Add comprehensive README files to all directories for improved documentation

applications/README.md

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+# Applications
+
+This directory contains model-specific implementations and examples for the ICESEE data assimilation framework.
+
+## Supported Models
+
+### Flowline Model
+A simple 1D ice flow simulation model used for testing and benchmarking data assimilation workflows.
+- **Location**: `flowline_model/`
+- **Status**: Integration underway
+
+### Icepack Model
+PDE-based ice sheet modeling using the Firedrake finite element framework.
+- **Location**: `icepack_model/`
+- **Status**: Fully supported
+- **Dependencies**: Firedrake
+
+### ISSM (Ice Sheet System Model)
+Finite-element ice sheet modeling using MATLAB interface.
+- **Location**: `issm_model/`
+- **Status**: Development underway
+- **Dependencies**: ISSM, MATLAB
+
+### Lorenz96 Model
+Idealized nonlinear dynamical system for data assimilation benchmarking and testing.
+- **Location**: `lorenz_model/`
+- **Status**: Fully supported
+
+## Model Registration
+
+Models are registered in `supported_models.py`, which provides a centralized interface for model discovery and initialization within the ICESEE framework.
+
+## Structure
+
+Each model directory typically contains:
+- Example configurations and run scripts
+- Model-specific utilities and helper functions
+- Integration code for connecting to the ICESEE EnKF framework

applications/flowline_model/README.md

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+# Flowline Model
+
+A simple 1D ice flow simulation model for testing and benchmarking ICESEE data assimilation workflows.
+
+## Overview
+
+The flowline model provides a lightweight ice sheet representation that is computationally efficient for rapid prototyping and testing of data assimilation algorithms. It simulates ice flow along a single flowline using simplified physics.
+
+## Files
+
+- `flowline_enkf.py` - Main EnKF implementation for the flowline model
+- `config_loader.py` - Configuration file loader
+- `params.yaml` - Model parameters and DA configuration
+- `EnKF.ipynb` - Jupyter notebook demonstrating EnKF usage
+- `run_flowline_enkf.ipynb` - Complete workflow notebook
+
+## Usage
+
+### Running in Jupyter
+
+Open `run_flowline_enkf.ipynb` to see a complete example of:
+1. Model initialization
+2. Ensemble generation
+3. Data assimilation cycles
+4. Results visualization
+
+### Command Line
+
+```bash
+python flowline_enkf.py --config params.yaml
+```
+
+## Status
+
+Integration with ICESEE framework is currently underway. The model is functional for standalone testing and demonstration purposes.
+
+## Configuration
+
+Model parameters are specified in `params.yaml`, including:
+- Ensemble size
+- Observation frequency
+- Model physics parameters
+- Data assimilation settings
+
+Refer to the configuration file for detailed parameter descriptions.

applications/icepack_model/README.md

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+# Icepack Model
+
+Integration of the Icepack ice sheet model with the ICESEE data assimilation framework.
+
+## Overview
+
+Icepack is a Python library for modeling ice sheets using finite element methods via the Firedrake framework. This directory provides the interface between Icepack and ICESEE's Ensemble Kalman Filter implementation.
+
+## Structure
+
+- `examples/` - Example configurations and test cases for different ice geometries and scenarios
+- `icepack_utils/` - Utilities specific to Icepack model integration
+
+## Dependencies
+
+- Firedrake finite element library
+- Icepack ice sheet modeling library
+- ICESEE core framework
+
+## Examples
+
+The `examples/` directory contains various test cases including:
+- Idealized geometries
+- Synthetic ice streams
+- Realistic glacier scenarios
+
+Each example typically includes:
+- Configuration files
+- Mesh generation scripts
+- Initial condition setup
+- Observation generation
+
+## Status
+
+Fully supported and actively used for ice sheet state and parameter estimation.
+
+## Getting Started
+
+Refer to the examples in the `examples/` directory for complete workflows. Each example contains its own README with specific instructions.
+
+## Resources
+
+- [Icepack Documentation](https://icepack.github.io/)
+- [Firedrake Documentation](https://www.firedrakeproject.org/)
+- [ICESEE Wiki](https://github.com/ICESEE-project/ICESEE/wiki)

