SplignCompartCommand options rename.

Options of SplignCompartCommand have been renamed from "reference" and
"target" to "genome" and "CDS", respectively.
Big update v0.9.0

Warning: This is a big commit that should have been split into several
minor commits.

The modifications included in this commit are:
	- Windows run scripts removed.
	- Linux run scripts changed. Now the "run.sh" runs the application
without data validation. The alternative run script is now
"run-validate.sh"
	- Reformat fasta modified to include sequence renaming.
	- Merge fasta operation added.
	- Help menu added with two options:
		- Help: still unimplemented.
		- About: showing information about the research groups involved.
	- Better operation dialog sizing.
	- Spling-compart bug that was causing empty result files fixed.
	- Repository tree bug that was causing duplicate and missing element
updates fixed.
Prefix renaming bug fix

A bug that was causing an incorrect fasta sequence name change when
using the "Prefix" method was repaired.
Fasta sequence renaming improvement

New options added to the fasta reformat operation. Now it is possible to
keep the sequence name and to include or not a counter after the prefix
when using the "Prefix" sequence name reformat method. In addition, the
"Separator" parameter allows user to select the separator to use when
several parts (e.g. prefix, counter, etc.) are used to create the new
name.

Minor source formating.