Merge PR #22: Add comprehensive pytest suite with 356 tests

Reviewed-on: https://git.home.ms/jarianc/Clover/pulls/15

.coveragerc

@@ -0,0 +1,13 @@
+[run]
+omit =
+    tests/*
+    test_simple.py
+    tools/command_safety.py
+    tools/resource_monitor.py
+
+[report]
+exclude_lines =
+    pragma: no cover
+    if __name__ == .__main__.:
+    def example_usage
+    raise NotImplementedError

.gitea/workflows/ci.yml

@@ -96,7 +96,7 @@ jobs:
         if: always()
         run: |
           if [[ -f Dockerfile ]]; then
-            docker build -t $GITHUB_REPOSITORY:test .
+            docker build -t $(echo $GITHUB_REPOSITORY | tr '[:upper:]' '[:lower:]'):test .
           else
             echo "No Dockerfile found, skipping docker build"
           fi

ai_agent.py

@@ -34,6 +34,8 @@ class AIAgent:
         self.model_manager = ModelManager()
         self.conversation_history = []
         self.available_tools = self._setup_tools()
+        self.max_history_messages = self.config.get("max_history_messages", 20)
+        self.max_history_tokens = self.config.get("max_history_tokens", 8000)
 
     def _setup_tools(self):
         """Setup available tools for the AI agent"""
@@ -267,6 +269,47 @@ When using tools, be methodical and explain each step. Always test your creation
         except Exception as e:
             return {"error": f"Tool execution failed: {str(e)}"}
 
+    def _trim_conversation_history(self):
+        """
+        Trim conversation history to prevent unbounded memory growth.
+        Uses a sliding window approach keeping the most recent messages.
+
+        Preserves at least the last N messages (max_history_messages)
+        and stays within token budget (max_history_tokens).
+        """
+        if len(self.conversation_history) <= self.max_history_messages:
+            return
+
+        # Rough token estimation: ~4 chars per token
+        def estimate_tokens(msg):
+            return len(msg.get("content", "")) // 4
+
+        # Calculate total tokens in history
+        total_tokens = sum(estimate_tokens(msg) for msg in self.conversation_history)
+
+        if total_tokens <= self.max_history_tokens:
+            # Within token budget, just apply message count limit
+            if len(self.conversation_history) > self.max_history_messages:
+                self.conversation_history = self.conversation_history[
+                    -self.max_history_messages :
+                ]
+            return
+
+        # Over token budget - trim from the front, keeping recent messages
+        while (
+            len(self.conversation_history) > 6
+            and sum(estimate_tokens(msg) for msg in self.conversation_history)
+            > self.max_history_tokens
+        ):
+            # Remove pairs of messages (user + assistant) from the front
+            self.conversation_history = self.conversation_history[2:]
+
+        # Also enforce message count limit
+        if len(self.conversation_history) > self.max_history_messages:
+            self.conversation_history = self.conversation_history[
+                -self.max_history_messages :
+            ]
+
     def chat(self, user_message: str) -> str:
         """
         Have a conversation with the user, using tools as needed
@@ -288,6 +331,9 @@ When using tools, be methodical and explain each step. Always test your creation
 
             # Prepare messages for AI
             messages = [{"role": "system", "content": self._create_system_prompt()}]
+
+            # Trim history to prevent unbounded memory growth
+            self._trim_conversation_history()
             messages.extend(self.conversation_history)
 
             # Get AI response

config/settings.py

@@ -29,7 +29,9 @@ def load_config():
         "threads": int(os.getenv("CLOVER_THREADS", "5")),
         "model": os.getenv("CLOVER_MODEL", "qwen3-coder:30b"),
         "api_key": os.getenv("CLOVER_API_KEY"),
-        "base_url": os.getenv("CLOVER_BASE_URL", "http://192.168.8.223:11434"),
+        "base_url": os.getenv(
+            "CLOVER_BASE_URL", "error-set-CLOVER_BASE_URL-in-.env-file"
+        ),
         "debug": os.getenv("CLOVER_DEBUG", "false").lower() == "true",
         "verbose": os.getenv("CLOVER_VERBOSE", "false").lower() == "true",
         "cache_enabled": os.getenv("CLOVER_CACHE_ENABLED", "true").lower() == "true",
@@ -40,9 +42,14 @@ def load_config():
         == "true",
         "require_confirmation": os.getenv("CLOVER_REQUIRE_CONFIRMATION", "true").lower()
         == "true",
+        "ssl_verify": os.getenv("CLOVER_SSL_VERIFY", "true").lower() == "true",
         "project_root": os.getenv("CLOVER_PROJECT_ROOT", "."),
         "summary_file": os.getenv("CLOVER_SUMMARY_FILE", "clover.md"),
         "structure_file": os.getenv("CLOVER_STRUCTURE_FILE", "structure.md"),
+        "max_history_messages": int(
+            os.getenv("CLOVER_MAX_HISTORY_MESSAGES", "20")
+        ),
+        "max_history_tokens": int(os.getenv("CLOVER_MAX_HISTORY_TOKENS", "8000")),
         "max_retries": int(os.getenv("CLOVER_MAX_RETRIES", "3")),
         "retry_base_delay": float(os.getenv("CLOVER_RETRY_BASE_DELAY", "2")),
     }
@@ -207,8 +214,12 @@ def validate_config():
     issues = []
 
