update biojava lib and PDB source
udpate fasta source to new library
update CDS source to new library
update uniprot fasta source
update UTR task
remove NCBI fasta source, it's not being used
a better solution for #123
test on loading dup chromosome regions
fixed template export button
Broke the law of Demeter - may she forgive me.

Don't fiddle with objects you don't control. In this case a method
added a value to a map it didn't create; and as we all know, maps
don't always support adding values, do they...
Make template json output useful for imjs.

We were not serialising all constraints, just editable ones. The way
imjs works means this is fairly pointless as it doesn't even use the
template query endpoints (and there is no benefit in doing so anyway).
This change means that imjs can natively consume available templates
listings now.
add incremental flag for builds (was implicit under certain conditions)
working version of worm gene expression scores
Fix user error being swallowed as HTTP 500.

addView throws IllegalArgumentException if the views are badly
formatted. This should be caught as user error.
publication url fix
changes the worm expression scores from gene to mRNA
Merge branch 'dev' of github.com:intermine/intermine into dev
update homology source to work with new data file content
change project XML config to accept true/false instead of summary/fullRecord. just to be consistent with the rest of the project XML attributes
merge dev into branch