Teknium b61d9b297a refactor: consolidate symlink-safe atomic replace into shared helper ... 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.		2026-04-28 04:58:22 -07:00
..
browser_providers	feat: ungate Tool Gateway — subscription-based access with per-tool opt-in	2026-04-16 12:36:49 -07:00
environments	fix: strip leaked declare-x env dump from terminal output on macOS (#15459)	2026-04-27 00:19:48 -07:00
neutts_samples	refactor(tts): replace NeuTTS optional skill with built-in provider + setup flow	2026-03-17 02:33:12 -07:00
__init__.py	Merge branch 'main' into rewbs/tool-use-charge-to-subscription	2026-03-31 08:48:54 +09:00
ansi_strip.py	fix: strip ANSI at the source — clean terminal output before it reaches the model	2026-03-23 07:43:12 -07:00
approval.py	feat(plugins): add pre_approval_request / post_approval_response hooks (#16776)	2026-04-27 20:08:33 -07:00
binary_extensions.py	fix(tools): address PR review — remove _extract_raw_output, BudgetConfig everywhere, read_file hardening	2026-04-08 02:24:32 -07:00
browser_camofox.py	refactor: remove remaining redundant local imports (comprehensive sweep)	2026-04-21 00:50:58 -07:00
browser_camofox_state.py	feat(browser): add persistent Camofox sessions and VNC URL discovery (salvage #4400) (#4419)	2026-04-01 04:18:50 -07:00
browser_cdp_tool.py	fix: sanitize tool schemas for llama.cpp backends; restore MCP in TUI (#15032)	2026-04-24 02:44:46 -07:00
browser_dialog_tool.py	feat(browser): CDP supervisor — dialog detection + response + cross-origin iframe eval (#14540)	2026-04-23 22:23:37 -07:00
browser_supervisor.py	feat(browser): CDP supervisor — dialog detection + response + cross-origin iframe eval (#14540)	2026-04-23 22:23:37 -07:00
browser_tool.py	improve(agent): guidance for plain-text URLs, subagent language/verification, hermes-config routing (#16325)	2026-04-26 20:57:19 -07:00
budget_config.py	fix: preserve existing thresholds, remove pre-read byte guard	2026-04-08 02:24:32 -07:00
checkpoint_manager.py	feat(checkpoints): auto-prune orphan and stale shadow repos at startup (#16303)	2026-04-26 19:05:52 -07:00
clarify_tool.py	refactor: add tool_error/tool_result helpers + read_raw_config, migrate 129 callsites	2026-04-07 13:36:38 -07:00
code_execution_tool.py	feat(terminal): collapse subagent task_ids to shared container (#16177)	2026-04-26 11:55:02 -07:00
credential_files.py	refactor: extract shared helpers to deduplicate repeated code patterns (#7917)	2026-04-11 13:59:52 -07:00
cronjob_tools.py	fix(cron): wire context_from through the update action	2026-04-25 04:49:28 -07:00
debug_helpers.py	refactor: codebase-wide lint cleanup — unused imports, dead code, and inefficient patterns (#5821)	2026-04-07 10:25:31 -07:00
delegate_tool.py	fix(delegate): clear acp_command when override_provider is set	2026-04-28 01:14:38 -07:00
discord_tool.py	fix(discord_tool): coerce limit parameter to int before min() call	2026-04-26 20:48:38 -07:00
env_passthrough.py	fix(env_passthrough): reject Hermes provider credentials from skill passthrough (#13523)	2026-04-21 06:14:25 -07:00
feishu_doc_tool.py	fix(feishu-comment): use get_hermes_home(); drop dead asyncio wrapper; AUTHOR_MAP	2026-04-17 19:04:11 -07:00
feishu_drive_tool.py	fix(feishu-comment): use get_hermes_home(); drop dead asyncio wrapper; AUTHOR_MAP	2026-04-17 19:04:11 -07:00
file_operations.py	feat(skills): add design-md skill for Google's DESIGN.md spec (#14876)	2026-04-23 21:51:19 -07:00
file_state.py	feat(delegate): cross-agent file state coordination for concurrent subagents (#13718)	2026-04-21 16:41:26 -07:00
file_tools.py	fix(file-tools): escalate to BLOCKED on repeated read_file dedup stubs (#16382)	2026-04-27 00:17:26 -07:00
fuzzy_match.py	fix(patch): gate 'did you mean?' to no-match + extend to v4a/skill_manage	2026-04-21 02:03:46 -07:00
homeassistant_tool.py	fix: clean up description escaping, add string-data tests	2026-04-13 04:45:07 -07:00
image_generation_tool.py	fix(image-gen): force-refresh plugin providers in long-lived sessions	2026-04-23 03:01:18 -07:00
interrupt.py	fix(interrupt): propagate to concurrent-tool workers + opt-in debug trace (#11907)	2026-04-17 20:39:25 -07:00
