ModSearchEngine and GlycanBox merging

[RayMSMS]

Summary of Changes

This PR introduces a new search engine for ModPair Search, supporting two distinct modes:

1. GlycoSearchEngine

• Database: Utilizes a glyco-only database with no non-glyco modifications.
• Motif Restriction: Specifically targets serine (S) and threonine (T) residues, optimized for O-glycan searches.

2. ModSearchEngine

• Database: Compatible with a general modification database, supporting broader search capabilities.
• Motif Extraction: Motifs are dynamically retrieved from the modBox via the getMotifs function.

Additional Changes

Unified Box Structure: The previously separate glycanBox has been merged into the more general-purpose modBox, since glycanBox did not contain any glycan-specific logic.