initialization of plugin repositories, online and local in pluginmanager module

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3816 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
fixed setting up local repository in case it doesn't exist

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3817 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
added missing libs to exe ant task

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3818 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
created bundle directory, install local plugins, also get started after pathvisio is restarted

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3819 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
implemented method to download plugins from the repository

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3820 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
added missing library

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3821 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
updating all manifests of the core modules with additional OSGi manifest headers

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3822 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
remove empty directories

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3823 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
disabled ensembl conversion to old ensembl identifiers

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3824 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
deprecated getGeneID(), setGeneID() ; see getElementID(), setElementID() instead


git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3827 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
moved GPML.xsd to GPML2013.xsd maintaining the naming convention


git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3828 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
New GPML xsd introduced, interaction annotation enabled and related changes


git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3832 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
bug fix #1528

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3834 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
changed namespace back to genmapp for now

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3837 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
added optional junit bundle dependency for core bundles with test implementation, fix bug with new schema

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3838 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
Changes for tickets 1520 , 1537, 1540

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3839 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
Added select all labels function

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3840 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
Reverted unintended change in get_defaults

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3841 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
added junit library to test path in build.xml file

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3842 4f21837e-9f06-0410-ae49-bac5c3a7b9b6
extended new plugin manager module and moved functionality to that module

git-svn-id: http://svn.bigcat.unimaas.nl/pathvisio/trunk@3843 4f21837e-9f06-0410-ae49-bac5c3a7b9b6