Each copy re-implemented temp+replace by hand and lacked one or more of
fsync, symlink preservation, atomic_replace's Windows-contention retry and
EXDEV/bind-mount fallback, mode preservation, or interrupt-safe temp
cleanup. Three (gateway/session_persistence, cron/suggestions,
agent/shell_hooks) were verbatim inlines of utils._atomic_write; two
modules defined their own directory-fsync helper, now utils.fsync_directory.
plugins/google_meet/_jsonfile.write_json_atomic is deleted (callers use the
canonical helper directly).
Behavior change: every one of these writers now fsyncs the payload, keeps a
pre-existing target's mode, cleans its temp file on BaseException, and
survives Windows AV/indexer contention and cross-device renames the way
config writes already did. cron/suggestions.json is 0600 from creation
(previously chmod'ed after the replace). Skipped on purpose: cron/jobs.py
two-phase staging, gateway/status._write_json_excl (create-only lock),
kanban_transfer staging (not atomic writers); tools/skill_usage.
_write_suppressed_names lives inside a PLUGIN-COMPAT block.
For each issue anchor present in BASE 63279301bc non-test .py and absent on HEAD, the BASE comment/docstring block was re-attached at the HEAD location of the code it explained (matched by the distinctive code line / enclosing def). Sentences already covered by an existing HEAD comment were deduped; the issue number always survives. Insert-only: no code lines changed.
Repo scanners (check_subprocess_stdin, check-windows-footguns --all) flagged 21 sites where
the r3 single-line collapses lost stdin=DEVNULL, encoding='utf-8'/errors='replace', the
'# windows-footgun: ok' same-line marker, or the getattr(os, 'geteuid') gate. Each guard is
restored at the call site (real portability/hang fixes, not suppressions).
