REIVEW: [NX-518] Orient database manager

This PR addresses the following issues:

https://issues.sonatype.org/browse/NX-518
https://issues.sonatype.org/browse/NX-519
https://issues.sonatype.org/browse/NX-542
for testing, it might be nice to have a way to init one of these with a custom uri instead of assuming it's always coming from applicationDirectories.