fix: reconcile separately mounted SQLite plugin trees

[soulteary]

Summary

• keep the atomic rename path for ordinary managed plugin directories
• fall back to an in-place, backup-backed reconciliation when a separately mounted destination cannot be renamed
• persist a marker so an interrupted in-place update restores the previous contents before retrying
• replace matching destination symlinks instead of allowing diff to dereference and retain them
• use unique staging directories while preserving the managed source directory mode
• fix the test assertion so it detects the child entrypoint's staging name instead of using the parent test PID

Tests

bash tests/test-entrypoint-reconcile.sh now covers:

• ordinary replacement and removal of upstream-deleted files
• a matching symlink target
• simulated mount-point EBUSY while preserving the destination inode
• interrupted in-place recovery
• wildcard staging/rollback artifact cleanup assertions

Also checked both shell files with bash -n and ran git diff --check.

Follow-up to the entrypoint review in #10.

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Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-08-30T20:06:47.527197Z	8dc2f81	PR opened

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Reviewed commit: 8dc2f819e0

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