fix(mcp): fix read tool to work with 2 arguments for agent compatibility

Fixed the read tool and all filesystem tools to properly work with agents
that call them with 2 positional arguments (ctx, file_path).

Changes:
- Updated auto_timeout decorator to handle instance methods properly
  - Changed wrapper signature to accept *args to handle both methods and functions
  - Properly extracts ctx from correct position (second arg for methods, first for functions)

- Made set_tool_context_info async and updated all callers
  - Changed from sync to async def
  - Added await for all calls to set_tool_context_info()
  - Fixed in: read, write, edit, multi_edit, ast_tool, rules_tool, symbols_tool

- Tests now pass without warnings
- Both run() and call() methods work correctly
- Agents can now properly invoke read tool with expected signature

Version: 0.9.1 -> 0.9.2

pkg/hanzo-mcp/hanzo_mcp/tools/common/auto_timeout.py

@@ -128,47 +128,67 @@ class MCPToolTimeoutManager:
 
 def with_auto_timeout(tool_name: str, timeout_manager: Optional[MCPToolTimeoutManager] = None):
     """Decorator to add automatic timeout and backgrounding to MCP tools.
-    
+
     Args:
         tool_name: Name of the tool (for logging and process tracking)
         timeout_manager: Optional timeout manager instance
-        
+
     Returns:
         Decorator function
     """
     if timeout_manager is None:
         timeout_manager = MCPToolTimeoutManager()
-    
+
     def decorator(func: Callable[..., Awaitable[Any]]) -> Callable[..., Awaitable[Any]]:
         @functools.wraps(func)
-        async def wrapper(ctx: MCPContext, **params: Any) -> Any:
+        async def wrapper(*args: Any, **params: Any) -> Any:
+            # Handle both method calls (with self) and function calls
+            # For methods: args = (self, ctx), For functions: args = (ctx,)
+            if len(args) >= 2:
+                # Method call: self, ctx, **params
+                self_or_ctx = args[0]
+                ctx = args[1]
+                call_func = lambda: func(self_or_ctx, ctx, **params)
+            elif len(args) == 1:
+                # Function call: ctx, **params
+                ctx = args[0]
+                call_func = lambda: func(ctx, **params)
+            else:
+                raise TypeError(f"Expected at least 1 argument (ctx), got {len(args)}")
+
             # Fast path for tests - skip timeout logic
             if os.getenv("HANZO_MCP_FAST_TESTS") == "1":
-                return await func(ctx, **params)
-            
+                return await call_func()
+
             # Get tool-specific timeout
             tool_timeout = timeout_manager._get_timeout_for_tool(tool_name)
-            
+
             # Create task for the tool execution
-            tool_task = asyncio.create_task(func(ctx, **params))
-            
+            tool_task = asyncio.create_task(call_func())
+
             try:
                 # Wait for completion with timeout
                 result = await asyncio.wait_for(tool_task, timeout=tool_timeout)
                 return result
-                
+
             except asyncio.TimeoutError:
                 # Tool timed out - background it
                 process_id = f"{tool_name}_{uuid.uuid4().hex[:8]}"
                 log_file = timeout_manager.process_manager.create_log_file(process_id)
-                
-                # Start background execution
+
+                # Start background execution (need to reconstruct the call)
+                async def background_call():
+                    if len(args) >= 2:
+                        return await func(args[0], ctx, **params)
+                    else:
+                        return await func(ctx, **params)
+
                 asyncio.create_task(
                     timeout_manager._background_tool_execution(
-                        func, tool_name, ctx, process_id, log_file, **params
+                        background_call, tool_name, ctx, process_id, log_file, **params
                     )
                 )
-                
+
                 # Return backgrounding message
                 timeout_formatted = format_timeout(tool_timeout)
                 return (
@@ -179,7 +199,7 @@ def with_auto_timeout(tool_name: str, timeout_manager: Optional[MCPToolTimeoutMa
                     f"Use 'process --action kill --id {process_id}' to cancel\\n\\n"
                     f"The {tool_name} operation is continuing in the background..."
                 )
-                
+
         return wrapper
     return decorator
 

pkg/hanzo-mcp/hanzo_mcp/tools/filesystem/ast_tool.py

@@ -114,7 +114,7 @@ Searches code structure intelligently, understanding syntax and providing semant
             Tool result
         """
         tool_ctx = self.create_tool_context(ctx)
-        self.set_tool_context_info(tool_ctx)
+        await self.set_tool_context_info(tool_ctx)
 
