Added a rebuild-graph operation that fixes errors in the graph database.
merge branch jdgarret/rebuild-graph
Add truncate() method to GraphDatabase and use it in RebuildGraphOpTest.java.

RebuildGraphOpTest.java was calling on File.delete() without checking for the return code
and with a non empty directory, so File.delete() was surely returning false, hence the graph
wasn't being deleted, hence the test succeeded cause the db didn't change at all.
Fixed an issue which caused rebuild-graph tests to fail.

GraphDatabase:put was incorrectly reporting that nodes
pointing to the root were being updated.
Merge branch 'rebuild-graph' of github.com:jdgarrett/GeoGit into jdgarrett-rebuild-graph