Refactor code structure for readability and maintainability

[alsmith151]

This pull request updates the documentation and example code for PlotNado, focusing on improving onboarding, clarifying workflows, and reorganizing the docs structure. The main changes include a major rewrite of the README.md to streamline installation and usage instructions, updates to the Quarto documentation navigation, and the addition of a new Python module for generating in-memory example data.

Documentation and onboarding improvements:

• README.md: Completely rewritten for clarity and ease of onboarding. The new README provides concise installation instructions, clearer separation between Python and CLI workflows, and emphasizes reproducible in-memory examples. It also updates feature lists, troubleshooting tips, and contribution guidelines. [1] [2] [3] [4]

Documentation structure and navigation:

• _quarto.yml: Refactored the navigation structure to improve the order and grouping of documentation sections, update descriptions, and clarify menu items. Some unused or redundant references were removed or renamed for clarity. [1] [2]

Example and utility code:

• docs/_examples.py: Added a new module containing utility functions for generating synthetic genomic signal, interval, and link data as pandas DataFrames. This module supports reproducible, in-memory examples for documentation and notebooks, and includes example figure-generating functions.

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 80.62%. Comparing base (3ec1d9f) to head (1a5982a).
⚠️ Report is 1 commits behind head on main.
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Additional details and impacted files

@@           Coverage Diff           @@
##             main      #32   +/-   ##
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  Coverage   80.62%   80.62%           
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  Files          41       41           
  Lines        5393     5393           
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  Hits         4348     4348           
  Misses       1045     1045           

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