Extract the islink/realpath guard from the 16743 fix into a single
atomic_replace() helper in utils.py, then migrate every os.replace()
call site in the codebase to use it.
The original PR #16777 correctly identified and fixed the bug, but
only patched 9 of ~24 call sites. The same bug class (managed
deployments that symlink state files silently losing the link on
every write) still existed at auth.json, sessions file, gateway
config, env_loader, webhook subscriptions, debug store, model
catalog, pairing, google OAuth, nous rate guard, and more.
Rather than add another 10+ copies of the same three-line guard,
consolidate into atomic_replace(tmp, target) which:
- resolves symlinks via os.path.realpath before os.replace
- returns the resolved real path so callers can re-apply permissions
- is a drop-in replacement for os.replace at the use sites
Changes:
- utils.py: new atomic_replace() helper + atomic_json_write /
atomic_yaml_write now call it instead of inlining the guard
- 16 files: all os.replace() call sites migrated to atomic_replace()
- agent/{google_oauth, nous_rate_guard, shell_hooks}.py
- cron/jobs.py
- gateway/{pairing, session, platforms/telegram}.py
- hermes_cli/{auth, config, debug, env_loader, model_catalog, webhook}.py
- tools/{memory_tool, skill_manager_tool, skills_sync}.py
Tests: tests/test_atomic_replace_symlinks.py pins the invariant for
atomic_replace + atomic_json_write + atomic_yaml_write, covers plain
files, first-time creates, broken symlinks, and permission preservation.
Refs #16743
Builds on #16777 by @vominh1919.
os.replace(tmp, path) replaces the symlink itself with a regular file,
breaking users who symlink config.yaml, SOUL.md, or .env from ~/.hermes/
to a dotfiles repo or managed profile package.
Fix: resolve symlinks via os.path.realpath() before os.replace(), so the
real file is overwritten in-place while the symlink survives.
Fixed in 7 files covering all os.replace call sites:
- utils.py (atomic_json_write, atomic_yaml_write — fixes save_config)
- hermes_cli/config.py (env sanitizer, save_env_value, remove_env_value)
- tools/skill_manager_tool.py (_atomic_write_text — SOUL.md writes)
- tools/memory_tool.py (memory file writes)
- tools/skills_sync.py (manifest writes)
- cron/jobs.py (job state + output file writes)
- agent/shell_hooks.py (hook file writes)
FixesNousResearch/hermes-agent#16743
`_resolve_effective_accept()` used `return bool(cfg_val)` for the
`hooks_auto_accept` config key. In Python, `bool("false")` is `True`,
so a user setting `hooks_auto_accept: "false"` (quoted YAML string)
in `config.yaml` would silently enable auto-approval of every shell
hook, bypassing the consent prompt entirely.
Replace the coercion with the same type-aware parsing already used for
the HERMES_ACCEPT_HOOKS env var three lines above: bool passthrough,
strings checked against {1,true,yes,on} case-insensitively, everything
else (including "false", None, 0, ints) rejected.
Add TestHooksAutoAcceptParsing guarding the regression across all four
value shapes (bool, string-truthy, string-falsy, missing/None).
Reported by @sprmn24 in #16244.
Users can declare shell scripts in config.yaml under a hooks: block that
fire on plugin-hook events (pre_tool_call, post_tool_call, pre_llm_call,
subagent_stop, etc). Scripts receive JSON on stdin, can return JSON on
stdout to block tool calls or inject context pre-LLM.
Key design:
- Registers closures on existing PluginManager._hooks dict — zero changes
to invoke_hook() call sites
- subprocess.run(shell=False) via shlex.split — no shell injection
- First-use consent per (event, command) pair, persisted to allowlist JSON
- Bypass via --accept-hooks, HERMES_ACCEPT_HOOKS=1, or hooks_auto_accept
- hermes hooks list/test/revoke/doctor CLI subcommands
- Adds subagent_stop hook event fired after delegate_task children exit
- Claude Code compatible response shapes accepted
Cherry-picked from PR #13143 by @pefontana.
