api: change JSON mediatype to include charset

Fix #639.
Don’t hide exceptions from `subprocess.call`. It raises an exception itself and we are hiding the original message which can be helpful when debugging.
Remove unused code
Use logging instead of printing
Aggregate the number of tuples sent between fragments.
Merge pull request #640 from uwescience/rest-json-encoding

api: change JSON mediatype to include charset
kill_all_java_processes.py: typo

missing space
Merge pull request #641 from uwescience/dont-hide-exceptions

Don't hide exceptions in deployment scripts
Fix query construction
QueryManager: cleanup active vs running, fix kill

1. In an earlier commit, I confused the notions of active queries (running, queued)
   with running queries. Rename 'activeQueries' to 'runningQueries' to explain
   the difference.

2. The user should be able to kill a queued query. Thus, make the 'kill(qId)' API
   call look at all active, not just running, queries.

3. Add the ability to kill/cancel queued queries.
QueryQueueTest: test canceling a query in the queue
Server.java: fix spacing, sadly

Would love to get Eclipse default without this, but for now
stick to repo standards.
LogResource.java: fix spacing, sadly

Would love to get Eclipse default without this, but for now
stick to repo standards.
Merge pull request #644 from uwescience/sent-aggregate

Aggregate the number of tuples sent between fragments.
Merge pull request #645 from uwescience/fix-643

Fix 643