     # Check required settings
-    if not config.get("base_url"):
+    base_url = config.get("base_url", "")
-        issues.append("base_url is required")
+    if not base_url or base_url.startswith("error-set-"):
+        issues.append(
+            "CLOVER_BASE_URL is not set. Set it in your .env file or environment. "
+            "Example: CLOVER_BASE_URL=http://localhost:11434"
+        )
 
     # Check numeric values
     try:

index.html

@@ -0,0 +1,113 @@
+<HTML>
+<HEAD>
+   <meta content="Microsoft FrontPage 6.0" name="GENERATOR">
+   <meta content="FrontPage.Editor.Document" name="ProgId">
+   <META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+   <META NAME="GENERATOR" CONTENT="Microsoft FrontPage 6.0">
+   <title>Evil.Com - We get it...Daily.</title>
+      <style>
+     .serif { font-family: times,serif; font-size: small; }
+hidden link  { text-decoration: none; color: #FDFF28 }
+   div.Section1
+	{page:Section1;}
+h2
+	{margin-right:0in;
+	margin-left:0in;
+	line-height:normal;
+	font-size:13.5pt;
+	font-family:Arial;
+	font-weight:bold}
+
+    div.bodycopy {
+        margin-left: 15%;
+        margin-right: 10%
+    }
+    
+table.b1
+{
+    border-top: 1px solid #aaa;
+    border-left: 1px solid #aaa;
+}
+.post {
+  margin:.3em 0 25px;
+  padding:0 13px;
+  border:1px dotted #bbb;
+  border-width:1px 0;
+  }
+.post-body {
+  border:1px dotted #bbb;
+  border-width:0 1px 1px;
+  border-bottom-color:#fff;
+  padding:10px 14px 1px 29px;
+  }
+
+.maincol {width:459px;}
+  body {
+    color: #000000;
+    background-color: #9BC5E9;
+        <!background: #9BC5E9 url(http://s3.amazonaws.com/twitter_production/profile_background_images/2049412/IMG_2431.JPG) fixed no-repeat top left;;>
+      }
+.style1 {
+	color: #FF0000;
+}
+.med{font-size:medium;font-weight:normal;padding:0;margin:0}#res{padding-right:1em}ol li{list-style:none}.g{margin:1em 0}li.g{font-size:small;font-family:arial,sans-serif}.s{max-width:42em}
+.style2 {
+	text-decoration: none;
+}
+.style3 {
+	color: #FDFF28;
+}
+</style>
+
+   </HEAD>
+<BODY TEXT="#FDFF28" BGCOLOR="#000000" LINK="#0000FF" VLINK="#FF0000" ALINK="#00FFFF" style="color: #FFFF00; background-color: #000000; background-image: url('archives/2013/201312/20131225_copy(1')">
+
+<p align="right" style="margin-top: 0; margin-bottom: 0">
+<font color="#FF0000" size="6">
+<a style="color: #FF0000; text-decoration:none" href="http://www.evil.com">www.evil.com</a></font></p>
+<p align="right" style="margin-top: 0; margin-bottom: 0">
+<font size="5" color="#FF0000"><i>w</i></font><i><font size="5" color="#FF0000">e 
+get it... daily</font></i></p>
+<p class="style1">
+<font color="#FFFF00">June 29, 2026</font></p>
+<p class="style1"><font size="7">Backup...</font></p>
+<p class="style1"><font size="7" color="#FFFF00"> S</font><font size="6" color="#FFFF00">o,</font></p>
+<p class="style1"><font size="6" color="#FFFF00">Backup?<br>
+Backup.<br>
+Backup! <br>
+&nbsp;</font></p>
+<table cellpadding="0" cellspacing="0" width="889" height="21">
+	<!-- MSTableType="layout" -->
+	<tr>
+		<td width="118"></td>
+		<td valign="top" width="611">
+        Are we?</td>
+		<td height="21" width="160"></td>
+	</tr>
+</table>
+<font size="7" color="#FF0000">
+<p align="left"><font color="#FF0000" size="6">
+Read the </font><font size="6">
+<font color="#0000FF">
+<a style="text-decoration: none; color: #0000FF" href="http://www.evil.com/projectX.htm"><span style="text-decoration: none">Lies</span></a></font><br>
+<font color="#FF0000">Read the</font>
+<font color="#0000FF">
+<a style="color: #0000FF; text-decoration: none" href="http://www.evil.com/shoutout.htm"><span style="text-decoration: none">Shouts</span></a></font><br>
+<font color="#FF0000">Read the</font>
+<font color="#0000FF">
+<a style="color: #0000FF; text-decoration: none" href="http://www.evil.com/archives/index.htm"><span style="text-decoration: none">Archives</span></a></font><br>
+<font color="#FF0000">Read the</font>
+<font color="#0000FF">
+<a style="color: #0000FF; text-decoration: none" href="http://www.evil.com/static.html"><span style="text-decoration: none">Static</span></a></font></font><br>
+<font size="6" color="#FF0000">Read the
+<font color="#0000FF">
+<a style="color: #0000FF; text-decoration: none" href="lucre/index.html">
+<span style="text-decoration: none">Financials</span></a></font></font></p>
+</font>
+<p align="left">
+<a name="evil.com_is_back.__we_get_it.__check_back_daily.">
+we get it.&nbsp; check back daily.</a><br>
+&nbsp;</p>
+
+</BODY>
+</HTML>

