Adopt some optimizations implemented by LIRMM in 2023

[jvendetti]

This pull request adopts some of the optimizations implemented by our LIRMM collaborators in their version of this library. The highlights include:

• Deprecate the find method in favor of get
• Modify the get method to add collection paths if not provided
• Stop refreshing the cache for all ontologies, submissions, and users when updating individual objects
• Cache the result of calls to top_level_links (the set of links never changes)

A more detailed explanation of these optimizations is available here: ontoportal-lirmm#14. The purpose of ingesting these optimizations now is part of a larger effort to address recent system instability in the BioPortal Ruby on Rails application: ncbo/bioportal-project#320.

Also included in this pull request:

• Remove the no longer used refresh_cache method
• Remove the no longer used spawnling dependency
• Bump minitest from 5.24.1 to 5.25.1
• Fix some RuboCop warnings