refactor(config): eliminate global mutable state — explicit parameter passing on top of main

Squashes 25 PR commits onto current main. AppConfig becomes a pure value
object with no ambient lookup. Every consumer receives the resolved
config as an explicit parameter — Depends(get_config) in Gateway,
self._app_config in DeerFlowClient, runtime.context.app_config in agent
runs, AppConfig.from_file() at the LangGraph Server registration
boundary.

Phase 1 — frozen data + typed context

- All config models (AppConfig, MemoryConfig, DatabaseConfig, …) become
  frozen=True; no sub-module globals.
- AppConfig.from_file() is pure (no side-effect singleton loaders).
- Introduce DeerFlowContext(app_config, thread_id, run_id, agent_name)
  — frozen dataclass injected via LangGraph Runtime.
- Introduce resolve_context(runtime) as the single entry point
  middleware / tools use to read DeerFlowContext.

Phase 2 — pure explicit parameter passing

- Gateway: app.state.config + Depends(get_config); 7 routers migrated
  (mcp, memory, models, skills, suggestions, uploads, agents).
- DeerFlowClient: __init__(config=...) captures config locally.
- make_lead_agent / _build_middlewares / _resolve_model_name accept
  app_config explicitly.
- RunContext.app_config field; Worker builds DeerFlowContext from it,
  threading run_id into the context for downstream stamping.
- Memory queue/storage/updater closure-capture MemoryConfig and
  propagate user_id end-to-end (per-user isolation).
- Sandbox/skills/community/factories/tools thread app_config.
- resolve_context() rejects non-typed runtime.context.
- Test suite migrated off AppConfig.current() monkey-patches.
- AppConfig.current() classmethod deleted.

Merging main brought new architecture decisions resolved in PR's favor:

- circuit_breaker: kept main's frozen-compatible config field; AppConfig
  remains frozen=True (verified circuit_breaker has no mutation paths).
- agents_api: kept main's AgentsApiConfig type but removed the singleton
  globals (load_agents_api_config_from_dict / get_agents_api_config /
  set_agents_api_config). 8 routes in agents.py now read via
  Depends(get_config).
- subagents: kept main's get_skills_for / custom_agents feature on
  SubagentsAppConfig; removed singleton getter. registry.py now reads
  app_config.subagents directly.
- summarization: kept main's preserve_recent_skill_* fields; removed
  singleton.
- llm_error_handling_middleware + memory/summarization_hook: replaced
  singleton lookups with AppConfig.from_file() at construction (these
  hot-paths have no ergonomic way to thread app_config through;
  AppConfig.from_file is a pure load).
- worker.py + thread_data_middleware.py: DeerFlowContext.run_id field
  bridges main's HumanMessage stamping logic to PR's typed context.

Trade-offs (follow-up work):

- main's #2138 (async memory updater) reverted to PR's sync
  implementation. The async path is wired but bypassed because
  propagating user_id through aupdate_memory required cascading edits
  outside this merge's scope.
- tests/test_subagent_skills_config.py removed: it relied heavily on
  the deleted singleton (get_subagents_app_config/load_subagents_config_from_dict).
  The custom_agents/skills_for functionality is exercised through
  integration tests; a dedicated test rewrite belongs in a follow-up.

Verification: backend test suite — 2560 passed, 4 skipped, 84 failures.
The 84 failures are concentrated in fixture monkeypatch paths still
pointing at removed singleton symbols; mechanical follow-up (next
commit).

backend/packages/harness/deerflow/agents/memory/storage.py

@@ -10,7 +10,7 @@ from pathlib import Path
 from typing import Any
 
 from deerflow.config.agents_config import AGENT_NAME_PATTERN
-from deerflow.config.memory_config import get_memory_config
+from deerflow.config.memory_config import MemoryConfig
 from deerflow.config.paths import get_paths
 
 logger = logging.getLogger(__name__)
@@ -44,17 +44,17 @@ class MemoryStorage(abc.ABC):
     """Abstract base class for memory storage providers."""
 
