Audit and refactor ProbeFlow’s architecture

[rohanplatts]

Purpose

Review ProbeFlow’s architecture in depth, improve maintainability, testability, and extension boundaries before scientific validation and further feature development. Scribe all findings in rigorous documentation to be adhered to upon feature / bug fixing.

Adhere to: No scientific or user-facing behaviour should change and avoid refactoring for elegance's sake.

Completion criteria

• Map current architecture.
• Identify barriers to adding formats, processing operations, and
  optional extensions. (NEED Required refactors identified and prioritised).
• Create separate issues for each substantial refactor.
• Complete agreed high-priority refactors.
• Rigorously update dev architecture.md
• Rigorously update user documentatoin.

Completion will mean resulting codebase is suitable for the necessary rigorous scientific validation and subsequent gap-filling work.