JAVA-1410: Javadoc for legacy API

Made a first pass through the com.mongodb package and the existing API classes.  I've added some jira tickets for missing tests and code we might be able to delete, and updated the [Jira ticket](https://jira.mongodb.org/browse/JAVA-1410) with the classes that I couldn't document without help.
"The encoder with which to encode the command document" ?