Plugin Manager is too optimisitic about dependencies when installing unrelated plugins

[yaauie]

When using the plugin manager to install a plugin, even a plugin that is already installed, the plugin manager updates the graph to pull in updates to unrelated dependencies.

This recently lead to our users consuming Sinatra 2.2.0 on its release day (#13777), despite it introducing a JRuby-specific bug, because our dependency was merely listed as ~>2.

We should investigate if we can cause bundler to update transitive dependencies of Logstash if and only if they are also dependencies of the new plugins being installed or updated.