Switch to using an iterator to avoid raw types / unchecked conversion warnings.
Upgrade libraries:
 - httpclient from 4.2.5 to 4.3.3
 - httpcore from 4.2.4 to 4.3.2

Both changes will be used in a later commit to add CT log retrieve
functionality to the Java client.
Use the protobuf jar file from the system.

Either sysjarsdir or jars.protobuf can be overridden in local.properties.
Remove warnings from several Java source files.