Added setPipelineParentSet to Pipeline, and Javadoc.
Fixed a bug with queries accepting whitespace.

Also added some tentative documentation to the Query class.
Update README.txt
meh
Added documentation notes
Merged some comments in query.java
Merging our visko repo with delrio's latest changes.
Merge remote-tracking branch 'upstream/master'
Update README.md
Merge branch 'master' of https://github.com/SEDTT/visko
Merge branch 'master' of https://github.com/nicholasdelrio/visko