Add in first pass at a DBOptions class that allows specifying the port (and any other mysqld command line option) when creating the database.
Relatively extensive re-write, mainly to make things easier for me to follow and to consolidate and organize functionality
Bump up the version number to 2.0-SNAPSHOT due to large amount of changes and non-backwards compatibility.  Make unit tests pass again.  Add ability to get connection from DB.
Add the configured port to the various directories in order to facilitate running more than one at a time on different ports.