Add secret_file::write_secret_0600: create the parent dir, write a
sibling temp file opened create_new + mode 0600, sync_all, rename over
the target. Use it for the matrix sender token, the space/chat room-id
files and the forge core token, which previously wrote at the process
umask, then chmod-ed with the error discarded, and dropped the
create_dir_all error. agent_identity::write_identity uses it too
instead of its own open-0600 loop; that loop opened with create +
truncate, so a pre-existing file kept its old mode.
Also log instead of discarding:
- the manager's applied-rev marker write in auto_update
- the knowledge `git remote set-url` scrub (spawn error and non-zero
exit; the exit status only, since stderr may echo the old URL)
- the parent create_dir_all in paths::move_if_legacy
Closes#5037
f53ccb2740