Follow-up to the salvaged #79323 commits. The three hand-rolled
stat -> atomic_write_text -> chmod blocks (xai migration, uninstaller
shell-rc rewrite, dashboard SOUL.md editor) collapse into an opt-in
preserve_mode=True kwarg on utils.atomic_write_text, plus create_mode=
on both atomic_write_text and atomic_yaml_write for first-create paths
(SOUL.md first save, write_manifest's allowlist create path).
Beyond deduplication this closes two gaps the hand-rolled copies had:
- Owner preservation: the old in-place writes kept the inode, so file
ownership survived root-run rewrites for free. atomic_write_text
swaps in a new inode owned by the writing user, and the hand-rolled
blocks restored only the mode -- a root-run 'hermes migrate xai' or
sudo uninstall on a user-owned Docker/NAS volume would flip
config.yaml / ~/.zshrc ownership to root. preserve_mode now routes
through the same _preserve_file_owner/_restore_file_owner helpers
atomic_yaml_write and atomic_json_write already use.
- chmod-after-replace window: the mode is applied to the temp fd via
fchmod BEFORE the replace (mirroring atomic_json_write's mode= param),
so the target never transits through mkstemp's 0600.
Also removes write_manifest's caller-side existed/chmod block (and its
small TOCTOU) in favor of atomic_yaml_write(create_mode=0o644), and
corrects the SOUL.md mode comment (the default profile's runtime seeder
does run it through _secure_file; named profiles do not).
preserve_mode defaults to False so the existing callers (memory store,
skill manager, cron, agent importer) keep their current semantics.
New tests in tests/test_atomic_write_text_metadata.py cover mode
preservation, owner restore through symlinks, fchmod-before-replace,
create_mode on both writers, and no-behavior-change without opt-in;
all mutation-checked.
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