Add comprehensive README files to all directories for improved documentation

[Copilot]

Overview

This PR adds comprehensive README.md files to all major directories in the ICESEE repository (up to 3 levels deep), significantly improving documentation and making the codebase more accessible to contributors and users.

Changes

Added 30 new README files covering:

Applications (11 files)

• Overview of all supported models (Flowline, Icepack, ISSM, Lorenz96)
• Individual model documentation with usage instructions
• Example directories with guidance on running test cases
• Model-specific utilities documentation

Scripts (5 files)

• Data management utilities for handling ICESEE output
• MATLAB process management tools
• Visualization and plotting utilities for performance analysis
• SLURM job submission scripts for HPC environments

Source Code (12 files)

• Core framework architecture overview
• EnKF implementations (both Python and Cython versions)
• Parallelization infrastructure with MPI
• Main data assimilation workflow entry points
• Test suite documentation for all test categories
• Common utilities documentation

Configuration (2 files)

• Spack environment setup for dependency management
• HDF5/h5py parallel I/O environment configuration

Documentation Structure

Each README provides:

• Clear Purpose: Explanation of the directory's role in the framework
• Contents Overview: Description of files and subdirectories
• Usage Instructions: Code examples and command-line usage
• Dependencies: Required packages and tools
• Best Practices: Tips for effective usage
• References: Links to related documentation and resources

Benefits

1. Improved Navigation: Users can quickly understand the purpose and contents of each directory
2. Better Onboarding: New contributors can familiarize themselves with the codebase structure efficiently
3. Comprehensive Coverage: All major components now have dedicated documentation
4. Consistent Format: Uniform structure across all READMEs for easy reading
5. Self-Contained: Each README provides complete information about its directory without requiring external documentation

Statistics

• Total README files: 41 (30 new + 11 existing)
• Documentation added: ~87 KB (~2,156 lines)
• Directory coverage: 100% of directories up to 3 levels deep
• Average README size: ~72 lines

Next Steps

As outlined in the original issue, this completes the README preparation phase. The next steps are:

• Work on GitHub Actions
• Code cleanup

Closes #[issue_number]

Original prompt

Prepare a README file for each directory, after that we shall work on git actions and code clean app

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