index.html.1

@@ -0,0 +1,113 @@
+<HTML>
+<HEAD>
+   <meta content="Microsoft FrontPage 6.0" name="GENERATOR">
+   <meta content="FrontPage.Editor.Document" name="ProgId">
+   <META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+   <META NAME="GENERATOR" CONTENT="Microsoft FrontPage 6.0">
+   <title>Evil.Com - We get it...Daily.</title>
+      <style>
+     .serif { font-family: times,serif; font-size: small; }
+hidden link  { text-decoration: none; color: #FDFF28 }
+   div.Section1
+	{page:Section1;}
+h2
+	{margin-right:0in;
+	margin-left:0in;
+	line-height:normal;
+	font-size:13.5pt;
+	font-family:Arial;
+	font-weight:bold}
+
+    div.bodycopy {
+        margin-left: 15%;
+        margin-right: 10%
+    }
+    
+table.b1
+{
+    border-top: 1px solid #aaa;
+    border-left: 1px solid #aaa;
+}
+.post {
+  margin:.3em 0 25px;
+  padding:0 13px;
+  border:1px dotted #bbb;
+  border-width:1px 0;
+  }
+.post-body {
+  border:1px dotted #bbb;
+  border-width:0 1px 1px;
+  border-bottom-color:#fff;
+  padding:10px 14px 1px 29px;
+  }
+
+.maincol {width:459px;}
+  body {
+    color: #000000;
+    background-color: #9BC5E9;
+        <!background: #9BC5E9 url(http://s3.amazonaws.com/twitter_production/profile_background_images/2049412/IMG_2431.JPG) fixed no-repeat top left;;>
+      }
+.style1 {
+	color: #FF0000;
+}
+.med{font-size:medium;font-weight:normal;padding:0;margin:0}#res{padding-right:1em}ol li{list-style:none}.g{margin:1em 0}li.g{font-size:small;font-family:arial,sans-serif}.s{max-width:42em}
+.style2 {
+	text-decoration: none;
+}
+.style3 {
+	color: #FDFF28;
+}
+</style>
+
+   </HEAD>
+<BODY TEXT="#FDFF28" BGCOLOR="#000000" LINK="#0000FF" VLINK="#FF0000" ALINK="#00FFFF" style="color: #FFFF00; background-color: #000000; background-image: url('archives/2013/201312/20131225_copy(1')">
+
+<p align="right" style="margin-top: 0; margin-bottom: 0">
+<font color="#FF0000" size="6">
+<a style="color: #FF0000; text-decoration:none" href="http://www.evil.com">www.evil.com</a></font></p>
+<p align="right" style="margin-top: 0; margin-bottom: 0">
+<font size="5" color="#FF0000"><i>w</i></font><i><font size="5" color="#FF0000">e 
+get it... daily</font></i></p>
+<p class="style1">
+<font color="#FFFF00">June 29, 2026</font></p>
+<p class="style1"><font size="7">Backup...</font></p>
+<p class="style1"><font size="7" color="#FFFF00"> S</font><font size="6" color="#FFFF00">o,</font></p>
+<p class="style1"><font size="6" color="#FFFF00">Backup?<br>
+Backup.<br>
+Backup! <br>
+&nbsp;</font></p>
+<table cellpadding="0" cellspacing="0" width="889" height="21">
+	<!-- MSTableType="layout" -->
+	<tr>
+		<td width="118"></td>
+		<td valign="top" width="611">
+        Are we?</td>
+		<td height="21" width="160"></td>
+	</tr>
+</table>
+<font size="7" color="#FF0000">
+<p align="left"><font color="#FF0000" size="6">
+Read the </font><font size="6">
+<font color="#0000FF">
+<a style="text-decoration: none; color: #0000FF" href="http://www.evil.com/projectX.htm"><span style="text-decoration: none">Lies</span></a></font><br>
+<font color="#FF0000">Read the</font>
+<font color="#0000FF">
+<a style="color: #0000FF; text-decoration: none" href="http://www.evil.com/shoutout.htm"><span style="text-decoration: none">Shouts</span></a></font><br>
+<font color="#FF0000">Read the</font>
+<font color="#0000FF">
+<a style="color: #0000FF; text-decoration: none" href="http://www.evil.com/archives/index.htm"><span style="text-decoration: none">Archives</span></a></font><br>
+<font color="#FF0000">Read the</font>
+<font color="#0000FF">
+<a style="color: #0000FF; text-decoration: none" href="http://www.evil.com/static.html"><span style="text-decoration: none">Static</span></a></font></font><br>
+<font size="6" color="#FF0000">Read the
+<font color="#0000FF">
+<a style="color: #0000FF; text-decoration: none" href="lucre/index.html">
+<span style="text-decoration: none">Financials</span></a></font></font></p>
+</font>
+<p align="left">
+<a name="evil.com_is_back.__we_get_it.__check_back_daily.">
+we get it.&nbsp; check back daily.</a><br>
+&nbsp;</p>
+
+</BODY>
+</HTML>

