fix: MCP call_tool threading.Lock held across await deadlocks event loop

[PaoloC68]

Fixes #1553

Problem

Three threading.Lock instances in helpers/mcp_handler.py are held across await calls. A threading.Lock is an OS-level blocking mutex — holding it across an await suspends the coroutine while keeping the lock acquired. Any other coroutine that tries to acquire the same lock blocks the entire event loop thread, making Agent Zero completely unresponsive to new chats while a slow MCP tool (e.g. Perplexity deep research) is running.

A secondary bug: MCPClientBase.call_tool always used the global mcp_client_tool_timeout, ignoring per-server tool_timeout overrides.

Changes

helpers/mcp_handler.py — 3 fixes, 1 file:

1. MCPServerRemote.call_tool: add asyncio.Lock instance (__async_lock), use async with self.__async_lock instead of with self.__lock. Sync methods (get_error, get_tools, has_tool, update) keep threading.Lock — correct, they're called from sync context.

2. MCPServerLocal.call_tool: same fix as above.

3. MCPConfig.call_tool: resolve the target server under threading.Lock (sync, instant list lookup), release the lock, then await server.call_tool() outside it. This is the outermost and most impactful site — it's the dispatcher that all MCP tool calls pass through.

4. MCPClientBase.call_tool: tool_timeout = self.server.tool_timeout or set["mcp_client_tool_timeout"] — per-server override now takes precedence over global default.

Tests

Verified on a live Agent Zero instance (Proxmox LXC, Docker):

• Triggered Perplexity deep research (1200s timeout configured)
• Opened new chat while research was running → responded immediately (previously: no response until timeout)
• Research completed successfully after ~3 minutes
• No regressions observed on sqlite, sequential-thinking, deep-wiki MCP servers

Existing test suite: pytest — no new failures introduced.

Notes

• No new dependencies
• No breaking changes
• threading.Lock is intentionally kept for all sync accessors — only the async call_tool path is changed