Quick fix for the context download issue #107
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This PR provides a quick fix for the context download issue, but storing the two most recent contexts in the JAR file so that they can used even without an internet connection. We will need the internet to download the Phyloref, CDAO and TCAN ontologies, but those can be stored in an
ontologies/
directory, so in theory this gets us to the point where JPhyloRef can be run without an internet connection. However, this has not yet been tested on HiPerGaTor as we are in the process of moving from one server to another there.WIP: Hopefully this will not be needed at all if I can get the more comprehensive solution in PR #106 to work. But I wanted to hold onto this code if it is needed as an intermediate solution.