Removes extension of archives by default and ensures that jar/war products are built by defaultJar is added to runtime configuration, so picked up by dependent products, and jar/war tasks can remain enabled all the time. Jar and War products are still not added to archives by default, but these changes make that more readily possible in the future.
Separated classes ouput directory from resources output directory. This requires a code review but I preferred to check in the changes. Updated the documentation, user guide and tests accordingly. New property is called resourcesDir (I somewhat don't like the name but that's what we agreed with Adam).