fix: remove legacy commits/ and snapshots/ dirs from muse init
muse init was creating .muse/commits/ and .muse/snapshots/ as legacy subdirectories. The unified object store lives entirely in .muse/objects/ (SHA-256 sharded). These directories are no longer created, and the _CRITICAL_MUSE_DIRS integrity check no longer expects them.
Updated _INIT_SUBDIRS in init.py, _CRITICAL_MUSE_DIRS in core/repo.py, and the two test files that asserted the old layout.
sha256:58e6d63233c0f6625660346e29fce21f52272ef3f349598df7d9fc2c1a8c3d1a
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sha256:4a0773660f75901c87f50918d109afcd44b6f92c3115d02e08e1c88a09640b64
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