Improvement and creation of operations

ORF entity is no longer used and replaced for a Fasta entity in the GetORF operation. In addition, the GetORF operation now incorporates the "no new line" option.

Entities in the tree view now can be exported. In addition, more entities can be deleted.

BLAST operations now include the option to delete the single sequence files created.
Version update in build.xml
NCBI merge operation support.
Query (SearchEntry) deletion support.

Queries of Search Entries can be deleted as other entities can.

As a minor change, "external" BLAST options now have the same order as
"internal" BLAST options.
Merge branch 'development'
Bug 131. Text appearance in the popup menus of the repository.

The text "Export Database Export Entry to..." was replaced by "Export
database entry to...". Additionally, the export messages now are showed
in lower case, except for the first letter.
Bug 134. ReformatFasta operation.

The ReformatFasta operation allows users to change the format of Fasta
files by changing the line width of the sequences.
SplignCompartCommand options rename.

Options of SplignCompartCommand have been renamed from "source" and
"target" to "reference" and "target".
Bug 133. Not all sequences are retrieved. Repository tree improvement.

This bug was causing that BLAST operations using a multiple sequence
FASTA file as query only generate results for the first sequence.

While solving this bug, an bug in the repository tree view was detected.
This bug hanged the application when several files were deleted (as
occurs in the BLAST operations). Repository tree was improved and, in
addition to the bugfix, now the items are sorted by alphabetical order.
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.