Fixing superposition bug in CeCPMain.invertAlignment
Adding CECPParameters class

Stores parameters for CeCPMain:
- __DuplicationHint__ controls which protein gets duplicated
- __minCPLength__ controls minimum block length

Tests run with DUPLICATE_RIGHT to simulate existing behavior,
but the default is DUPLICATE_SHORTER for performance and
(hopefully) quality.
Adding Enums to ParameterGUI
Added nice names to DuplicationHints

The toString method is displayed now, while the name() method
identifies the enum internally.
Fix infinite recursion with DUPLICATE_LEFT

Also improves JavaDocs