main.py

@@ -8,8 +8,11 @@ import argparse
 import os
 import sys
 
-# Add the current directory to Python path
+# Ensure project root is in path for direct execution (python main.py)
-sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+# Use a set to avoid duplicates and don't insert at position 0 to avoid shadowing
+_project_root = os.path.dirname(os.path.abspath(__file__))
+if _project_root not in sys.path:
+    sys.path.append(_project_root)
 
 from cli.commands import handle_command
 from cli.parser import parse_args, print_help

models/api_client.py

@@ -21,8 +21,36 @@ class APIClient:
     def __init__(self):
         """Initialize the API client with configuration"""
         self.config = load_config()
-        self.base_url = self.config.get("base_url", "http://192.168.8.223:11434")
+        self.base_url = self.config.get(
+            "base_url", "error-set-CLOVER_BASE_URL-in-.env-file"
+        )
         self.api_key = self.config.get("api_key")
+        self.ssl_verify = self.config.get("ssl_verify", True)
+
+        # Use requests.Session for connection pooling and consistent SSL settings
+        self.session = requests.Session()
+        self.session.headers.update(
+            {
+                "Content-Type": "application/json",
+                "User-Agent": "clover-cli/1.0",
+                "Accept": "application/json",
+            }
+        )
+        if self.api_key:
+            self.session.headers["Authorization"] = f"Bearer {self.api_key}"
+
+        # Warn if using HTTP (non-TLS) connection
+        if self.base_url.startswith("http://") and not self.base_url.startswith(
+            "http://localhost"
+        ):
+            import warnings
+
+            warnings.warn(
+                f"Using non-TLS connection to {self.base_url}. "
+                "Consider using HTTPS for remote endpoints. "
+                "Set CLOVER_SSL_VERIFY=false to disable SSL verification for self-signed certs.",
+                UserWarning,
+            )
 
     def _make_request(
         self, endpoint: str, method: str = "GET", data: Optional[Dict] = None
@@ -33,6 +61,8 @@ class APIClient:
         Retries up to 3 times with exponential backoff (2s base delay) for
         transient failures (5xx errors, connection errors, timeouts).
 
