refactor: replace CommandExecutor with BashSessionExecutor for persistent shell execution

BREAKING CHANGE: Removed CommandExecutor in favor of BashSessionExecutor. All shell tools now use persistent sessions by default. The run_command tool interface has been updated to support session-based execution with new parameters (is_input, blocking). CommandResult now includes additional metadata about the execution context.

Author: SDGLBL

mcp_claude_code/server.py

@@ -8,7 +8,6 @@
 from mcp_claude_code.tools import register_all_tools
 from mcp_claude_code.tools.common.context import DocumentContext
 from mcp_claude_code.tools.common.permissions import PermissionManager
-from mcp_claude_code.tools.shell.command_executor import CommandExecutor
 
 
 @final

mcp_claude_code/tools/__init__.py

@@ -19,7 +19,6 @@
 from mcp_claude_code.tools.filesystem import register_filesystem_tools
 from mcp_claude_code.tools.jupyter import register_jupyter_tools
 from mcp_claude_code.tools.shell import register_shell_tools
-from mcp_claude_code.tools.shell.command_executor import CommandExecutor
 from mcp_claude_code.tools.todo import register_todo_tools
 
 
@@ -77,7 +76,6 @@ def register_all_tools(
             mcp_server,
             document_context,
             permission_manager,
-            CommandExecutor(permission_manager),
             agent_model=agent_model,
             agent_max_tokens=agent_max_tokens,
             agent_api_key=agent_api_key,

mcp_claude_code/tools/agent/__init__.py

@@ -10,14 +10,12 @@
 from mcp_claude_code.tools.common.base import BaseTool, ToolRegistry
 from mcp_claude_code.tools.common.context import DocumentContext
 from mcp_claude_code.tools.common.permissions import PermissionManager
-from mcp_claude_code.tools.shell.command_executor import CommandExecutor
 
 
 def register_agent_tools(
     mcp_server: FastMCP,
     document_context: DocumentContext,
     permission_manager: PermissionManager,
-    command_executor: CommandExecutor,
     agent_model: str | None = None,
     agent_max_tokens: int | None = None,
     agent_api_key: str | None = None,
@@ -31,7 +29,6 @@ def register_agent_tools(
         mcp_server: The FastMCP server instance
         document_context: Document context for tracking file contents
         permission_manager: Permission manager for access control
-        command_executor: Command executor for running shell commands
         agent_model: Optional model name for agent tool in LiteLLM format
         agent_max_tokens: Optional maximum tokens for agent responses
         agent_api_key: Optional API key for the LLM provider
@@ -46,7 +43,6 @@ def register_agent_tools(
     agent_tool = AgentTool(
         document_context=document_context,
         permission_manager=permission_manager,
-        command_executor=command_executor,
         model=agent_model,
         api_key=agent_api_key,
         base_url=agent_base_url,

mcp_claude_code/tools/agent/agent_tool.py

@@ -36,7 +36,6 @@
 from mcp_claude_code.tools.common.permissions import PermissionManager
 from mcp_claude_code.tools.filesystem import get_read_only_filesystem_tools
 from mcp_claude_code.tools.jupyter import get_read_only_jupyter_tools
-from mcp_claude_code.tools.shell.command_executor import CommandExecutor
 
 Prompt = Annotated[
     str,
@@ -107,7 +106,6 @@ def __init__(
         self,
         document_context: DocumentContext,
         permission_manager: PermissionManager,
-        command_executor: CommandExecutor,
         model: str | None = None,
         api_key: str | None = None,
         base_url: str | None = None,
@@ -120,7 +118,6 @@ def __init__(
         Args:
             document_context: Document context for tracking file contents
             permission_manager: Permission manager for access control
-            command_executor: Command executor for running shell commands
             model: Optional model name override in LiteLLM format (e.g., "openai/gpt-4o")
             api_key: Optional API key for the model provider
             base_url: Optional base URL for the model provider API endpoint
@@ -130,7 +127,6 @@ def __init__(
         """
         self.document_context = document_context
         self.permission_manager = permission_manager
-        self.command_executor = command_executor
         self.model_override = model
         self.api_key_override = api_key
         self.base_url_override = base_url
@@ -390,17 +386,10 @@ async def _execute_agent_with_tools(
 
         # If we've reached the limit, add a warning and get final response
         if total_tool_use_count >= max_tool_uses or iteration_count >= max_iterations:
-            limit_ = (
-                "tool usage" if total_tool_use_count >= max_tool_uses else "iterations"
-            )
-            await tool_ctx.info(
-                f"Reached maximum {limit_type} limit. Getting final response."
-            )
-
             messages.append(
                 {
                     "role": "system",
-                    "content": f"You have reached the maximum number of {limit_type}. Please provide your final response.",
+                    "content": "You have reached the maximum iteration. Please provide your final response.",
                 }
             )
 
@@ -416,7 +405,7 @@ async def _execute_agent_with_tools(
 
                 return (
                     final_response.choices[0].message.content
-                    or f"Agent reached {limit_type} limit without a response."
+                    or "Agent reached max iteration limit without a response."
                 )  # pyright: ignore
             except Exception as e:
                 await tool_ctx.error(f"Error in final model call: {str(e)}")

mcp_claude_code/tools/filesystem/grep.py

@@ -14,7 +14,6 @@
 
 from fastmcp import Context as MCPContext
 from fastmcp import FastMCP
-from fastmcp.server.dependencies import get_context
 from pydantic import Field
 
 from mcp_claude_code.tools.common.context import ToolContext
@@ -37,10 +36,10 @@
 ]
 
 Include = Annotated[
-    str | None,
+    str,
     Field(
         description='File pattern to include in the search (e.g. "*.js", "*.{ts,tsx}")',
-        default=None,
+        default="*",
     ),
 ]
 
@@ -387,7 +386,7 @@ async def call(
         pattern = params.get("pattern")
         path: str = params.get("path", ".")
         # Support both 'include' and legacy 'file_pattern' parameter for backward compatibility
-        include: str = params.get("include") or params.get("file_pattern", "*")
+        include: str = params.get("include")
 
         # Validate required parameters for direct calls (not through MCP framework)
         if pattern is None:

mcp_claude_code/tools/jupyter/notebook_edit.py

@@ -38,10 +38,10 @@
 ]
 
 CellType = Annotated[
-    Literal["code", "markdown"] | None,
+    Literal["code", "markdown"],
     Field(
         description="The of the cell (code or markdown). If not specified, it defaults to the current cell type. If using edit_mode=insert, this is required.",
-        default=None,
+        default="code",
     ),
 ]
 

mcp_claude_code/tools/shell/__init__.py

@@ -7,13 +7,13 @@
 
 from mcp_claude_code.tools.common.base import BaseTool, ToolRegistry
 from mcp_claude_code.tools.common.permissions import PermissionManager
-from mcp_claude_code.tools.shell.command_executor import CommandExecutor
+from mcp_claude_code.tools.shell.bash_session_executor import BashSessionExecutor
 from mcp_claude_code.tools.shell.run_command import RunCommandTool
 
 # Export all tool classes
 __all__ = [
     "RunCommandTool",
-    "CommandExecutor",
+    "BashSessionExecutor",
     "get_shell_tools",
     "register_shell_tools",
 ]
@@ -31,7 +31,7 @@ def get_shell_tools(
         List of shell tool instances
     """
     # Initialize the command executor
-    command_executor = CommandExecutor(permission_manager)
+    command_executor = BashSessionExecutor(permission_manager)
 
     return [
         RunCommandTool(permission_manager, command_executor),