Fixes https://github.com/BeehiveInnovations/gemini-mcp-server/issues/6

docker-compose.yml

@@ -31,7 +31,9 @@ services:
     environment:
       - GEMINI_API_KEY=${GEMINI_API_KEY}
       - REDIS_URL=redis://redis:6379/0
-      - WORKSPACE_ROOT=${WORKSPACE_ROOT:-/workspace}
+      # Use HOME not PWD: Claude needs access to any absolute file path, not just current project,
+      # and Claude Code could be running from multiple locations at the same time
+      - WORKSPACE_ROOT=${WORKSPACE_ROOT:-${HOME}}
     volumes:
       - ${HOME:-/tmp}:/workspace:ro
     stdin_open: true

setup-docker.sh

@@ -37,8 +37,12 @@ GEMINI_API_KEY=$API_KEY_VALUE
 # Redis configuration (automatically set for Docker Compose)
 REDIS_URL=redis://redis:6379/0
 
-# Workspace root (automatically set for Docker Compose)
+# Workspace root - host path that maps to /workspace in container
-WORKSPACE_ROOT=/workspace
+# This should be the host directory path that contains all files Claude might reference
+# We use $HOME (not $PWD) because Claude needs access to ANY absolute file path,
+# not just files within the current project directory. Additionally, Claude Code
+# could be running from multiple locations at the same time.
+WORKSPACE_ROOT=$HOME
 EOF
     echo "✅ Created .env file with Redis configuration"
     echo ""

tests/test_collaboration.py

@@ -235,9 +235,9 @@ class TestCollaborationWorkflow:
         )
 
         response = json.loads(result[0].text)
-        assert (
+        assert response["status"] == "requires_clarification", (
-            response["status"] == "requires_clarification"
+            "Should request clarification when asked about dependencies without package files"
-        ), "Should request clarification when asked about dependencies without package files"
+        )
 
         clarification = json.loads(response["content"])
         assert "package.json" in str(clarification["files_needed"]), "Should specifically request package.json"

tests/test_conversation_memory.py

@@ -300,7 +300,7 @@ class TestConversationFlow:
         # REQUEST 6: Try to exceed MAX_CONVERSATION_TURNS limit - should fail
         turns_at_limit = [
             ConversationTurn(
-                role="assistant" if i % 2 == 0 else "user", content=f"Turn {i+1}", timestamp="2023-01-01T00:00:30Z"
+                role="assistant" if i % 2 == 0 else "user", content=f"Turn {i + 1}", timestamp="2023-01-01T00:00:30Z"
             )
             for i in range(MAX_CONVERSATION_TURNS)
         ]
@@ -423,7 +423,9 @@ class TestConversationFlow:
             # Mock context with current turns
             turns = [
                 ConversationTurn(
-                    role="user" if i % 2 == 0 else "assistant", content=f"Turn {i+1}", timestamp="2023-01-01T00:00:00Z"
+                    role="user" if i % 2 == 0 else "assistant",
+                    content=f"Turn {i + 1}",
+                    timestamp="2023-01-01T00:00:00Z",
                 )
                 for i in range(turn_num)
             ]
@@ -445,7 +447,7 @@ class TestConversationFlow:
         # Now we should be at the limit - create final context
         final_turns = [
             ConversationTurn(
-                role="user" if i % 2 == 0 else "assistant", content=f"Turn {i+1}", timestamp="2023-01-01T00:00:00Z"
+                role="user" if i % 2 == 0 else "assistant", content=f"Turn {i + 1}", timestamp="2023-01-01T00:00:00Z"
             )
             for i in range(MAX_CONVERSATION_TURNS)
         ]

tests/test_thinking_modes.py

@@ -32,9 +32,9 @@ class TestThinkingModes:
         ]
 
         for tool, expected_default in tools:
-            assert (
+            assert tool.get_default_thinking_mode() == expected_default, (
-                tool.get_default_thinking_mode() == expected_default
+                f"{tool.__class__.__name__} should default to {expected_default}"
-            ), f"{tool.__class__.__name__} should default to {expected_default}"
+            )
 
     @pytest.mark.asyncio
     @patch("tools.base.BaseTool.create_model")

utils/file_utils.py

@@ -28,8 +28,9 @@ from .token_utils import MAX_CONTEXT_TOKENS, estimate_tokens
 logger = logging.getLogger(__name__)
 
 # Get workspace root for Docker path translation
-# When running in Docker with a mounted workspace, WORKSPACE_ROOT contains
+# IMPORTANT: WORKSPACE_ROOT should contain the HOST path (e.g., /Users/john/project)
-# the host path that corresponds to /workspace in the container
+# that gets mounted to /workspace in the Docker container. This enables proper
+# path translation between host absolute paths and container workspace paths.
 WORKSPACE_ROOT = os.environ.get("WORKSPACE_ROOT")
 CONTAINER_WORKSPACE = Path("/workspace")
 
@@ -43,6 +44,7 @@ DANGEROUS_WORKSPACE_PATHS = {
     "/var",
     "/root",
     "/home",
+    "/workspace",  # Container path - WORKSPACE_ROOT should be host path
     "C:\\",
     "C:\\Windows",
     "C:\\Program Files",
@@ -54,7 +56,17 @@ if WORKSPACE_ROOT:
     # Resolve to canonical path for comparison
     resolved_workspace = Path(WORKSPACE_ROOT).resolve()
 
-    # Check against dangerous paths
+    # Special check for /workspace - common configuration mistake
+    if str(resolved_workspace) == "/workspace":
+        raise RuntimeError(
+            f"Configuration Error: WORKSPACE_ROOT should be set to the HOST path, not the container path. "
+            f"Found: WORKSPACE_ROOT={WORKSPACE_ROOT} "
+            f"Expected: WORKSPACE_ROOT should be set to your host directory path (e.g., $HOME) "
+            f"that contains all files Claude might reference. "
+            f"This path gets mounted to /workspace inside the Docker container."
+        )
+
+    # Check against other dangerous paths
     if str(resolved_workspace) in DANGEROUS_WORKSPACE_PATHS:
         raise RuntimeError(
             f"Security Error: WORKSPACE_ROOT '{WORKSPACE_ROOT}' is set to a dangerous system directory. "
@@ -181,12 +193,17 @@ def translate_path_for_environment(path_str: str) -> str:
 
     This is the unified path translation function that should be used by all
     tools and utilities throughout the codebase. It handles:
-    1. Docker host-to-container path translation
+    1. Docker host-to-container path translation (host paths -> /workspace/...)
     2. Direct mode (no translation needed)
     3. Security validation and error handling
 
+    Docker Path Translation Logic:
+    - Input: /Users/john/project/src/file.py (host path from Claude)
+    - WORKSPACE_ROOT: /Users/john/project (host path in env var)
+    - Output: /workspace/src/file.py (container path for file operations)
+
     Args:
-        path_str: Original path string from the client
+        path_str: Original path string from the client (absolute host path)
 
     Returns:
         Translated path appropriate for the current environment