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
Aslaaen's fix in the original PR covered _detect_api_mode_for_url and the
two openai/xai sites in run_agent.py. This finishes the sweep: the same
substring-match false-positive class (e.g. https://api.openai.com.evil/v1,
https://proxy/api.openai.com/v1, https://api.anthropic.com.example/v1)
existed in eight more call sites, and the hostname helper was duplicated
in two modules.
- utils: add shared base_url_hostname() (single source of truth).
- hermes_cli/runtime_provider, run_agent: drop local duplicates, import
from utils. Reuse the cached AIAgent._base_url_hostname attribute
everywhere it's already populated.
- agent/auxiliary_client: switch codex-wrap auto-detect, max_completion_tokens
gate (auxiliary_max_tokens_param), and custom-endpoint max_tokens kwarg
selection to hostname equality.
- run_agent: native-anthropic check in the Claude-style model branch
and in the AIAgent init provider-auto-detect branch.
- agent/model_metadata: Anthropic /v1/models context-length lookup.
- hermes_cli/providers.determine_api_mode: anthropic / openai URL
heuristics for custom/unknown providers (the /anthropic path-suffix
convention for third-party gateways is preserved).
- tools/delegate_tool: anthropic detection for delegated subagent
runtimes.
- hermes_cli/setup, hermes_cli/tools_config: setup-wizard vision-endpoint
native-OpenAI detection (paired with deduping the repeated check into
a single is_native_openai boolean per branch).
Tests:
- tests/test_base_url_hostname.py covers the helper directly
(path-containing-host, host-suffix, trailing dot, port, case).
- tests/hermes_cli/test_determine_api_mode_hostname.py adds the same
regression class for determine_api_mode, plus a test that the
/anthropic third-party gateway convention still wins.
Also: add asslaenn5@gmail.com → Aslaaen to scripts/release.py AUTHOR_MAP.
atomic_yaml_write() and atomic_json_write() used tempfile.mkstemp()
which creates files with 0o600 (owner-only). After os.replace(), the
original file's permissions were destroyed. Combined with _secure_file()
forcing 0o600, this broke Docker/NAS setups where volume-mounted config
files need broader permissions (e.g. 0o666).
Changes:
- atomic_yaml_write/atomic_json_write: capture original permissions
before write, restore after os.replace()
- _secure_file: skip permission tightening in container environments
(detected via /.dockerenv, /proc/1/cgroup, or HERMES_SKIP_CHMOD env)
- save_env_value: preserve original .env permissions, remove redundant
third os.chmod call
- remove_env_value: same permission preservation
On desktop installs, _secure_file() still tightens to 0o600 as before.
In containers, the user's original permissions are respected.
Reported by Cedric Weber (Docker/Portainer on NAS).
Remove read_json_file, read_jsonl, append_jsonl, env_str, env_lower —
all added in #7917 but never imported anywhere in the codebase. Also
remove unused List and Optional typing imports.
env_int, env_bool, and the other helpers that have real consumers are
kept.
- add regression coverage for BaseException cleanup in atomic_json_write
- add dedicated atomic_yaml_write tests, including interrupt cleanup
- document why BaseException is intentional in both helpers
