fix(stage): make code add idempotent for deletions and dir sentinels
Running 'muse code add .' on an already-staged repo was re-staging deletions and empty-dir sentinels unconditionally — only modified files had the 'skip if already staged' guard. Now all three paths check first: deletions skip if mode==D in stage, dir sentinels skip if object_id==dir:. Result: second 'muse code add .' on a clean stage prints 'Nothing new to stage' instead of reporting false counts.
sha256:9b4ea477b4ddf7b5285f01c12622078dc5cdb14fbdf35ab046d8d170556d285f
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sha256:84d36909c40116f306676101fc9cd7227fdae2cb6ffbc8b12dec6a2d4471f462
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fix(stage): compute total after dir sentinels are staged
sha256:7fb3690c362340890e70b510ad8d7a5dfc1261e43f7d3522c9c72137bc3bd58c
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fix(stage,status): don't re-stage or surface already-committed e…
sha256:00518230287e4eef5012e619cd030beb8883260e0b170ee53d68d89bbe058928
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