candidate file has the same link_to_path as the grouping, then just link to that file
and skip any remaining files in the group. The rest of the group's files are skipped
because none of them can contribute links anymore:

• If they have the same path, then they are ignored (first set wins)
• If they are a sub-path, then it violates the preconditions of the group (all files
  in the group should be exact matches or sub-paths of a common prefix)
• If they aren't under the common prefix, then it violates the preconditions of the
  group and are skipped.

[gemini-code-assist]

Summary of Changes

Hello @rickeylev, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses a critical bug in the virtual environment (venv) merging logic where individual files were erroneously processed as directories when conflicts arose. The core change introduces a precise path equality check to ensure that when a file's path exactly matches a conflicting entry, it is correctly linked as a file, overriding any directory-based interpretations. This prevents unintended behavior, such as accidental implicit namespace package creation. Alongside this fix, the PR also includes a substantial update to the documentation's Python dependencies, incorporating torch and its associated NVIDIA CUDA libraries, and refines existing test cases to validate the improved conflict resolution.

Highlights

• Venv Conflict Resolution: Correctly handles conflicting virtual environment files, preventing files from being mistakenly treated as directories during merging, especially for __init__.py files.
• Exact Path Matching: Introduces a precise check for exact path equality when resolving venv conflicts, ensuring that a file is directly linked if its path matches, and skipping other conflicting entries in the group.
• Dependency Updates: Updates several Python dependencies in docs/requirements.txt and adds torch along with its associated NVIDIA CUDA libraries to the documentation build.
• Test Refinements: Refactors test helpers and adds a specific test case to validate the new file-level conflict merging logic, ensuring the fix behaves as expected.

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[gemini-code-assist]

Code Review

This pull request correctly fixes an issue with merging conflicting venv files, particularly when a file is duplicated instead of a directory. The core logic change in python/private/venv_runfiles.bzl is sound, using rf_root_path == entry.link_to_path to handle direct file links and partition for more robust prefix matching. The refactoring of the tests in tests/venv_site_packages_libs/app_files_building/app_files_building_tests.bzl improves clarity and the new test case for conflicting files is a great addition. I've found one minor typo in a test comment. Overall, this is a good fix.