chore(docker): Refactor sandbox state management and improve Docker integration (#1068)

* Refactor sandbox state management and improve Docker integration

- Removed FileSandboxStateStore and SandboxStateStore classes for a cleaner architecture.
- Enhanced LocalContainerBackend to handle port allocation retries and introduced environment variable support for sandbox host configuration.
- Updated Paths class to include host_base_dir for Docker volume mounts and ensured proper permissions for sandbox directories.
- Modified ExtensionsConfig to improve error handling when loading configuration files and adjusted environment variable resolution.
- Updated sandbox configuration to include a replicas option for managing concurrent sandbox containers.
- Improved logging and context management in SandboxMiddleware for better sandbox lifecycle handling.
- Enhanced network port allocation logic to bind to 0.0.0.0 for compatibility with Docker.
- Updated Docker Compose files to ensure proper volume management and environment variable configuration.
- Created scripts to ensure necessary configuration files are present before starting services.
- Cleaned up unused MCP server configurations in extensions_config.example.json.

* Address Copilot review suggestions from PR #1068 (#9)

---------

Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>

backend/src/sandbox/tools.py

@@ -135,6 +135,8 @@ def sandbox_from_runtime(runtime: ToolRuntime[ContextT, ThreadState] | None = No
     sandbox = get_sandbox_provider().get(sandbox_id)
     if sandbox is None:
         raise SandboxNotFoundError(f"Sandbox with ID '{sandbox_id}' not found", sandbox_id=sandbox_id)
+
+    runtime.context["sandbox_id"] = sandbox_id  # Ensure sandbox_id is in context for downstream use
     return sandbox
 
 
@@ -169,6 +171,7 @@ def ensure_sandbox_initialized(runtime: ToolRuntime[ContextT, ThreadState] | Non
         if sandbox_id is not None:
             sandbox = get_sandbox_provider().get(sandbox_id)
             if sandbox is not None:
+                runtime.context["sandbox_id"] = sandbox_id  # Ensure sandbox_id is in context for releasing in after_agent
                 return sandbox
             # Sandbox was released, fall through to acquire new one
 
@@ -188,6 +191,7 @@ def ensure_sandbox_initialized(runtime: ToolRuntime[ContextT, ThreadState] | Non
     if sandbox is None:
         raise SandboxNotFoundError("Sandbox not found after acquisition", sandbox_id=sandbox_id)
 
+    runtime.context["sandbox_id"] = sandbox_id  # Ensure sandbox_id is in context for releasing in after_agent
     return sandbox