Freeze branch for the BridgeDb 1.2.0 release

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@722 e3f1d335-44b1-4163-9530-9b341189ae98
Also delete target/ dirs when 'clean'-ing

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@723 e3f1d335-44b1-4163-9530-9b341189ae98
Bumped the version for the upcoming release

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@724 e3f1d335-44b1-4163-9530-9b341189ae98
Updated the MANIFEST.MF files for the upcoming release

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@725 e3f1d335-44b1-4163-9530-9b341189ae98
Ignore more autogenerated stuff

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@730 e3f1d335-44b1-4163-9530-9b341189ae98
Include the build-common.xml in the source distrib

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@731 e3f1d335-44b1-4163-9530-9b341189ae98
Bumped the version

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@732 e3f1d335-44b1-4163-9530-9b341189ae98
Add the MANIFEST.MF files

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@733 e3f1d335-44b1-4163-9530-9b341189ae98
Embed the required jars for starting the server

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@734 e3f1d335-44b1-4163-9530-9b341189ae98
Added a script to see if a jar is an OSGi jar (see http://stackoverflow.com/questions/19455486/how-can-i-test-if-a-jar-is-an-osgi-jar)

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@746 e3f1d335-44b1-4163-9530-9b341189ae98
Move OSGi bundles to transient

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@747 e3f1d335-44b1-4163-9530-9b341189ae98
Include transient deps in the distribution

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@748 e3f1d335-44b1-4163-9530-9b341189ae98
Copy the derby properly into the dist too

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@749 e3f1d335-44b1-4163-9530-9b341189ae98
Various updates: server.jar does not exist, mysql-connector-java-5.1.7-bin.jar is now embedded, and commons-cli-1.2.jar, org.restlet.ext.servlet.jar, and org.restlet.jar are OSGi jars (to be best of my knowledge)

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@750 e3f1d335-44b1-4163-9530-9b341189ae98
Fixed a typo in a test method

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@751 e3f1d335-44b1-4163-9530-9b341189ae98
Copied the Uniprot ID pattern from MIRIAM (via Christian)

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@752 e3f1d335-44b1-4163-9530-9b341189ae98
Addressed some issues identified by Christian in the deprecated API

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@753 e3f1d335-44b1-4163-9530-9b341189ae98
Added taxonomy support for Organism's (implementing an API suggested by Igor and Martijn in 2010; see issue #55)

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@754 e3f1d335-44b1-4163-9530-9b341189ae98
Updated the MIRIAM urn for the Gene Ontology (via Christian)

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@759 e3f1d335-44b1-4163-9530-9b341189ae98
Updated the unit tests for the updated GO MIRIAM urn

git-svn-id: http://svn.bigcat.unimaas.nl/bridgedb/branches/1.2.x@760 e3f1d335-44b1-4163-9530-9b341189ae98