Prepare ProbeFlow for JOSS publication

[rohanplatts]

Goal

Prepare Probeflow for submission to Journal of Open Source Software. The Preparation requires: established human accountabitility, scientific validation, publication-quality documentation, and documented research use.

This is a parent / tracking issue. Individual tasks should be commpleted through separate sub-issues, and pull requests targeting develop. The final release will be erged from develop into main.

Completion criteria

Note: - [x] marks completed.

• Scientific AI-written code and tests have been
  independently reviewed and validated by humans.
• Supported formats, scientific claims, and known limitations
  explicitly documented.
• Third-party code and licensing audited.
• Research workflow and representative data have
  been archived with a DOI (Gustavo / Suhani zenodo ?)
• Genuine user feedback and resulting fixes publicly documented (from external lab)
• A stable JOSS candidate release has been tested and archived.
• paper.md and paper.bib included in repo and satisfy the JOSS requirements.
• The repository has passed an internal review against the JOSS
  review checklist.
• Rigorous Documentation of ProbeFLow architecture for add-ons / plug-ins / its Modularity.
• Some integration with existing software, e.g., Gwyddion / WsXM hooks for loaded image
• Citation, changelog, validation, contribution, and research-use
  documentation are complete.

Note: For Current phase, see the ordered sub-issues below. Sub-issue descriptions elaborated on as scope.md / required tasks become more clear.

Dev workflow

Sub-issues of the JOSS issue are stages. Real substantive work is to be done in sub-sub-issues, with the target branch being default.

Each substantive unit of work receives:

1. A linked sub-issue; any commentary on the sub-issue in the comments, and any applied alterations of comments should be acknowledged in the comments.
2. A branch created from develop; titled according to <type>/<issue-number>-<short-description>.
3. A pull request targeting develop linked to its JOSS sub-issue; Pull request description / title not AI written. feedback / commentary on the PR written in the PR's comments. Applied alterations acknowledged in the comments.
4. human review.
5. Closure after the accepted change is merged.