Major refactoring for new release.

[ypriverol]

Description of feature

The following error #459 triggered a discussion about the new OpenMS version and quantms. We should refactor the pipeline for the new OpenMS version.

• CI/CD ci.yml testing in dev PRs should always use the newest version of OpenMS dev profile singularity and docker. Conda must be only tested in PRs against master
• ProteinInference should always make sure that will be using the PEP score: -Algorithm:score_type "PEP"
• Remove IDFilter after PercolatorAdapter, Percolator adapter will have this possibility now.
• IDSwitcher is not needed.
• Remove PSMFeatureExtractor All the search engines will have the features afterwards. No need to rerun this.

Feedback @timosachsenberg @jpfeuffer

[jpfeuffer]

Do we really have an IDFilter after the search engines? I thought only after Percolator.
And we added filtering to the PercolatorAdapter

[ypriverol]

Yes sorry, I edited the original post.

[ypriverol]

One of the errors is back https://github.com/bigbio/quantms/actions/runs/12435901319/job/34722665635?pr=464 @daichengxin