chore: migrate from qs to qs2 package (GDR-3351)

[gladkia]

Description

What changed?

Related JIRA issue: GDR-3351

Replaced all usage of the archived qs package with qs2:

• qs::qread() → qs2::qs_read()
• qs::qsave() → qs2::qs_save()
• File extensions updated from .qs to .qs2
• Dependency in DESCRIPTION updated accordingly
• Tests and vignettes updated to reflect the new API

Why was it changed?

The qs package was archived on CRAN on January 17, 2026 and will not be included in Bioconductor 3.23.
The qs2 package is its official successor with an incompatible binary format.

Checklist for sustainable code base

• I added tests for any code changed/added
• I added documentation for any code changed/added
• I made sure naming of any new functions is self-explanatory and consistent

Logistic checklist

• Package version bumped
• Changelog updated

[gemini-code-assist]

Code Review

This pull request migrates the package from the qs dependency to qs2, updating function calls and file extensions across the codebase, tests, and vignettes. Feedback indicates that qs2 should be moved from Suggests to Imports since it is used in exported functions. Additionally, a bug was identified in the 384-well plate test where 96-well data variables were incorrectly reused, and a misleading variable name in the test suite should be renamed for clarity.

[j-smola]

Please, update doc with devtools::document().

What with RUN Rscript -e 'BiocManager::install(c("BiocStyle", "qs"))' in DOCKERFILE?

[gladkia]

Please, update doc with devtools::document().

What with RUN Rscript -e 'BiocManager::install(c("BiocStyle", "qs"))' in DOCKERFILE?
Done.

[bczech]

Please reoxygenate