Stop using deprecated Server.connect method.

Just use the Server constructor instead.
Workflows are now passed in as byte[] not String.
Baclava output is now returned as a byte array.
Catch new exception if inputs are not set.

Run.start now throws a RunInputsNotSetException if any runs are not set when it
is called. Catch it and do the right thing.
Update for use of InputPort.setFile().

This now throws a FileNotFoundException if the file does not exist or is not
readable so handle this.
ServerInfo: Minor update to reflect change in Server API.

Server.getUri() renamed to Server.getURI().
RunWorkflow and GetOutput changes for new OutputPort API.
Update RunWorkflow and GetOutput for new streaming data API.

Data is streamed and baclava outputs can be streamed directly to a file if
requested.
GetOutput: Get baclava output if appropriate.

If the run was configured to output baclava, get it rather than trying to read
the non-existing output port data.
RunWorkflow: Save outputs to zip file

A new option switch, -z or --zip, is added so that outputs can be streamed to a
file in zip format.
DeleteRuns: Update for adjusted Server delete methods.
Rename, bump version and use latest client lib.

Rename this artifact taverna-server-java-cli and bump the version number to
0.9.0. The client lib has also been renamed and bumped to version 0.9.0.
Minor changes to reflect changes in the client library API.
Merge branch 'rh/comments' into next

* rh/comments:
  Minor changes to reflect changes in the client library API.
  Rename, bump version and use latest client lib.
  DeleteRuns: Update for adjusted Server delete methods.
  RunWorkflow: Save outputs to zip file
  GetOutput: Get baclava output if appropriate.
  Update RunWorkflow and GetOutput for new streaming data API.
  RunWorkflow and GetOutput changes for new OutputPort API.
  ServerInfo: Minor update to reflect change in Server API.
  Update for use of InputPort.setFile().
  Catch new exception if inputs are not set.
  Baclava output is now returned as a byte array.
  Workflows are now passed in as byte[] not String.
  Stop using deprecated Server.connect method.
Merge remote-tracking branch 'origin/next' into next

* origin/next:
  Correct snapshot repository XML..
  Snapshot repository
  Use Client lib 0.1

Conflicts:
	pom.xml