managed_tool_gateway.py	fix(tools): add debug logging for token refresh and tighten domain check	2026-04-02 12:40:03 +11:00
mcp_oauth.py	fix(mcp-oauth): preserve server_url path for protected-resource validation (#16031)	2026-04-26 05:43:54 -07:00
mcp_oauth_manager.py	fix(mcp-oauth): preserve server_url path for protected-resource validation (#16031)	2026-04-26 05:43:54 -07:00
mcp_tool.py	refactor(schema): consolidate nullable-union stripping in schema_sanitizer	2026-04-28 04:58:03 -07:00
memory_tool.py	refactor: consolidate symlink-safe atomic replace into shared helper	2026-04-28 04:58:22 -07:00
mixture_of_agents_tool.py	Fix (mixture_of_agents): replace deprecated Gemini model and forward max_tokens to OpenRouter (#6621)	2026-04-23 15:14:11 -07:00
neutts_synth.py	fix(tts): document NeuTTS provider and align install guidance (#1903)	2026-03-18 02:55:30 -07:00
openrouter_client.py	refactor: route ad-hoc LLM consumers through centralized provider router	2026-03-11 20:02:36 -07:00
osv_check.py	feat: OSV malware check for MCP extension packages (#5305)	2026-04-05 12:46:07 -07:00
patch_parser.py	fix(patch): gate 'did you mean?' to no-match + extend to v4a/skill_manage	2026-04-21 02:03:46 -07:00
path_security.py	refactor: extract shared helpers to deduplicate repeated code patterns (#7917)	2026-04-11 13:59:52 -07:00
process_registry.py	chore: extend [SYSTEM:→[IMPORTANT: rename + AUTHOR_MAP	2026-04-26 08:44:58 -07:00
registry.py	fix: tighten AST check to module-level only	2026-04-14 21:12:29 -07:00
rl_training_tool.py	refactor: codebase-wide lint cleanup — unused imports, dead code, and inefficient patterns (#5821)	2026-04-07 10:25:31 -07:00
schema_sanitizer.py	refactor(schema): consolidate nullable-union stripping in schema_sanitizer	2026-04-28 04:58:03 -07:00
send_message_tool.py	fix(email): add required Date header to outbound mail	2026-04-27 06:41:11 -07:00
session_search_tool.py	fix(session-search): exclude current lineage root deterministically in recent mode	2026-04-26 19:03:17 -07:00
skill_manager_tool.py	refactor: consolidate symlink-safe atomic replace into shared helper	2026-04-28 04:58:22 -07:00
skills_guard.py	feat(skills-guard): gate agent-created scanner on config.skills.guard_agent_created (default off)	2026-04-23 06:20:47 -07:00
skills_hub.py	feat(skills): install skills from a direct HTTP(S) URL (#16323)	2026-04-26 20:57:10 -07:00
skills_sync.py	refactor: consolidate symlink-safe atomic replace into shared helper	2026-04-28 04:58:22 -07:00
skills_tool.py	fix(skills): drop raw_content to avoid doubling skill payload	2026-04-24 15:15:07 -07:00
terminal_tool.py	fix(security): isolate interactive sudo password cache per session	2026-04-28 01:34:16 -07:00
tirith_security.py	fix: guard against None tirith path in security scanner	2026-04-23 03:08:53 -07:00
todo_tool.py	fix(tools): enforce ID uniqueness in TODO store during replace operations	2026-04-11 16:22:50 -07:00
tool_backend_helpers.py	fix(cli): coerce use_gateway config flags in tool routing	2026-04-26 19:02:55 -07:00
tool_output_limits.py	feat(skills): add design-md skill for Google's DESIGN.md spec (#14876)	2026-04-23 21:51:19 -07:00
tool_result_storage.py	fix(tools): neutralize shell injection in _write_to_sandbox via path quoting (#7940)	2026-04-11 14:26:11 -07:00
transcription_tools.py	fix(transcription): fall back to CPU when CUDA runtime libs are missing	2026-04-24 02:50:14 -07:00
tts_tool.py	fix(tts): use per-provider input-character caps instead of global 4000 (#13743)	2026-04-21 17:49:39 -07:00
url_safety.py	fix(security): treat quoted false as false in browser SSRF guards	2026-04-26 18:27:13 -07:00
vision_tools.py	feat(image-input): native multimodal routing based on model vision capability (#16506)	2026-04-27 06:27:59 -07:00
voice_mode.py	fix: point optional-dep install hints at the venv's python (#11938)	2026-04-17 21:16:33 -07:00
web_tools.py	✨ feat(web): expose search result limit	2026-04-28 02:09:30 -07:00
website_policy.py	refactor: codebase-wide lint cleanup — unused imports, dead code, and inefficient patterns (#5821)	2026-04-07 10:25:31 -07:00
xai_http.py	feat(xai): upgrade to Responses API, add TTS provider	2026-04-16 02:24:08 -07:00
yuanbao_tools.py	yuanbao platform (#16298)	2026-04-26 18:50:49 -07:00