Migrate upload and qsee preprocessing to playbase.preprocess

[phisanti]

Summary

The app stops calling preprocessing primitives scattered across playbase and talks to one boundary instead. Two consequences shape this PR:

1. One options object describes a run. The QC/BC panel builds a single canonical option list; staged previews and the submitted matrix are the same description with stages switched off. What you see in the panel is what
   compute runs.
2. counts is the pure user input, so boards must ask for it aligned. pgx$counts keeps its uploaded shape and no longer matches pgx$X. .opg_pgx_analysis_counts() is the only supported way to read counts on X's axes — never index pgx$counts directly in a board.

components/
├── board.upload/R/
│   ├── upload_preprocess.R          # NEW, 487 lines — the boundary:
│   │                                #   option builder · staged previews
│   │                                #   createPGX handoff · aligned counts
│   ├── upload_module_normalization.R  # QC/BC panel emits the canonical options
│   ├── upload_module_computepgx.R     # splits the batch selector for createPGX
│   └── upload_server.R                # reanalysis payload + contract gate
│
├── app_qsee/R/                      # compute files repointed at the leaf;
│                                    #   plot files migrated to omicsplots bundles
├── board.dataview/  (9 sites) ┐
├── board.expression/(3 sites) ├─ read counts via .opg_pgx_analysis_counts()
└── app_qsee/        (1 site)  ┘

Merge order

Depends on bigomics/playbase#526
playbase → this PR.

Testing

• 66 contract tests pass (tests/testthat/test-upload-preprocess-contract.R)
• Verified against example-data.pgx, mouse-example.pgx, arabidopsis.pgx
  and the AML multi-omics dataset
• Parser-level scan confirms no remaining bad omicsplots:: arguments
• Single-cell, methylomics (BMIQ) and Olink/NuLISA NPX paths were not tested.

[phisanti]

Please @ivokwee confirm if we close this PR in favour of using the branch as reference for fanta.

[phisanti]

Implementation in shiny OPG cancelled. This will go directly to fanta