refactor(config): eliminate global mutable state, wire DeerFlowContext into runtime

- Freeze all config models (AppConfig + 15 sub-configs) with frozen=True
- Purify from_file() — remove 9 load_*_from_dict() side-effect calls
- Replace mtime/reload/push/pop machinery with single ContextVar + init_app_config()
- Delete 10 sub-module globals and their getters/setters/loaders
- Migrate 50+ consumers from get_*_config() to get_app_config().xxx

- Expand DeerFlowContext: app_config + thread_id + agent_name (frozen dataclass)
- Wire into Gateway runtime (worker.py) and DeerFlowClient via context= parameter
- Remove sandbox_id from runtime.context — flows through ThreadState.sandbox only
- Middleware/tools access runtime.context directly via Runtime[DeerFlowContext] generic
- resolve_context() retained at server entry points for LangGraph Server fallback

backend/packages/harness/deerflow/skills/manager.py

@@ -9,7 +9,7 @@ from datetime import UTC, datetime
 from pathlib import Path
 from typing import Any
 
-from deerflow.config import get_app_config
+from deerflow.config.app_config import AppConfig
 from deerflow.skills.loader import load_skills
 from deerflow.skills.validation import _validate_skill_frontmatter
 
@@ -21,7 +21,7 @@ _SKILL_NAME_PATTERN = re.compile(r"^[a-z0-9]+(?:-[a-z0-9]+)*$")
 
 
 def get_skills_root_dir() -> Path:
-    return get_app_config().skills.get_skills_path()
+    return AppConfig.current().skills.get_skills_path()
 
 
 def get_public_skills_dir() -> Path: