Documentation Expansion & Update

## Description
Expand and update the project documentation. Create new docs for:
- General project structure and workflows
- Step-by-step guides for all Python tools (combiner, plot GUI, etc.)
- Usage examples and best practices
- Troubleshooting and FAQ

## Motivation
- Improve onboarding for new users and contributors
- Make all features and workflows easy to understand
- Ensure Python scripts are well documented for analysis and visualization

## Tasks
- [ ] Create new documentation pages for project structure and workflows
- [ ] Update existing docs for accuracy and completeness
- [ ] Write detailed guides for each Python tool (usage, options, output)
- [ ] Add example workflows and screenshots
- [ ] Document troubleshooting steps and common issues

## Benefit
- Easier for users to get started and use all features
- More contributors can help with development
- Python tools become more accessible for data analysis

---
*Please prioritize documentation improvements to support the growing user base and future development.*

No files or existing documentation pages are named. Begin by inventorying the repository structure and the Python tools mentioned, including the combiner and plot GUI, then identify the existing documentation to update. Done means the requested guides, examples, screenshots, FAQs, troubleshooting steps, and workflow documentation are complete and accurate.

Written by the indexing model from the issue text.