changed imports as a result of moving various classes to org.pfaat
imports changes as result of moving classes to org.pfaat.
Moved to org.pfaat.core
Moved src/com/neogenesis/pfaat/common/progressbar to src/org/pfaat/gui/common/
copied over from pls module
Moved Version.java to src/org/pfaat/core/msa/help
removed import that is no longer used
comment out dead code
No longer used
