This was because that package depends on a different version of jersey-jackson or whatever, which was discovered by classpath scanning, and so because Eclipse doesn't keep a separate test classpath, we'd be discovering a new MessageBodyWriter which Jersey would be using to override the Dropwizard supplied MessageBodyWriter, which would not have the appropriate Jackson modules.
It was a mess.
It is a littlebit sad, that there are no javac warnings enabled by default that at least check known classes for conflicts in the classpath. An IDE should do that by default, too.
Where does bytecode manipulation or code generation happen in Dropwizard? Reflection for sure, but not any more so than any major web framework in a dynamically typed language.
Maybe you're referring to the SQL library they suggest (which I've admittedly never used heavily). But I don't see how you can have a SQL library without generating SQL.