fix(file_read): skip hidden directories during os.walk traversal

[dosvk]

Description using their template:

Filter directories starting with '.' in-place during os.walk to
prevent descending into .venv, .git, .mypy_cache, etc. This matches
the existing hidden file filter and prevents token explosion when
file_read is called on directories containing large hidden trees.

Closes #405

Description

find_files() uses os.walk() and filters hidden files but not hidden
directories. This causes traversal into .venv, .git, .mypy_cache, etc.,
collecting thousands of irrelevant files and exploding the context window.

The fix modifies dirs in-place during os.walk (the standard Python
approach for pruning traversal) to skip directories starting with .,
consistent with the existing hidden file filter on the same line.

Before: 13,769 files (97% from hidden dirs)
After: 1,257 files (hidden dirs skipped)

Related Issues

Closes #405

Type of Change

Bug fix

Testing

• All 17 existing file_read tests pass

• Verified manually: hidden directory files no longer returned

• I ran hatch run prepare

Checklist

• I have read the CONTRIBUTING document
• I have added any necessary tests that prove my fix is effective or my feature works
• I have updated the documentation accordingly
• I have added an appropriate example to the documentation to outline the feature
• My changes generate no new warnings
• Any dependent changes have been merged and published

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