fix(server): checkpoints no longer rehash every file when one entry is skip-worktree or assume-unchanged#23624

fix(server): flagged checkpoint entries stay rehashable under core.ignorestat

Merge remote-tracking branch 'origin/main' into fix/issue-13741

fix(server): checkpoints no longer rehash every file when an entry is flagged

test(server): reproduce #13741 checkpoint rehash with manually flagged entries