Corrected the function GetDegeneracy

The function did not work when there was indeed degeneracy
(accessor problem with array).
File renamed to follow bioconductor guidelines
Rene is added as an autor in all documentation

Removed 'hello world' files.
Modifications to Makevar and README for compilation on Windows.
Deleted data and part of fasta file to meet bioconductor 2M limit.
Correction of typos and small mistakes in the documentation.
Adjusted date, version and 'news' for first submission to bioconductor
Added version dependency on data.table.

Changed procedure for linking against expat during windows build.
Changed the PKG_LIBS definition

Change suggesteb by Simon Urbanek:
change PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"`
to PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` -lpthread -lexpat
to prevent configure problems.
Added xtandem license information
Added examples to the accessors and convertors man pages.
revision change
Disabled R C-stack checking
Corrected the Rprintf commands for better display of output.

Variables were not correctly interpolated in messages.
Added a setter for rTParam: setParamValue().

All examples were modified to use the new function.
Documenation was updated to include the new function.
Version change
Made the NAMESPACE more exhaustive

Changes suggested by Martin Morgan following 'codetoolsBioC'.
Import the latest from bioconductor's SVN. (rTANDEM version 1.1.1)
rTANDEM is now based on X!Tandem Jackhammer

Manually did a three-way merge between X!Tandem-
Cyclone, X!Tandem-Jackhammer and rTANDEM
Merge branch 'master' of ssh://gh/Frederic-bioinfo/rTANDEM