Fix Flow registration schema and publish a tested advanced-model runtime

[CharlotteAnne]

Flow registration used the legacy schema, and explicit DESeq2/CAMERA execution had no default container. This change makes flow/schema/main.json the sole current-format schema and supplies a tested, publicly downloadable immutable runtime in both the schema and Nextflow defaults.

• Remove the duplicate schema and guard uploaded inputs, custom sample columns, output declarations and default-image agreement with a schema contract test.
• Pin the Bioconductor base digest and assert R 4.4.1, DESeq2 1.44.0, limma 3.60.6 and edgeR 4.2.2. Preserve all installed-package versions and R session information.
• Run the synthetic statistical suite inside each image, compare both Docker-backed Nextflow paths against direct R outputs, then publish eligible candidates only after tests pass. Fork PRs cannot publish.
• Pull the registered default with an empty Docker credential configuration in CI to catch private or unavailable releases.

Default runtime: ghcr.io/charlotteanne/differential-analysis/advanced-model@sha256:6555b85f0de65ad43a31968014e8f2913b005dfeaf67fbd4a372199068f0a611.

The public package is hosted under CharlotteAnne. Its build, statistical tests, both Docker integration tests and publication passed. The full installed-package manifest matches the earlier tested organisation build. Anonymous manifest/configuration access returned HTTP 200, and the image digest was verified. The default stays pinned to this tested release; later candidate builds do not change it automatically.

All 18 checks passed on final commit e24f94e, including the full anonymous Docker pull, synthetic statistics, both Docker integration paths, installed-R integration and the legacy regression suites. There is no remaining package-visibility prerequisite.

No statistical methods changed. Flow registration and biological validation remain separate; no biological data were imported or analysed.