applications/icepack_model/examples/README.md

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+# Icepack Examples
+
+This directory contains example configurations and test cases for the Icepack model integration with ICESEE.
+
+## Available Examples
+
+Each subdirectory contains a complete example workflow with:
+- Model configuration
+- Mesh/geometry setup
+- Initial conditions
+- Observation specifications
+- Data assimilation configuration
+
+## Example Types
+
+Examples range from idealized test cases to realistic glacier scenarios, providing templates for various data assimilation applications with ice sheet models.
+
+## Running Examples
+
+Each example directory typically contains:
+1. Configuration files (YAML)
+2. Python scripts or Jupyter notebooks
+3. Documentation (README.md)
+4. Results/output directories
+
+Refer to individual example READMEs for specific instructions.
+
+## Requirements
+
+- Firedrake and Icepack installed
+- ICESEE framework
+- Sufficient computational resources (varies by example)
+
+## Contributing
+
+When adding new examples:
+- Include a README describing the scenario
+- Provide clear configuration files
+- Document expected results
+- Keep examples self-contained

applications/icepack_model/icepack_utils/README.md

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+# Icepack Utilities
+
+This directory contains utilities specific to the Icepack model integration with ICESEE.
+
+## Purpose
+
+These utilities provide helper functions and tools for:
+- Model initialization and setup
+- Data conversion between Icepack and ICESEE formats
+- Mesh handling and geometry operations
+- Firedrake-specific operations
+- Result post-processing
+
+## Structure
+
+Utilities are organized to support:
+- Model preprocessing
+- Runtime operations
+- Post-processing and analysis
+
+## Usage
+
+Import these utilities in your Icepack-ICESEE workflows:
+
+```python
+from applications.icepack_model.icepack_utils import ...
+```
+
+## Dependencies
+
+- Firedrake
+- Icepack
+- ICESEE core framework
+
+Refer to individual utility modules for specific dependencies and usage examples.

applications/issm_model/README.md

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+# ISSM Model
+
+Integration of the Ice Sheet System Model (ISSM) with the ICESEE data assimilation framework.
+
+## Overview
+
+ISSM is a comprehensive finite-element ice sheet model that includes a wide range of physics and capabilities. This directory provides the interface between ISSM and ICESEE's ensemble-based data assimilation methods.
+
+## Structure
+
+- `examples/` - Example configurations and test cases using ISSM
+- `issm_utils/` - Utilities for ISSM model integration and MATLAB-Python interfacing
+
+## Dependencies
+
+- ISSM (Ice Sheet System Model)
+- MATLAB with ISSM installed
+- ICESEE core framework
+- Python-MATLAB bridge
+
+## Status
+
+Development underway. The integration is being actively developed and tested.
+
+## Examples
+
+The `examples/` directory contains test cases including:
+- ISMIP benchmark experiments
+- Realistic ice sheet configurations
+- Parameter estimation scenarios
+
+## MATLAB Interface
+
+Since ISSM primarily operates through MATLAB, special utilities are provided in `issm_utils/` to facilitate:
+- MATLAB-Python communication
+- Data conversion between MATLAB and Python formats
+- Process management for MATLAB instances
+
+## Getting Started
+
+Refer to the examples in the `examples/` directory. Note that ISSM must be properly installed and configured in your MATLAB environment.
+
+## Resources
+
+- [ISSM Website](https://issm.jpl.nasa.gov/)
+- [ISSM Documentation](https://issm.jpl.nasa.gov/documentation/)
+- [ICESEE Wiki](https://github.com/ICESEE-project/ICESEE/wiki)