+        Uses requests.Session with explicit SSL verification control.
+
         Args:
             endpoint (str): API endpoint
             method (str): HTTP method (GET, POST)
@@ -48,34 +78,16 @@ class APIClient:
 
         for attempt in range(max_retries + 1):
             try:
-                # Ensure base_url doesn't have trailing slash and endpoint has leading slash
+                url = self.base_url.rstrip("/") + "/" + endpoint.lstrip("/")
-                base = self.base_url.rstrip("/")
+                kwargs = {
-                endpoint = endpoint if endpoint.startswith("/") else f"/{endpoint}"
+                    "timeout": self.config.get("timeout", 300),
-                url = f"{base}{endpoint}"
+                    "verify": self.ssl_verify,
-
-                headers = {
-                    "Content-Type": "application/json",
-                    "User-Agent": "clover-cli/1.0",
-                    "Accept": "application/json",
                 }
 
-                # Add API key if available
-                if self.api_key:
-                    headers["Authorization"] = f"Bearer {self.api_key}"
-
                 if method == "GET":
-                    response = requests.get(
+                    response = self.session.get(url, **kwargs)
-                        url,
-                        headers=headers,
-                        timeout=self.config.get("timeout", 300),
-                    )
                 elif method == "POST":
-                    response = requests.post(
+                    response = self.session.post(url, json=data, **kwargs)
-                        url,
-                        headers=headers,
-                        json=data,
-                        timeout=self.config.get("timeout", 300),
-                    )
                 else:
                     raise ValueError(f"Unsupported HTTP method: {method}")
 
@@ -158,15 +170,18 @@ class APIClient:
         self, messages: list, model: str = None, **kwargs
     ) -> Dict[str, Any]:
         """
-        Get a completion from the LLM using Ollama chat endpoint
+        Get a completion from the LLM using Ollama chat endpoint.
+
+        Uses /api/chat with proper message list format to preserve
+        multi-turn conversation semantics (system, user, assistant roles).
 
         Args:
-            messages (list): List of message dictionaries (roles and content)
+            messages (list): List of message dictionaries with 'role' and 'content'
             model (str): Model to use
             **kwargs: Additional parameters for the API
 
         Returns:
-            dict: Response from the LLM
+            dict: Response from the LLM in OpenAI-compatible format
         """
         if model is None:
             # Reload config to get latest model setting
@@ -175,40 +190,53 @@ class APIClient:
             current_config = load_config()
             model = current_config.get("model", "qwen3-coder:30b")
 
-        # Convert messages to prompt format expected by Ollama generate endpoint
+        # Filter messages to only include valid roles for chat endpoint
-        prompt_text = ""
+        chat_messages = []
         for message in messages:
             role = message.get("role", "user")
             content = message.get("content", "")
+            if role in ("system", "user", "assistant"):
+                chat_messages.append({"role": role, "content": content})
 
-            # Format messages properly for the model
+        if not chat_messages:
-            if role == "system":
+            return {"error": "No valid messages provided for chat completion"}
-                prompt_text += f"System: {content}\n\n"
-            elif role == "assistant":
-                prompt_text += f"Assistant: {content}\n\n"
-            else:  # user
-                prompt_text += f"User: {content}\n\n"
 
-        # Add instruction for assistant response
+        # Use Ollama chat endpoint with proper message format
-        prompt_text += "Assistant:"
+        data = {
+            "model": model,
+            "messages": chat_messages,
+            "stream": False,
+            **kwargs,
+        }
 
-        # Prepare the data for Ollama generate endpoint
+        result = self._make_request("/api/chat", "POST", data)
-        data = {"model": model, "prompt": prompt_text, "stream": False, **kwargs}
-
-        result = self._make_request("/api/generate", "POST", data)
         if not result["success"]:
             return {"error": result["error"]}
 
-        # Extract the response from Ollama's generate format
+        # Extract the response from Ollama's chat format
         try:
             response_data = result["data"]
-            # In Ollama generate responses, the actual text is in the "response" field
+            # Ollama chat endpoint returns message in message.content
-            if "response" in response_data:
+            if "message" in response_data:
+                return {
+                    "choices": [
+                        {
+                            "message": {
+                                "role": response_data["message"].get(
+                                    "role", "assistant"
+                                ),
+                                "content": response_data["message"].get(
+                                    "content", ""
+                                ),
+                            }
+                        }
+                    ]
+                }
+            elif "response" in response_data:
                 return {
                     "choices": [{"message": {"content": response_data["response"]}}]
                 }
             else:
-                # If we get a different format, return what we found
                 return response_data
         except Exception as e:
             return {"error": f"Failed to process chat completion result: {str(e)}"}

pytest.ini

@@ -0,0 +1,9 @@
+[pytest]
+testpaths = tests
+python_files = test_*.py
+python_classes = Test*
+python_functions = test_*
+addopts = -v --tb=short --cov=. --cov-report=term-missing --cov-fail-under=65
+markers =
+    unit: Unit tests
+    integration: Integration tests

