refactor(harness): remove old persistence layer from deerflow package

Remove the following deprecated modules:
- deerflow/persistence/ - old SQL persistence models and repositories
- deerflow/config/checkpointer_config.py - checkpointer configuration
- deerflow/config/database_config.py - database configuration
- deerflow/runtime/checkpointer/ - checkpointer providers
- deerflow/runtime/store/ - store providers
- deerflow/runtime/events/ - event store implementations
- deerflow/runtime/journal.py - run journal

These components are replaced by the new storage layer in app/infra/.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

backend/packages/harness/deerflow/config/checkpointer_config.py

@@ -1,46 +0,0 @@
-"""Configuration for LangGraph checkpointer."""
-
-from typing import Literal
-
-from pydantic import BaseModel, Field
-
-CheckpointerType = Literal["memory", "sqlite", "postgres"]
-
-
-class CheckpointerConfig(BaseModel):
-    """Configuration for LangGraph state persistence checkpointer."""
-
-    type: CheckpointerType = Field(
-        description="Checkpointer backend type. "
-        "'memory' is in-process only (lost on restart). "
-        "'sqlite' persists to a local file (requires langgraph-checkpoint-sqlite). "
-        "'postgres' persists to PostgreSQL (requires langgraph-checkpoint-postgres)."
-    )
-    connection_string: str | None = Field(
-        default=None,
-        description="Connection string for sqlite (file path) or postgres (DSN). "
-        "Required for sqlite and postgres types. "
-        "For sqlite, use a file path like '.deer-flow/checkpoints.db' or ':memory:' for in-memory. "
-        "For postgres, use a DSN like 'postgresql://user:pass@localhost:5432/db'.",
-    )
-
-
-# Global configuration instance — None means no checkpointer is configured.
-_checkpointer_config: CheckpointerConfig | None = None
-
-
-def get_checkpointer_config() -> CheckpointerConfig | None:
-    """Get the current checkpointer configuration, or None if not configured."""
-    return _checkpointer_config
-
-
-def set_checkpointer_config(config: CheckpointerConfig | None) -> None:
-    """Set the checkpointer configuration."""
-    global _checkpointer_config
-    _checkpointer_config = config
-
-
-def load_checkpointer_config_from_dict(config_dict: dict) -> None:
-    """Load checkpointer configuration from a dictionary."""
-    global _checkpointer_config
-    _checkpointer_config = CheckpointerConfig(**config_dict)

backend/packages/harness/deerflow/config/database_config.py

@@ -1,102 +0,0 @@
-"""Unified database backend configuration.
-
-Controls BOTH the LangGraph checkpointer and the DeerFlow application
-persistence layer (runs, threads metadata, users, etc.). The user
-configures one backend; the system handles physical separation details.
-
-SQLite mode: checkpointer and app share a single .db file
-({sqlite_dir}/deerflow.db) with WAL journal mode enabled on every
-connection. WAL allows concurrent readers and a single writer without
-blocking, making a unified file safe for both workloads.  Writers
-that contend for the lock wait via the default 5-second sqlite3
-busy timeout rather than failing immediately.
-
-Postgres mode: both use the same database URL but maintain independent
-connection pools with different lifecycles.
-
-Memory mode: checkpointer uses MemorySaver, app uses in-memory stores.
-No database is initialized.
-
-Sensitive values (postgres_url) should use $VAR syntax in config.yaml
-to reference environment variables from .env:
-
-    database:
-      backend: postgres
-      postgres_url: $DATABASE_URL
-
-The $VAR resolution is handled by AppConfig.resolve_env_variables()
-before this config is instantiated -- DatabaseConfig itself does not
-need to do any environment variable processing.
-"""
-
-from __future__ import annotations
-
-import os
-from typing import Literal
-
-from pydantic import BaseModel, Field
-
-
-class DatabaseConfig(BaseModel):
-    backend: Literal["memory", "sqlite", "postgres"] = Field(
-        default="memory",
-        description=("Storage backend for both checkpointer and application data. 'memory' for development (no persistence across restarts), 'sqlite' for single-node deployment, 'postgres' for production multi-node deployment."),
-    )
-    sqlite_dir: str = Field(
-        default=".deer-flow/data",
-        description=("Directory for the SQLite database file. Both checkpointer and application data share {sqlite_dir}/deerflow.db."),
-    )
-    postgres_url: str = Field(
-        default="",
-        description=(
-            "PostgreSQL connection URL, shared by checkpointer and app. "
-            "Use $DATABASE_URL in config.yaml to reference .env. "
-            "Example: postgresql://user:pass@host:5432/deerflow "
-            "(the +asyncpg driver suffix is added automatically where needed)."
-        ),
-    )
-    echo_sql: bool = Field(
-        default=False,
-        description="Echo all SQL statements to log (debug only).",
-    )
-    pool_size: int = Field(
-        default=5,
-        description="Connection pool size for the app ORM engine (postgres only).",
-    )
-
-    # -- Derived helpers (not user-configured) --
-
-    @property
-    def _resolved_sqlite_dir(self) -> str:
-        """Resolve sqlite_dir to an absolute path (relative to CWD)."""
-        from pathlib import Path
-
-        return str(Path(self.sqlite_dir).resolve())
-
-    @property
-    def sqlite_path(self) -> str:
-        """Unified SQLite file path shared by checkpointer and app."""
-        return os.path.join(self._resolved_sqlite_dir, "deerflow.db")
-
-    # Backward-compatible aliases
-    @property
-    def checkpointer_sqlite_path(self) -> str:
-        """SQLite file path for the LangGraph checkpointer (alias for sqlite_path)."""
-        return self.sqlite_path
-
-    @property
-    def app_sqlite_path(self) -> str:
-        """SQLite file path for application ORM data (alias for sqlite_path)."""
-        return self.sqlite_path
-
-    @property
-    def app_sqlalchemy_url(self) -> str:
-        """SQLAlchemy async URL for the application ORM engine."""
-        if self.backend == "sqlite":
-            return f"sqlite+aiosqlite:///{self.sqlite_path}"
-        if self.backend == "postgres":
-            url = self.postgres_url
-            if url.startswith("postgresql://"):
-                url = url.replace("postgresql://", "postgresql+asyncpg://", 1)
-            return url
-        raise ValueError(f"No SQLAlchemy URL for backend={self.backend!r}")