Fix the blockers for the next denbi run

[rcannood]

Describe your changes

Sweep of main before the next full run on de.NBI. Fixes everything that would make a method or metric silently not run, or not build.

• Fix methods/liger failing to build: drop the github: welch-lab/RcppPlanc install, whose cmake step no longer configures. rliger 2.2.1 already imports RcppPlanc (>= 2.0.0) from CRAN, so the line was redundant. Every Build on main today failed on liger and the build_main image dated from 2025-10-15. viash test green locally.
• Register methods/condo, methods/drvi, methods/limma_removebatcheffect, methods/seurat_cca, methods/seurat_rpca, methods/stacas, metrics/bras and metrics/cilisi in run_benchmark (both config.vsh.yaml dependencies and the lists in main.nf). They were all in src/ and the CHANGELOG, but the workflow never ran them.
• Add metric_type: embedding to metrics/cilisi and method_types: [embedding] to methods/drvi; without those the workflow filter never schedules them. cilisi viash test green.
• Give methods/scimilarity a gpu label and pass use_gpu=torch.cuda.is_available() to CellEmbedding; it was running CPU-only on a 5-cpu slot. Verified the component end-to-end on the test dataset with the model archive from s3://openproblems-work/cache/ (CPU path; no CUDA card here, so the GPU branch is first exercised on denbi).

Not in this PR: the flaky Bioconductor index fetches in the R image builds (unable to access index for repository https://bioconductor.org/packages/3.23/...) that hit batchelor_*, limma_removebatcheffect, scmerge2 and ss_stacas today. viash-actions' build workflow has no retry input, so the only cheap option is re-running the job; all their build_main images are fresh as of today.

Heads-up: CRAN lists RcppPlanc as "issues need fixing before 2026-08-26". If it gets archived, liger will need the CRAN archive tarball pinned explicitly.

Checklist before requesting a review

• I have performed a self-review of my code

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• CI Tests succeed and look good!