`hermes worktree prune` (and the startup/cron pruner) classified every clean tree in a
repository with no remote as "clean and fully merged/pushed" and force-deleted its branch,
even when the branch carried commits that exist nowhere else. `audit_branches` returned []
in the same repos, so a unique local-only branch was invisible to the audit as well.
Root cause: `_worktree_has_unpushed_commits` answered False when `refs/remotes` was empty
("nothing to be unpushed against") and both consumers — `worktree_gc._classify_tree` and
`worktree_ops._classify_prune_candidates` — read False as "safe to reap".
The preceding commit (#111897) flips that branch to True, which is safe but also means a
no-remote repo can never reclaim anything (a tree sitting at trunk, or squash-merged into
it, stays "unpushed" forever because `_worktree_commits_all_merged_upstream` finds no
origin/* base). This commit replaces the unconditional True with a real baseline:
- `_worktree_local_trunk`: `main`/`master`, else the branch checked out in the main
worktree; None when no trunk exists.
- `_worktree_merge_base_ref`: origin/HEAD|origin/main|origin/master, falling back to the
local trunk ONLY when the repo has no remote-tracking refs at all. Single resolver used
by `_worktree_commits_all_merged_upstream` and `worktree_gc.audit_branches`.
- `_worktree_has_unpushed_commits`: with no remote refs, `git log HEAD --not <trunk>`;
no trunk -> True (preserve), matching the docstring's fail-safe promise.
Net effect in a no-remote repo: unique work is kept ("unpushed commits not found
upstream"), trees at/merged into the local trunk still reap, branch audit reports unique
branches as keep and merged ones as delete, and `git branch -D` can only run on a branch
whose every commit is reachable from or patch-equivalent to the trunk.
Tests: the salvaged no-remote keep test now uses a shared `local_repo` fixture; a control
test proves trunk-merged trees still reclaim and the branch audit reports in the same
repo; `test_merged_predicate_fails_safe_without_upstream` now pins both halves of the
contract (trunk resolves -> merged; no trunk at all -> False/preserve).
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).
teknium1