Add modular system package installation support

Implemented SYSTEM_PACKAGES environment variable for flexible system library installation:

Key Features:
- Users specify packages in .env: SYSTEM_PACKAGES="libopenslide0 libgdal-dev"
- Packages installed during Docker build (secure, no runtime mounting)
- Automatic rebuild detection when packages change
- Documentation with common scientific computing packages

Technical Implementation:
- ARG SYSTEM_PACKAGES in Dockerfile with conditional apt-get install
- Build argument passed from claude-docker.sh script
- Clean package management with cache cleanup

Benefits:
- Secure: No system directory mounting required
- Flexible: Users choose exactly what they need
- Documented: Common packages listed in README
- Clean: Packages baked into image, not mounted at runtime

Tested successfully with OpenSlide: conda run -n prism python -c "import openslide"

.env.example

@@ -13,6 +13,16 @@ 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)
+# Directories are mounted to the same path inside the container
+# Automatic detection:
+#   - Paths with "*env*" are added to CONDA_ENVS_DIRS (for environments)
+#   - Paths with "*pkg*" are added to CONDA_PKGS_DIRS (for package cache)
 # 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=
+CONDA_EXTRA_DIRS=
+
+# Optional: System packages to install in Docker container (space-separated)
+# Common scientific packages: libopenslide0 libgdal-dev libproj-dev libopencv-dev
+# Example: SYSTEM_PACKAGES="libopenslide0 libgdal-dev"
+SYSTEM_PACKAGES=

Dockerfile

@@ -12,6 +12,17 @@ RUN apt-get update && apt-get install -y \
     sudo \
     && rm -rf /var/lib/apt/lists/*
 
+# Install additional system packages if specified
+ARG SYSTEM_PACKAGES=""
+RUN if [ -n "$SYSTEM_PACKAGES" ]; then \
+    echo "Installing additional system packages: $SYSTEM_PACKAGES" && \
+    apt-get update && \
+    apt-get install -y $SYSTEM_PACKAGES && \
+    rm -rf /var/lib/apt/lists/*; \
+else \
+    echo "No additional system packages specified"; \
+fi
+
 # Create a non-root user with matching host UID/GID
 ARG USER_UID=1000
 ARG USER_GID=1000

README.md

@@ -113,6 +113,12 @@ This workflow gives you:
 - Configurable via MCP integration
 - Optional - works without if Twilio not configured
 
+### 🐍 Conda Integration
+- Supports custom conda installations (ideal for academic/lab environments)
+- Mounts conda directories to preserve original paths and configurations
+- Automatic environment variable configuration for seamless conda usage
+- Works with environments and package caches in non-standard locations
+
 ### 🗂️ Context Persistence
 - Maintains scratchpad.md files for project memory
 - Persistent across container sessions
@@ -181,7 +187,49 @@ claude-docker
 Rebuild when you:
 - Update your .env file with new credentials
 - Update the Claude Docker repository
-- Want to refresh the authentication files
+
+### Conda Configuration
+
+For custom conda installations (common in academic/lab environments), add these to your `.env` file:
+
+```bash
+# Main conda installation
+CONDA_PREFIX=/vol/biomedic3/username/miniconda3
+
+# Additional conda directories (space-separated)
+CONDA_EXTRA_DIRS="/vol/biomedic3/username/.conda/envs /vol/biomedic3/username/conda_envs /vol/biomedic3/username/.conda/pkgs /vol/biomedic3/username/conda_pkgs"
+```
+
+**How it works:**
+- `CONDA_PREFIX`: Mounts your conda installation to the same path in container
+- `CONDA_EXTRA_DIRS`: Mounts additional directories and automatically configures conda
+
+**Automatic Detection:**
+- Paths containing `*env*` → Added to `CONDA_ENVS_DIRS` (conda environment search)
+- Paths containing `*pkg*` → Added to `CONDA_PKGS_DIRS` (package cache search)
+
+**Result:** All your conda environments and packages work exactly as they do on your host system.
+
+### System Package Installation
+
+For scientific computing packages that require system libraries, add them to your `.env` file:
+
+```bash
+# Install OpenSlide for medical imaging
+SYSTEM_PACKAGES="libopenslide0"
+
+# Install multiple packages (space-separated)
+SYSTEM_PACKAGES="libopenslide0 libgdal-dev libproj-dev libopencv-dev"
+```
+
+**Common packages:**
+- `libopenslide0` - OpenSlide for whole slide imaging
+- `libgdal-dev` - GDAL for geospatial data
+- `libproj-dev` - PROJ for cartographic projections  
+- `libopencv-dev` - OpenCV for computer vision
+- `libfftw3-dev` - FFTW for fast Fourier transforms
+
+**Note:** Adding system packages requires rebuilding the Docker image (`docker rmi claude-docker:latest`).
 
 ## Requirements