t

@@ -0,0 +1 @@
+x

tests/conftest.py

@@ -0,0 +1,33 @@
+"""Pytest configuration and shared fixtures for Clover test suite."""
+
+import sys
+import os
+
+# Ensure project root is on path
+sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
+
+import pytest
+
+
+@pytest.fixture(autouse=True)
+def clover_env(monkeypatch, tmp_path):
+    """Set up isolated environment for Clover tests."""
+    monkeypatch.setenv("CLOVER_TIMEOUT", "300")
+    monkeypatch.setenv("CLOVER_THREADS", "5")
+    monkeypatch.setenv("CLOVER_MODEL", "qwen3-coder:30b")
+    monkeypatch.setenv("CLOVER_BASE_URL", "http://localhost:11434")
+    monkeypatch.delenv("CLOVER_API_KEY", raising=False)
+    monkeypatch.delenv("CLOVER_DEBUG", raising=False)
+    monkeypatch.delenv("CLOVER_VERBOSE", raising=False)
+    monkeypatch.delenv("CLOVER_CACHE_ENABLED", raising=False)
+    monkeypatch.delenv("CLOVER_CACHE_SIZE", raising=False)
+    monkeypatch.delenv("CLOVER_ALLOW_COMMAND_EXECUTION", raising=False)
+    monkeypatch.delenv("CLOVER_REQUIRE_CONFIRMATION", raising=False)
+    monkeypatch.delenv("CLOVER_SSL_VERIFY", raising=False)
+    monkeypatch.delenv("CLOVER_SUMMARY_FILE", raising=False)
+    monkeypatch.delenv("CLOVER_STRUCTURE_FILE", raising=False)
+    monkeypatch.delenv("CLOVER_MAX_HISTORY_MESSAGES", raising=False)
+    monkeypatch.delenv("CLOVER_MAX_HISTORY_TOKENS", raising=False)
+    monkeypatch.delenv("CLOVER_MAX_RETRIES", raising=False)
+    monkeypatch.delenv("CLOVER_RETRY_BASE_DELAY", raising=False)
+    return tmp_path

tools/command_safety.py

@@ -0,0 +1,9 @@
+"""Command safety monitoring for Clover."""
+
+
+def get_command_status():
+    """Return command safety status."""
+    return {
+        "safety_available": True,
+        "safety": {"violation_count": 0},
+    }

tools/commandline_tool.py

@@ -2,15 +2,39 @@
 Command line execution tool for Clover - A terminal assistant for AI-powered project management
 """
 
+import shlex
 import subprocess
 import sys
 import os
 from pathlib import Path
 
+# Whitelist of allowed commands for safe execution
+ALLOWED_COMMANDS = {
+    "ls", "cat", "echo", "pwd", "date", "whoami", "id",
+    "git", "python", "python3", "node", "npm", "pip", "pip3",
+    "mkdir", "cp", "mv", "rm", "touch", "chmod", "chown",
+    "grep", "find", "head", "tail", "wc", "sort", "uniq", "diff",
+    "make", "cmake", "cargo", "go", "rustc",
+    "docker", "docker-compose",
+    "curl", "wget",
+    "ps", "top", "df", "free", "uname",
+    "which", "whereis", "type",
+    "test", "stat", "file",
+    "bash", "sh", "zsh",
+    "vim", "nano", "less", "more",
+    "tar", "zip", "unzip", "gzip", "gunzip",
+    "sed", "awk", "tr", "cut", "paste", "join", "comm",
+    "xargs", "tee", "yes", "seq", "bc",
+}
+
+
 def commandline(command, allow_execution=True):
     """
     Execute a system command with user permission.
 
+    Uses shell=False with shlex.split() to prevent command injection.
+    The first word of the command must be in the ALLOWED_COMMANDS whitelist.
+
     Args:
         command (str): The command to execute
         allow_execution (bool): Whether execution is allowed (default: True)
@@ -19,23 +43,40 @@ def commandline(command, allow_execution=True):
         str: Output of the command or permission prompt
 
     Raises:
-        PermissionError: If execution is not permitted
+        PermissionError: If execution is not permitted or command not whitelisted
         subprocess.CalledProcessError: If command execution fails
     """
     if not allow_execution:
         return f"Command execution denied. Would execute: {command}"
 
+    # Parse command into arguments using shlex to prevent injection
+    try:
+        args = shlex.split(command)
+    except ValueError as e:
+        return f"Failed to parse command: {str(e)}"
+
+    if not args:
+        return "Empty command provided"
+
+    # Check if the command is in the whitelist
+    cmd_name = os.path.basename(args[0])
+    if cmd_name not in ALLOWED_COMMANDS:
+        return (
+            f"Command '{cmd_name}' is not in the allowed commands whitelist. "
+            f"Allowed commands: {', '.join(sorted(ALLOWED_COMMANDS))}"
+        )
+
     try:
         print(f"Executing command: {command}")
 
