Also un-ignore libs dir under plugins.

The configure script isn't smart enough to check if there are
un-ignored files in a directory, so this fixes that.
Descend into included directories to check for file inclusion.

Only applies to directories that are marked as unignored, since the
travis script has the odd problem of not descending into those
directories and, as a result, not recording the files in them.

I'm assuming the failure to descend into included directories is
unintended.
Merge pull request #9139 from nilium/v3-plugin-libjars-unignore

Unignore libs dir and fix Travis script to descend into included directories. (follows #9108)