New package structure
Moved from a analysis (I think)
Moved to org/pfaat/core/msa/analysis/
Moved to src/org/pfaat//core/msa/analysis/
Moved to src/org/pfaat//gui/msa/analysis/action/ExtractProfileDialog.java
No longer used
Moved to src/org/pfaat/gui/msa/analysis and src/org/pfaat/core/msa/analysis
Moved to src/org/pfaat/gui/msa/colorscheme
Moved to src/org/pfaat/commandline
