docs(remove50Missing): Clarify documentation regarding remove50Missing parameter

[tonywu1999]

Motivation and Context

I got questions regarding the remove50Missing parameter, and then realized that the documentation is a bit hard to follow and doesn't define the feature well. Adjusted the parameter definition.

Changes

• Adjusted the documentation regarding the remove50Missing parameter to be more clear on what it actually does.
• Cleaned up documentation setup for MSstatsSummarize

Testing

• Manuals have been updated with new information.

Checklist Before Requesting a Review

• [x] I have read the MSstats contributing guidelines
• [x] My changes generate no new warnings
• [x] Any dependent changes have been merged and published in downstream modules

[tonywu1999]

Looking into the dry run errors right now. I think they're unrelated to my changes.

Fix: https://github.com/Vitek-Lab/MSstats/pull/124

[mstaniak]

Thank @tonywu1999. @devonjkohler I think we discussed this some time ago. Was the conclusion that it's better to actually remove this parameter? There's a question about it in the google group again, I'll double check the behavior of this and related options [counts].