I have found the reason this bug happens. Document...

# kobalt

[dimsuz]

I have found the reason this bug happens. Documented in the issue.

In short: for some reason when using 'directory = customdir' class files are still being put to kobaltBuild at the root directory, rather than to customdir/kobaltBuild. So they are never found by an assemble task and don't get put to the resulting jar...