Small stuff. I'm fine if you want to kill the binary & bundle goals' jar goal dependency / use in a follow up.
This is a lie, there is no such thing as a bundle's classes dir. Needs some rewording, maybe: Create a single jar with all internal and 3rdparty classfiles at the root of the bundle. If unset, the root jar will contain internal classfiles only and link 3rdparty jars via a Class-Path manifest entry to copies in the bundle libs/ dir.
fat_jar, mono_jar ... all jars are loose classfile jars. I cannot come up with a name I like either :/
Have a single internal classes dir even in a non-deployjar bundle.
Review Request #358 — Created May 15, 2014 and submitted
This restores the status quo ante. This turns out to make the code a lot simpler too. The terminology 'deployjar' is confusing, so I changed the name of the internal method deployjar() to loose_classfiles_jar(), which is more descriptive. However I left the term 'deployjar' in the cmd-line flag name, for backwards compatibility.
All unittests pass. Manually ran binary and bundle creation with and without deployjar flag. Inspected jar and MANIFEST.MF contents manually to ensure that they're as expected. We should really buff up the tests for these...