         # Extract parameters
         pattern: Pattern = params["pattern"]

pkg/hanzo-mcp/hanzo_mcp/tools/filesystem/base.py

@@ -104,10 +104,10 @@ class FilesystemBaseTool(FileSystemTool, ABC):
         tool_ctx = create_tool_context(ctx)
         return tool_ctx
 
-    def set_tool_context_info(self, tool_ctx: ToolContext) -> None:
+    async def set_tool_context_info(self, tool_ctx: ToolContext) -> None:
         """Set the tool info on the context.
 
         Args:
             tool_ctx: Tool context
         """
-        tool_ctx.set_tool_info(self.name)
+        await tool_ctx.set_tool_info(self.name)

pkg/hanzo-mcp/hanzo_mcp/tools/filesystem/edit.py

@@ -108,7 +108,7 @@ Usage:
             Tool result
         """
         tool_ctx = self.create_tool_context(ctx)
-        self.set_tool_context_info(tool_ctx)
+        await self.set_tool_context_info(tool_ctx)
 
         # Extract parameters
         file_path: FilePath = params["file_path"]

pkg/hanzo-mcp/hanzo_mcp/tools/filesystem/multi_edit.py

@@ -152,7 +152,7 @@ If you want to create a new file, use:
             Tool result
         """
         tool_ctx = self.create_tool_context(ctx)
-        self.set_tool_context_info(tool_ctx)
+        await self.set_tool_context_info(tool_ctx)
 
         # Extract parameters
         file_path: FilePath = params["file_path"]

pkg/hanzo-mcp/hanzo_mcp/tools/filesystem/read.py

@@ -94,8 +94,6 @@ Usage:
 
     @override
     @auto_timeout("read")
-
-
     async def call(
         self,
         ctx: MCPContext,
@@ -111,7 +109,7 @@ Usage:
             Tool result
         """
         tool_ctx = self.create_tool_context(ctx)
-        self.set_tool_context_info(tool_ctx)
+        await self.set_tool_context_info(tool_ctx)
 
         # Extract parameters
         file_path = params.get("file_path")

pkg/hanzo-mcp/hanzo_mcp/tools/filesystem/rules_tool.py

@@ -94,7 +94,7 @@ understand project-specific requirements and preferences."""
             Tool result
         """
         tool_ctx = self.create_tool_context(ctx)
-        self.set_tool_context_info(tool_ctx)
+        await self.set_tool_context_info(tool_ctx)
 
         # Extract parameters
         search_path = params.get("path", ".")

pkg/hanzo-mcp/hanzo_mcp/tools/filesystem/symbols_tool.py

@@ -138,7 +138,7 @@ Finds code structures (functions, classes, methods) with full context."""
     ) -> str:
         """Execute symbols operation."""
         tool_ctx = self.create_tool_context(ctx)
-        self.set_tool_context_info(tool_ctx)
+        await self.set_tool_context_info(tool_ctx)
 
         # Extract action
         action = params.get("action", "search")

pkg/hanzo-mcp/hanzo_mcp/tools/filesystem/write.py

@@ -92,7 +92,7 @@ Usage:
             Tool result
         """
         tool_ctx = self.create_tool_context(ctx)
-        self.set_tool_context_info(tool_ctx)
+        await self.set_tool_context_info(tool_ctx)
 
         # Extract parameters
         file_path: FilePath = params["file_path"]

pkg/hanzo-mcp/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "hanzo-mcp"
-version = "0.9.1"
+version = "0.9.2"
 description = "The Zen of Hanzo MCP: One server to rule them all. The ultimate MCP that orchestrates all others."
 readme = "README.md"
 requires-python = ">=3.12"

pkg/hanzo-mcp/uv.lock

@@ -1003,7 +1003,7 @@ wheels = [
 
 [[package]]
 name = "hanzo-mcp"
-version = "0.8.14"
+version = "0.9.1"
 source = { editable = "." }
 dependencies = [
     { name = "bashlex" },