*: carefully check and fix to make baby happy

.pre-commit-config.yaml

@@ -14,6 +14,12 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
+  - repo: https://github.com/jendrikseipp/vulture
+    rev: "v2.14"
+    hooks:
+      - id: vulture
+        stages: [manual]
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: "v0.11.5"
     hooks:

Makefile

@@ -13,6 +13,11 @@ check: ## Run code quality tools.
 	@echo "🚀 Static type checking: Running mypy"
 	@uv run mypy
 
+.PHONY: vulture
+vulture: ## Run vulture to check for unused code.
+	@echo "🚀 Checking for unused code with vulture"
+	@uv run pre-commit run vulture --hook-stage manual --all-files
+
 .PHONY: test
 test: ## Test the code with pytest
 	@echo "🚀 Testing code: Running pytest"

pyproject.toml

@@ -52,6 +52,10 @@ build-backend = "hatchling.build"
 [tool.hatch.build.targets.wheel]
 packages = ["src/bub"]
 
+[tool.vulture]
+ignore_names = ["test_*", "Test*"]
+paths = ["src"]
+
 [tool.mypy]
 files = ["src"]
 disallow_untyped_defs = true

src/bub/agent/core.py

@@ -73,9 +73,14 @@ def __init__(
         # Store custom system prompt if provided
         self.custom_system_prompt = system_prompt
 
-        # Use ReAct principles as the main system prompt
         self.prompt_formatter = ReActPromptFormatter()
-        self.system_prompt = self.prompt_formatter.REACT_PRINCIPLES
+        # Use format_prompt to generate the full system prompt
+        if self.custom_system_prompt:
+            self.system_prompt = self.prompt_formatter.format_prompt(self.custom_system_prompt)
+        else:
+            # Use config default if not provided
+            config_prompt = self.context.get_system_prompt()
+            self.system_prompt = self.prompt_formatter.format_prompt(config_prompt)
 
     def reset_conversation(self) -> None:
         """Reset the conversation history."""
@@ -88,11 +93,6 @@ def chat(self, message: str, on_step: Optional[Callable[[str, str], None]] = Non
         while True:
             context_msg = self.context.build_context_message()
 
-            # Add system prompt to context if available
-            system_prompt = self.custom_system_prompt or self.context.get_system_prompt()
-            if system_prompt:
-                context_msg += f"\n\n[System Instructions]\n{system_prompt}"
-
             messages = [
                 {"role": "system", "content": self.system_prompt},
                 {"role": "system", "content": context_msg},

src/bub/tools/run_command.py

@@ -20,6 +20,7 @@ class RunCommandTool(Tool):
     Parameters:
         command: The shell command to execute (e.g., 'ls', 'cat file.txt').
         cwd: Optional. The working directory to run the command in. Defaults to workspace root.
+        timeout: Optional. The timeout in seconds for the command to run. Defaults to 30 seconds.
     """
 
     name: str = Field(default="run_command", description="The internal name of the tool")
@@ -32,6 +33,9 @@ class RunCommandTool(Tool):
     cwd: Optional[str] = Field(
         default=None, description="Optional. The working directory to run the command in. Defaults to workspace root."
     )
+    timeout: int = Field(
+        default=30, description="The timeout in seconds for the command to run. Defaults to 30 seconds."
+    )
 
     # List of dangerous commands that should be blocked
     DANGEROUS_COMMANDS: ClassVar[set[str]] = {
@@ -104,7 +108,7 @@ def execute(self, context: Context) -> ToolResult:
                 cwd=working_dir,
                 capture_output=True,
                 text=True,
-                timeout=30,
+                timeout=self.timeout,
             )
             return ToolResult(
                 success=(result.returncode == 0),