full code refactoring using the Vue.js framework

[martin-raden]

goals

refactor the whole code base of the project using the Vue.js framework

details goals are:

• segment website and source into logical parts and reflect this decomposition by folder and file hierachies
• reduce individual file sizes to less than 500 lines each
• improve readability by AI agents and reduce required context sizes to work on tasks
• refactor redundant and inefficient code work and simplify where appropiate
• do a clear separation of model and views and ma
  • model = all data that defines the visualization (rna sequences, colors, highlightings, ...)
  • "canvas view" = varri-js library part to render the model
  • "ui view" = user interface to set and update the model
  • allow for exporting and importing the model via url parameters
  • examples are stored models with additional meta data
• rewrite all testing respectively
• also decompose varri-js source respectively but ensure a single js artifact is compiled via github actions on respective source changes
• extract and refactor the required fornac core functions into the new varri-js src framework without fornac dependency and full control and understanding of the visualization graph and d3 settings
  • add individual markdown documentation files for
    • the underlying force fied graph
    • the visualization architecture and workflow of generation
• rewrite the library with a focus on efficiency, code reusability and understandabilty by ai coding agents
• add guiding information for ai coding agents also in form of AGENTS.md directives
• ensure implemented all features of the original version are maintained
• generate a markdown protocol of changes, relations of old and new code, open issues, potential problems,

open a respective pull request to protocoll the progress or this issue and where the created detailed markdown protocol is linked respectively for inspection