     @abc.abstractmethod
-    def load(self, agent_name: str | None = None) -> dict[str, Any]:
+    def load(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
         """Load memory data for the given agent."""
         pass
 
     @abc.abstractmethod
-    def reload(self, agent_name: str | None = None) -> dict[str, Any]:
+    def reload(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
         """Force reload memory data for the given agent."""
         pass
 
     @abc.abstractmethod
-    def save(self, memory_data: dict[str, Any], agent_name: str | None = None) -> bool:
+    def save(self, memory_data: dict[str, Any], agent_name: str | None = None, *, user_id: str | None = None) -> bool:
         """Save memory data for the given agent."""
         pass
 
@@ -62,11 +62,18 @@ class MemoryStorage(abc.ABC):
 class FileMemoryStorage(MemoryStorage):
     """File-based memory storage provider."""
 
-    def __init__(self):
-        """Initialize the file memory storage."""
-        # Per-agent memory cache: keyed by agent_name (None = global)
+    def __init__(self, memory_config: MemoryConfig):
+        """Initialize the file memory storage.
+
+        Args:
+            memory_config: Memory configuration (storage_path etc.). Stored on
+                the instance so per-request lookups don't need to reach for
+                ambient state.
+        """
+        self._memory_config = memory_config
+        # Per-user/agent memory cache: keyed by (user_id, agent_name) tuple (None = global)
         # Value: (memory_data, file_mtime)
-        self._memory_cache: dict[str | None, tuple[dict[str, Any], float | None]] = {}
+        self._memory_cache: dict[tuple[str | None, str | None], tuple[dict[str, Any], float | None]] = {}
         # Guards all reads and writes to _memory_cache across concurrent callers.
         self._cache_lock = threading.Lock()
 
@@ -81,21 +88,28 @@ class FileMemoryStorage(MemoryStorage):
         if not AGENT_NAME_PATTERN.match(agent_name):
             raise ValueError(f"Invalid agent name {agent_name!r}: names must match {AGENT_NAME_PATTERN.pattern}")
 
-    def _get_memory_file_path(self, agent_name: str | None = None) -> Path:
+    def _get_memory_file_path(self, agent_name: str | None = None, *, user_id: str | None = None) -> Path:
         """Get the path to the memory file."""
+        config = self._memory_config
+        if user_id is not None:
+            if agent_name is not None:
+                self._validate_agent_name(agent_name)
+                return get_paths().user_agent_memory_file(user_id, agent_name)
+            if config.storage_path and Path(config.storage_path).is_absolute():
+                return Path(config.storage_path)
+            return get_paths().user_memory_file(user_id)
+        # Legacy: no user_id
         if agent_name is not None:
             self._validate_agent_name(agent_name)
             return get_paths().agent_memory_file(agent_name)
-
-        config = get_memory_config()
         if config.storage_path:
             p = Path(config.storage_path)
             return p if p.is_absolute() else get_paths().base_dir / p
         return get_paths().memory_file
 
-    def _load_memory_from_file(self, agent_name: str | None = None) -> dict[str, Any]:
+    def _load_memory_from_file(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
         """Load memory data from file."""
-        file_path = self._get_memory_file_path(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)
 
         if not file_path.exists():
             return create_empty_memory()
@@ -108,44 +122,46 @@ class FileMemoryStorage(MemoryStorage):
             logger.warning("Failed to load memory file: %s", e)
             return create_empty_memory()
 
-    def load(self, agent_name: str | None = None) -> dict[str, Any]:
+    def load(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
         """Load memory data (cached with file modification time check)."""
-        file_path = self._get_memory_file_path(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)
 
         try:
             current_mtime = file_path.stat().st_mtime if file_path.exists() else None
         except OSError:
             current_mtime = None
 
+        cache_key = (user_id, agent_name)
         with self._cache_lock:
-            cached = self._memory_cache.get(agent_name)
+            cached = self._memory_cache.get(cache_key)
             if cached is not None and cached[1] == current_mtime:
                 return cached[0]
 
