Add comprehensive conda integration for academic environments

Enhanced conda support to handle custom environment and package directories:

Key Changes:
- Mount conda installation at original path (not /opt/miniconda3)
- Add CONDA_EXTRA_DIRS for mounting additional search paths
- Mount all conda-configured directories to preserve existing setup
- Update CLAUDE.md to use ${CONDA_EXE} environment variable

Technical Details:
- Preserves original conda paths so existing configuration works
- Handles multiple envs_dirs and pkgs_dirs automatically
- Provides feedback about which directories are mounted
- Falls back gracefully for missing directories

Example usage: CONDA_EXTRA_DIRS="/vol/path/.conda/envs /vol/path/conda_envs /vol/path/.conda/pkgs"
Result: All conda environments and packages accessible in container.

.env.example

@@ -9,3 +9,10 @@ TWILIO_ACCOUNT_SID=your_twilio_account_sid
 TWILIO_AUTH_TOKEN=your_twilio_auth_token
 TWILIO_FROM_NUMBER=+1234567890
 TWILIO_TO_NUMBER=+0987654321
+
+# Optional: Custom conda installation (for academic/lab environments)
+# Example: CONDA_PREFIX=/vol/biomedic3/username/miniconda3
+CONDA_PREFIX=
+# Optional: Additional conda directories (space-separated list)
+# Example: CONDA_EXTRA_DIRS="/vol/biomedic3/username/.conda/envs /vol/biomedic3/username/conda_envs /vol/biomedic3/username/.conda/pkgs /vol/biomedic3/username/conda_pkgs /homes/username/.conda/envs"
+CONDA_EXTRA_DIRS=

scripts/claude-docker.sh

@@ -28,6 +28,10 @@ fi
 ENV_FILE="$PROJECT_ROOT/.env"
 if [ -f "$ENV_FILE" ]; then
     echo "✓ Found .env file with credentials"
+    # Source .env to get configuration variables
+    set -a
+    source "$ENV_FILE" 2>/dev/null || true
+    set +a
 else
     echo "⚠️  No .env file found at $ENV_FILE"
     echo "   Twilio MCP features will be unavailable."
@@ -61,11 +65,41 @@ fi
 # Ensure the claude-home directory exists
 mkdir -p "$HOME/.claude-docker/claude-home"
 
+# Prepare additional mount arguments
+MOUNT_ARGS=""
+ENV_ARGS=""
+
+# Mount conda installation if specified
+if [ -n "$CONDA_PREFIX" ] && [ -d "$CONDA_PREFIX" ]; then
+    echo "✓ Mounting conda installation from $CONDA_PREFIX"
+    MOUNT_ARGS="$MOUNT_ARGS -v $CONDA_PREFIX:$CONDA_PREFIX:ro"
+    ENV_ARGS="$ENV_ARGS -e CONDA_PREFIX=$CONDA_PREFIX -e CONDA_EXE=$CONDA_PREFIX/bin/conda"
+else
+    echo "No conda installation configured"
+fi
+
+# Mount additional conda directories if specified
+if [ -n "$CONDA_EXTRA_DIRS" ]; then
+    echo "✓ Mounting additional conda directories..."
+    for dir in $CONDA_EXTRA_DIRS; do
+        if [ -d "$dir" ]; then
+            echo "  - Mounting $dir"
+            MOUNT_ARGS="$MOUNT_ARGS -v $dir:$dir:ro"
+        else
+            echo "  - Skipping $dir (not found)"
+        fi
+    done
+else
+    echo "No additional conda directories configured"
+fi
+
 # Run Claude Code in Docker
 echo "Starting Claude Code in Docker..."
 docker run -it --rm \
     -v "$CURRENT_DIR:/workspace" \
     -v "$HOME/.claude-docker/claude-home:/home/claude-user/.claude:rw" \
+    $MOUNT_ARGS \
+    $ENV_ARGS \
     --workdir /workspace \
     --name claude-docker-session \
     claude-docker:latest "$@"

templates/.claude/CLAUDE.md

@@ -9,10 +9,14 @@ This is a containerized Claude Code environment with full autonomous permissions
    - Update it throughout your work to track progress
    - Use it to maintain context between sessions
 
-2. **Task Completion Notifications**: When you complete a major task:
-   - Send an SMS notification using the Twilio MCP server
-   - Format: "✅ Task complete | Task: [brief description] | Done: [what was accomplished]"
-   - Keep it concise - just the essentials
+2. **Task Completion Notifications**: ALWAYS send SMS when you complete significant work:
+   - **When to notify**: After completing any substantial task, debugging session, or reaching a milestone
+   - **How to send**: Use `twilio__send_text` command with the message
+   - **Message format**: "✅ [PROJECT] | [TASK] | [RESULT]"
+   - **Examples**: 
+     - "✅ MyApp | Bug fix complete | Fixed login validation issue"
+     - "✅ Website | Feature added | User dashboard now responsive"
+     - "✅ API | Tests passing | All 15 unit tests now green"
 
 3. **Working Environment**: You have full permissions to:
    - Execute any bash commands
@@ -20,9 +24,27 @@ This is a containerized Claude Code environment with full autonomous permissions
    - Access web resources
    - Manage the project autonomously
 
-## MCP Server Available
-- Twilio MCP server is running and available for SMS notifications
-- Use natural language to send SMS messages
-- Example: "Send SMS to notify that the task is complete"
+## Available Tools
+- **Twilio SMS**: `twilio__send_text` command available for notifications
+- **Full Bash Access**: All commands available with --dangerously-skip-permissions
+- **Context Persistence**: Use scratchpad.md for session memory
+- **Python/Conda**: Custom conda installation mounted (if configured)
+
+## Python/Conda Environment
+- When running Python commands or managing conda environments, use the mounted conda binary (if available) or fall back to system `conda`
+- ALWAYS use this exact format when running scripts in conda environments:
+```bash
+${CONDA_EXE:-conda} run --live-stream -n ENVIRONMENT_NAME python -u your_script.py [args]
+```
+- ALWAYS ensure the --live-stream and -u flags are enabled for real-time output and logs
+- Check available environments: `${CONDA_EXE:-conda} env list`
+- The conda installation preserves original paths so your existing environments and packages are accessible
+
+## SMS Notification Examples
+```
+twilio__send_text "✅ Docker Setup | Authentication fixed | Zero-friction login now working"
+twilio__send_text "✅ Bug Hunt | Memory leak resolved | App now stable under load"
+twilio__send_text "✅ Deployment | Production ready | Tests pass, security reviewed"
+```
 
 Remember: You're working in a safe containerized environment, so you can operate with full autonomy.