refactor: change pathTrie per-file to per-directory

[jbedard]

This way the pathTrie aligns with the directory structure, excluding files. This should make it easier to do things in parallel per-directory.

Depends on https://github.com/bazel-contrib/bazel-gazelle/pull/1932

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Other

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all

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Which issues(s) does this PR fix?

Fixes #

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