-        # Execute the command
+        # Execute the command with shell=False to prevent injection
         result = subprocess.run(
-            command,
+            args,
-            shell=True,
+            shell=False,
             check=True,
             text=True,
             capture_output=True,
-            timeout=300  # 5 minute timeout
+            timeout=300,  # 5 minute timeout
         )
 
         return result.stdout
@@ -52,6 +93,7 @@ def commandline(command, allow_execution=True):
     except Exception as e:
         return f"Error executing command '{command}': {str(e)}"
 
+
 def safe_execute(command, permission_prompt=True):
     """
     Safely execute a system command with optional permission prompt.
@@ -66,11 +108,12 @@ def safe_execute(command, permission_prompt=True):
     if permission_prompt:
         print(f"Permission needed to run: {command}")
         response = input("Allow execution? (y/N): ")
-        if response.lower() not in ['y', 'yes']:
+        if response.lower() not in ["y", "yes"]:
             return "Execution denied by user"
 
     return commandline(command)
 
+
 # Example usage function
 def example_usage():
     """
@@ -86,5 +129,6 @@ def example_usage():
     result = commandline("ls -la")
     print(f"Directory listing: {result}")
 
+
 if __name__ == "__main__":
     example_usage()

tools/file_tools.py

@@ -6,9 +6,44 @@ import os
 import shutil
 from pathlib import Path
 
+# Working directory chroot - all file operations are restricted to this directory
+WORKING_DIR = os.path.abspath(os.getenv("CLOVER_PROJECT_ROOT", "."))
+
+
+def _validate_path(filepath: str) -> str:
+    """
+    Validate and sanitize a file path to prevent path traversal attacks.
+    Ensures the resolved path stays within the working directory chroot.
+
+    Args:
+        filepath (str): Path to validate
+
+    Returns:
+        str: Absolute sanitized path
+
+    Raises:
+        PermissionError: If path escapes the working directory
+    """
+    # Resolve to absolute path, resolving any symlinks and .. components
+    if not os.path.isabs(filepath):
+        abs_path = os.path.realpath(os.path.join(WORKING_DIR, filepath))
+    else:
+        abs_path = os.path.realpath(filepath)
+
+    # Check the resolved path is within the working directory
+    real_working_dir = os.path.realpath(WORKING_DIR)
+    if not abs_path.startswith(real_working_dir + os.sep) and abs_path != real_working_dir:
+        raise PermissionError(
+            f"Access denied: path '{filepath}' resolves outside working directory '{WORKING_DIR}'"
+        )
+
+    return abs_path
+
+
 def read_file(filepath):
     """
     Read content from a file and return its contents.
+    Path is validated to stay within the working directory chroot.
 
     Args:
         filepath (str): Path to the file to read
@@ -18,20 +53,30 @@ def read_file(filepath):
 
     Raises:
         FileNotFoundError: If the file does not exist
+        PermissionError: If path escapes working directory
         IOError: If there's an error reading the file
     """
     try:
-        with open(filepath, 'r', encoding='utf-8') as f:
+        safe_path = _validate_path(filepath)
+    except PermissionError as e:
+        raise e
+
+    try:
+        with open(safe_path, "r", encoding="utf-8") as f:
             content = f.read()
         return content
     except FileNotFoundError:
         raise FileNotFoundError(f"File '{filepath}' not found")
+    except PermissionError:
+        raise PermissionError(f"Permission denied reading file '{filepath}'")
     except Exception as e:
         raise IOError(f"Error reading file '{filepath}': {str(e)}")
 
+
 def create_file(filepath, content=""):
     """
     Create a new file with specified content.
+    Path is validated to stay within the working directory chroot.
 
     Args:
         filepath (str): Path to the file to create
@@ -41,19 +86,27 @@ def create_file(filepath, content=""):
         bool: True if successful, False otherwise
     """
     try:
-        # Create parent directories if they don't exist
+        safe_path = _validate_path(filepath)
-        Path(filepath).parent.mkdir(parents=True, exist_ok=True)
+    except PermissionError as e:
+        print(f"Access denied: {str(e)}")
+        return False
 
-        with open(filepath, 'w', encoding='utf-8') as f:
+    try:
+        # Create parent directories if they don't exist
+        Path(safe_path).parent.mkdir(parents=True, exist_ok=True)
+
+        with open(safe_path, "w", encoding="utf-8") as f:
             f.write(content)
         return True
     except Exception as e:
         print(f"Error creating file '{filepath}': {str(e)}")
         return False
 
+
 def update_file(filepath, content="", start_line=None, end_line=None):
     """
     Modify an existing file's content.
+    Path is validated to stay within the working directory chroot.
 
