shell: only skip system-log subtree in fs.meta.save, not fsck/verify
The SystemLogDir skip lived in the shared BFS traversal, so volume.fsck
built its in-use set without the /topic/.system/log chunks and flagged
every referenced log needle as orphan. -reallyDeleteFromVolume would then
delete live log data and leave dangling filer entries. Gate the skip
behind a flag that only fs.meta.save sets.