Recreated Evosuite tests. Updated README from master branch. Various pom changes including removing the ssh plugin jar. Removed latex files from docs directory as these are no superceded by docx manuals that can be exported to html/pdf

Changed EBI DbFetch code so that the function works again. Added latest picard jar. More work on CRAM file loading. Updated/added scripts for application start. Small tweaks to makefile/ant. Removed gff2embl and gene_builder. Recreated evosuite tests.

Rather than testing the Ant build under multiple JDKs, I've arbitrarily
decided to test it only under openjdk7.  This keeps us to 4 builds
rather than 6 before the build is reported as green which should be a
bit quicker.

ant builds copy everything in the pwd into ant_build and then try to
build all of the java files copied, including those of the dependencies
which are built separately.  This does not end well.

We don't