Hope it's OK for me to chime in on this.

I would strongly vote for generating files into separate directories. 
Following are some thoughts:

* Combining static files with generated files is going to lead to
hacks...like including the same class files twice on the IDE classpath and
becoming dependent on classpath order.  IMHO that is asking for trouble.

* I'm not so sure generating files into the "build" directory is a good idea
either.  Why not treat these things like 1st class source folders and put
them under "src".  If not, why not put them under another top level
folder...say "genSrc".

* For the Java plugin at least it would be great it there could be full
support for all of the following: "main" source files, "main" resource
files, "test" source files, and "test" resource files.  I have a project
which has a use case for all of these.

Here's a concrete proposal for what the Java plugin could support:

src/codeGenMain/java -- Generated production Java source
src/codeGenMain/resources -- Generated production resources
src/codeGenTest/java -- Generated test java source
src/codeGenTest/resources -- Generated test resources

Another alternative is:

genSrc/main/java -- Generated production Java source
genSrc/main/resources -- Generated production resources
genSrc/test/java -- Generated test java source
genSrc/test/resources -- Generated test resources

In either case:

* Gradle would wipe out the contents of these directories when the "clean"
task was run.
* Gradle would generate the files for the java directories BEFORE the
appropriate "compile***" or "process***Resources" task was run.  Gradle
would compile or process these files just as it does the static files.
* Gradle would add these folders to the IDE classpath.


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