[JAVA-1410] Adding @mongodb.driver.manual tag to classes in com.mongodb ...

Adding `@mongodb.driver.manual` tag to classes in com.mongodb - covered classes up to DBCollection. Most classes have a tag at the class level, for DB and DBCollection most methods also point to manual documentation.

Conventions I have tried to follow:
 - Where possible, manual points to core documentation
 - If no extensive documentation, points to the glossary
 - If there's no documentation on the core concepts or tutorials, docs point to corresponding shell methods, as these often have very complete documentation that is helpful to those using the corresponding Java methods.

Also tried to add `@mongodb.server.release` where known.
Link to 

reference/command/update/#update.upserted

instead of shell example