Repository cleanup and publication hardening.

[Huq2090]

The NanoPSD repository is now public and serves as the main codebase for the project.
To improve usability, reproducibility, and collaboration, the repository needs cleanup and the addition of standard documentation files to guide contributors.

Planned improvements include:

Repository cleanup

• Remove unused or obsolete files
• Improve directory structure
• Standardize file naming conventions
• Ensure outputs and temporary files are excluded from version control

Contributor guidance files

• Add or improve README.md
• Add or improve CONTRIBUTING.md with contribution workflow
• Add or improve CODE_OF_CONDUCT.md
• Add or improve CITATION.cff to guide citation of the software
• Add or improve LICENSE file (if not already present)
• Add or improve .gitignore improvements if needed

Goal
Provide a clean, well-structured, and professional public repository that facilitates collaboration and reproducible research.

This issue will track the repository cleanup and documentation improvements needed to support external contributors.