I can buy that....generating to the build directory.  There are two remaining
points then: 

1) Should the files be generated to their own separate directories?

My opinion is an emphatic "yes".  How about something like:

build/codeGen/main/java -- Generated production Java source
build/codeGen/main/resources -- Generated production resources
build/codeGen/test/java -- Generated test java source
build/codeGen/test/resources -- Generated test resources

2) Should the folder which is added to the IDE contain the generated source
or the classes compiled from the generated source?

My opinion is "the generated source".  This allows the IDE to fully control
the compilation and/or processing of the source files.  I would think it
would also simplify the internal Gradle architecture since, once these
additional directories are added to the sourceSet, they don't need any
special handling to compile/process them.  The existing compileJava*** and
process***Resources tasks can handle them.

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