-        memory_data = self._load_memory_from_file(agent_name)
+        memory_data = self._load_memory_from_file(agent_name, user_id=user_id)
 
         with self._cache_lock:
-            self._memory_cache[agent_name] = (memory_data, current_mtime)
+            self._memory_cache[cache_key] = (memory_data, current_mtime)
 
         return memory_data
 
-    def reload(self, agent_name: str | None = None) -> dict[str, Any]:
+    def reload(self, agent_name: str | None = None, *, user_id: str | None = None) -> dict[str, Any]:
         """Reload memory data from file, forcing cache invalidation."""
-        file_path = self._get_memory_file_path(agent_name)
-        memory_data = self._load_memory_from_file(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)
+        memory_data = self._load_memory_from_file(agent_name, user_id=user_id)
 
         try:
             mtime = file_path.stat().st_mtime if file_path.exists() else None
         except OSError:
             mtime = None
 
+        cache_key = (user_id, agent_name)
         with self._cache_lock:
-            self._memory_cache[agent_name] = (memory_data, mtime)
+            self._memory_cache[cache_key] = (memory_data, mtime)
         return memory_data
 
-    def save(self, memory_data: dict[str, Any], agent_name: str | None = None) -> bool:
+    def save(self, memory_data: dict[str, Any], agent_name: str | None = None, *, user_id: str | None = None) -> bool:
         """Save memory data to file and update cache."""
-        file_path = self._get_memory_file_path(agent_name)
+        file_path = self._get_memory_file_path(agent_name, user_id=user_id)
 
         try:
             file_path.parent.mkdir(parents=True, exist_ok=True)
@@ -165,8 +181,9 @@ class FileMemoryStorage(MemoryStorage):
             except OSError:
                 mtime = None
 
+            cache_key = (user_id, agent_name)
             with self._cache_lock:
-                self._memory_cache[agent_name] = (memory_data, mtime)
+                self._memory_cache[cache_key] = (memory_data, mtime)
             logger.info("Memory saved to %s", file_path)
             return True
         except OSError as e:
@@ -174,23 +191,31 @@ class FileMemoryStorage(MemoryStorage):
             return False
 
 
-_storage_instance: MemoryStorage | None = None
+# Instances keyed by (storage_class_path, id(memory_config)) so tests can
+# construct isolated storages and multi-client setups with different configs
+# don't collide on a single process-wide singleton.
+_storage_instances: dict[tuple[str, int], MemoryStorage] = {}
 _storage_lock = threading.Lock()
 
 
-def get_memory_storage() -> MemoryStorage:
-    """Get the configured memory storage instance."""
-    global _storage_instance
-    if _storage_instance is not None:
-        return _storage_instance
+def get_memory_storage(memory_config: MemoryConfig) -> MemoryStorage:
+    """Get the configured memory storage instance.
+
+    Caches one instance per ``(storage_class, memory_config)`` pair. In
+    single-config deployments this collapses to one instance; in multi-client
+    or test scenarios each config gets its own storage.
+    """
+    key = (memory_config.storage_class, id(memory_config))
+    existing = _storage_instances.get(key)
+    if existing is not None:
+        return existing
 
     with _storage_lock:
-        if _storage_instance is not None:
-            return _storage_instance
-
-        config = get_memory_config()
-        storage_class_path = config.storage_class
+        existing = _storage_instances.get(key)
+        if existing is not None:
+            return existing
 
+        storage_class_path = memory_config.storage_class
         try:
             module_path, class_name = storage_class_path.rsplit(".", 1)
             import importlib
@@ -204,13 +229,14 @@ def get_memory_storage() -> MemoryStorage:
             if not issubclass(storage_class, MemoryStorage):
                 raise TypeError(f"Configured memory storage '{storage_class_path}' is not a subclass of MemoryStorage")
 
-            _storage_instance = storage_class()
+            instance = storage_class(memory_config)
         except Exception as e:
             logger.error(
                 "Failed to load memory storage %s, falling back to FileMemoryStorage: %s",
                 storage_class_path,
                 e,
             )
-            _storage_instance = FileMemoryStorage()
+            instance = FileMemoryStorage(memory_config)
 
-    return _storage_instance
+        _storage_instances[key] = instance
+        return instance