applications/issm_model/examples/README.md

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+# ISSM Examples
+
+This directory contains example configurations and test cases for the ISSM model integration with ICESEE.
+
+## Available Examples
+
+Examples demonstrate various ISSM capabilities with data assimilation, including:
+- Benchmark experiments (ISMIP)
+- Realistic ice sheet scenarios
+- State and parameter estimation workflows
+
+## Example Structure
+
+Each example typically includes:
+- MATLAB scripts for ISSM model setup
+- Python scripts for ICESEE integration
+- Configuration files
+- Documentation
+
+## Requirements
+
+- ISSM installed and configured in MATLAB
+- MATLAB with Python interface
+- ICESEE framework
+
+## Running Examples
+
+Since ISSM operates primarily through MATLAB:
+1. Ensure ISSM is properly installed in your MATLAB environment
+2. Configure Python-MATLAB interface
+3. Follow example-specific instructions in individual READMEs
+
+## Notes
+
+The ISSM integration is under active development. Some examples may require specific ISSM versions or configurations.
+
+## Resources
+
+- [ISSM Documentation](https://issm.jpl.nasa.gov/documentation/)
+- [ISMIP Protocols](http://www.climate-cryosphere.org/wiki/index.php?title=ISMIP6)

applications/issm_model/issm_utils/README.md

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+# ISSM Utilities
+
+This directory contains utilities for ISSM model integration with ICESEE.
+
+## Purpose
+
+These utilities facilitate:
+- MATLAB-Python communication
+- ISSM data conversion to ICESEE formats
+- Process management for MATLAB instances
+- Model state and parameter handling
+- Results extraction and post-processing
+
+## Key Components
+
+### matlab2python/
+Tools for converting MATLAB data structures to Python formats and vice versa.
+
+### containers/
+Container configurations for running ISSM with ICESEE in containerized environments.
+
+## Usage
+
+These utilities bridge the gap between ISSM's MATLAB environment and ICESEE's Python framework, enabling seamless data exchange during data assimilation cycles.
+
+## MATLAB Interface
+
+Special consideration is given to:
+- Efficient data transfer between MATLAB and Python
+- Proper MATLAB process lifecycle management
+- Error handling across the MATLAB-Python boundary
+
+## Dependencies
+
+- MATLAB
+- ISSM (properly configured in MATLAB)
+- Python MATLAB Engine API
+- ICESEE core framework
+
+Refer to individual utility modules for specific usage patterns and requirements.

applications/lorenz_model/README.md

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+# Lorenz Model
+
+Implementation of the Lorenz96 model for data assimilation testing and benchmarking.
+
+## Overview
+
+The Lorenz96 model is a simplified dynamical system originally designed to study atmospheric predictability. It serves as an excellent testbed for data assimilation algorithms due to its chaotic behavior and computational efficiency.
+
+## Structure
+
+- `examples/` - Example configurations and test cases
+- `lorenz_utils/` - Utilities specific to Lorenz96 model integration
+
+## Model Description
+
+The Lorenz96 model is a system of ordinary differential equations with the form:
+
+```
+dX_i/dt = (X_{i+1} - X_{i-2}) * X_{i-1} - X_i + F
+```
+
+where:
+- `X_i` represents the state variable at location i
+- `F` is a forcing parameter (typically 8)
+- Cyclic boundary conditions are applied
+
+## Use Cases
+
+This model is ideal for:
+- Testing new data assimilation algorithms
+- Benchmarking EnKF performance
+- Understanding nonlinear DA behavior
+- Educational demonstrations
+- Algorithm parameter tuning
+
+## Status
+
+Fully supported and extensively tested.
+
+## Examples
+
+The `examples/` directory contains various scenarios including:
+- Different system sizes (number of variables)
+- Various observation configurations
+- Perfect and imperfect model experiments
+- Parameter estimation tests
+
+## Getting Started
+
+See the examples in `examples/lorenz96/` for complete workflows demonstrating:
+- Model initialization
+- Ensemble generation
+- Observation simulation
+- EnKF application
+- Results analysis
+
+## Resources
+
+- Original Lorenz96 paper: Lorenz, E. N. (1996). "Predictability: A problem partly solved"
+- [ICESEE Wiki](https://github.com/ICESEE-project/ICESEE/wiki)