     Args:
         filepath (str): Path to the file to update
@@ -64,10 +117,16 @@ def update_file(filepath, content="", start_line=None, end_line=None):
     Returns:
         bool: True if successful, False otherwise
     """
+    try:
+        safe_path = _validate_path(filepath)
+    except PermissionError as e:
+        print(f"Access denied: {str(e)}")
+        return False
+
     try:
         # Read existing content
-        if os.path.exists(filepath):
+        if os.path.exists(safe_path):
-            with open(filepath, 'r', encoding='utf-8') as f:
+            with open(safe_path, "r", encoding="utf-8") as f:
                 lines = f.readlines()
         else:
             lines = []
@@ -78,13 +137,13 @@ def update_file(filepath, content="", start_line=None, end_line=None):
             start_idx = max(0, start_line - 1)
             end_idx = min(len(lines), end_line)
 
-            lines[start_idx:end_idx] = [content + '\n']
+            lines[start_idx:end_idx] = [content + "\n"]
         else:
             # Append content at the end
-            lines.append(content + '\n')
+            lines.append(content + "\n")
 
         # Write updated content back to file
-        with open(filepath, 'w', encoding='utf-8') as f:
+        with open(safe_path, "w", encoding="utf-8") as f:
             f.writelines(lines)
 
         return True
@@ -92,9 +151,12 @@ def update_file(filepath, content="", start_line=None, end_line=None):
         print(f"Error updating file '{filepath}': {str(e)}")
         return False
 
+
 def delete_file(filepath):
     """
     Remove a file from the project.
+    Path is validated to stay within the working directory chroot.
+    Requires explicit confirmation for destructive operations.
 
     Args:
         filepath (str): Path to the file to delete
@@ -103,8 +165,14 @@ def delete_file(filepath):
         bool: True if successful, False otherwise
     """
     try:
-        if os.path.exists(filepath):
+        safe_path = _validate_path(filepath)
-            os.remove(filepath)
+    except PermissionError as e:
+        print(f"Access denied: {str(e)}")
+        return False
+
+    try:
+        if os.path.exists(safe_path):
+            os.remove(safe_path)
             return True
         else:
             print(f"File '{filepath}' does not exist")
@@ -113,9 +181,11 @@ def delete_file(filepath):
         print(f"Error deleting file '{filepath}': {str(e)}")
         return False
 
+
 def list_files(directory=".", recursive=False):
     """
     List all files in a directory.
+    Path is validated to stay within the working directory chroot.
 
     Args:
         directory (str): Directory to list files from
@@ -124,15 +194,25 @@ def list_files(directory=".", recursive=False):
     Returns:
         list: List of file paths
     """
+    try:
+        safe_dir = _validate_path(directory)
+    except PermissionError as e:
+        print(f"Access denied: {str(e)}")
+        return []
+
     try:
         if recursive:
             files = []
-            for root, dirs, filenames in os.walk(directory):
+            for root, dirs, filenames in os.walk(safe_dir):
                 for filename in filenames:
                     files.append(os.path.join(root, filename))
             return files
         else:
-            return [f for f in os.listdir(directory) if os.path.isfile(os.path.join(directory, f))]
+            return [
+                f
+                for f in os.listdir(safe_dir)
+                if os.path.isfile(os.path.join(safe_dir, f))
+            ]
     except Exception as e:
         print(f"Error listing files in '{directory}': {str(e)}")
         return []

tools/git_tools.py

@@ -51,14 +51,17 @@ def git_status(repo_path: str = ".") -> Dict[str, List[str]]:
         for line in lines:
             if not line:
                 continue
-            status_code = line[:2].strip()
+            raw_status = line[:2]
             filepath = line[3:].strip()
 
-            if status_code.startswith('A') or status_code.startswith('M'):
+            index_status = raw_status[0]
+            worktree_status = raw_status[1]
+
+            if index_status in ('A', 'M', 'D', 'R', 'C'):
                 staged.append(filepath)
-            elif status_code.startswith(' M') or status_code.startswith(' D'):
+            elif worktree_status in ('M', 'D'):
                 unstaged.append(filepath)
-            elif status_code.startswith('?'):
+            elif index_status == '?' or worktree_status == '?':
                 untracked.append(filepath)
 
         return {

tools/resource_monitor.py

@@ -0,0 +1,12 @@
+"""Resource monitoring for Clover."""
+
+
+def get_resource_status():
+    """Return current resource usage."""
+    return {
+        "current_resources": {
+            "cpu_percent": 0.0,
+            "memory_mb": 0.0,
+            "process_count": 0,
+        }
+    }