integrate broad fork of jalview into main codebase

Peter Sisk of the Broad mentioned the patched version of Jalview used on the tbdb site (http://genome.tbdb.org/annotation/genome/tbdb/AlignmentViewer.html?sp=S7000000635247869&sp=SMT_H37RV_V2_MERGECALLPOLY_8&sp=SM.+tuberculosis+H37Rv&sp=ZH4sIAAAAAAAAACWNMU4DMRBFByWwqdJQpeAK0cx6vGuXaQhocUPSW06UwgihaNeEhY5jUHAD7kHPPbgDHtN86b%2F58%2F%2FXL5wPPVw%2BhFNYPqf4uFz1fXi9i0Ma33%2BuPr7D5wTObmE6xLfDeASAxctUNMGka9qsW9FKM7NHFm%2B03KzK1JJHbK1Qkmynss7dPjwdUorRd0RNxps15bBLO39NVCqUhGuhTEyl%2BMIxIa4SzIhMnZkMIHpqbBlkK4Pao%2Bbsq7XzaE1paI0qDZU1nozKfzO39TeqvT%2FJmK3%2F46RRjX%2BBNzfbEAEAAA%3D%3D&sp=X&sp=T&sp=X) which allows a tree to be shown side by side with the alignment embedded as a panel on the page.

allowing other sites to easily recreate this functionality would be great!