Fix issue where generated config-classes was not propogated.

Fixes #1568.

This is the fallout of attempting not to leak config-file classes. Since
we DO NOT have valid incremental compiler for config-classes, we've instituted
workaround to ensure that regular incremental compilation *AND* our own
sbt loader do not hose each other.   A full solution will eventually be
to find a way for .sbt files to participate in regular compilation of a
project.

For now, we fix the tracking of generated.class files throughout an sbt
"loadProjects" call, and then clean any .class files that were not
generated for a full reload.   This commit just fixes
a minor tracking issue.
Merge pull request #1581 from sbt/wip/fix-config-class-gc

Fix issue where generated config-classes was not propogated.