Remove Mascot search and import support

[labkey-jeckels]

Rationale

Remove Mascot support from the MS2 module, which has gone unused for years.

Related Pull Requests

• Remove Mascot test infrastructure testAutomation#3231

Changes

• Remove the Mascot search pipeline, the Mascot server configuration and connection test, and native .dat result import, viewing, and search indexing
• Remove the Mascot run type, so Mascot-exported pepXML now imports as an unknown search engine
• Upgrade script permanently drops the Mascot-only file columns from ms2.Runs and deletes the stored Mascot server settings
• Existing Mascot runs stay in the database but display as an unknown run type, without their peptide grid, Mascot scores, MS2 search listing, experiment-run link for pipeline searches, or spectra for native .dat imports
• Saved views, reports, and queries that reference the removed Mascot tables or columns will no longer resolve
• Remove the Mascot test and sample data
• Drop the unused opencsv and Lombok dependencies

Tasks

• Claude Code Review
• Manual Testing - N/A
• Test Automation - N/A
• User Education @labkey-hannah @labkey-keith
  • I (Josh) don't think that anyone will care

[labkey-adam]

We still have full support for Phenyx?!

[labkey-keith]

@labkey-hannah, one note about user education. I think we archived all of the MS2 docs after 24.11.