Refactor filesystem tools into per-tool modules #123

Job	Run time
Build wheel, install & CLI smoke test	24s
Ruff (lint + format)	18s
Tests (py3.11)	1m 17s
Tests (py3.12)	1m 23s
Pyright	32s
pip-audit (dependency CVEs)	15s
Tests (py3.13)	1m 19s
	5m 28s

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