fix(commit,checkout): Phase 5/6 cleanup — non-fatal clear_stage + checkout docstring
Phase 5: wrap clear_stage in try/except after write_branch_ref succeeds. A clear_stage failure must not hide a successful commit or leave staged index entries that would produce a duplicate commit on next muse commit.
Phase 6: update _checkout_snapshot docstring to document clear_marker=False semantics — caller contract for keeping CHECKOUT_HEAD alive through write_head_branch.
sha256:711b44ed69a0c34641cc4245ba8c84602ba6b098b456974c688b60c62f4b3850
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sha256:94b38e0617e28d8b2db4b85f678006ed4647d21d5e674c42bd03aed13556e1e5
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