Resolve "upgrade 3rd party libraries"

Closes #538 (closed)

added 28 commits

• 08f8fcc8 - dependcy versions are centralized
• e6adad94 - xeres version upgraded
• bd607032 - version of com.sun.xml.ws upgraded
• 10dcd0bc - miriam library upgraded
• 762b42fa - version of org.apache.httpcomponents upgraded
• e503dcb6 - fix on httpcomponents library upgrade
• 80879fa1 - mockito upgraded
• b1ff55db - spring upgraded to the newest 4.3
• 860feb0b - commons-io upgraded
• 72da92af - apache commons lang3 upgraded
• c969dc52 - commons-cli upgraded
• 8de7767b - batik upgraded
• 2f156a29 - itext upgraded
• 614fcfdb - hibernate upgraded
• 119ba9b8 - flyway upgraded
• 8e9e9529 - commons-net upgraded
• 79914841 - postgres driver upgraded
• b89495f3 - cglib upgraded
• ffa9b004 - gson upgraded
• 41e4b544 - jersey and jacskon upgraded
• 8246fe7d - servlet api upgraded to 3.1
• c2f2af02 - primefaces updated
• d0cd1a3e - jsf version upgraded
• fb045524 - commons-fileupload and commons-validator updated
• 4e175ff4 - chebi vesion upgraded
• 12c9e790 - junit dependecy included properly
• 184b9094 - when file is downloaded partially isCached returns false
• 92308cad - changes required due to library upgrades

Compare with previous version

added 3 commits

• 9e3652a5 - debug removed
• 9dbcc830 - homo sapiens was changed into homo sapien in ncbi database
• 1bea1514 - bundle plugin upgraded

Compare with previous version

added 1 commit

• 0cc78275 - junit dependency was removed

Compare with previous version

added 5 commits

• cd38d400 - configuration of spring security changed
• 5bd22f5a - urls don't contain double / characters
• 2a41e4de - base url doesn't contain double "/"
• c7ab4050 - jquery outerheight value changed for undefiend elements
• 41c30e47 - jquery vesion changed

Compare with previous version

unmarked as a Work In Progress

mentioned in commit cc19aaf1

merged