Unify HaplotypeCaller debugging arguments.

[jamesemery]

As part of #8083 we have added yet another heterogenous way of spitting out detailed debugging logs from yet another part of the HaplotypeCaller (namely in this case a toggle that prints to Stdout). This is in contrast to the existing (mostly assembly region position information) --verbosity DEBUG debug arguments and the various debug output stream arguments like --debug-assembly-region-state. These debug modes have proliferated and it has become difficult/confusing to know which ones are relevant if you are developing the code.

At some point it might be worth creating some sort of static debug manager class that manages the various specific output streams and saves us from having to pass debugger state to all of the various subclasses/utility methods of the HaplotypeCallerEngine. Importantly using DEBUG to stderr is not entirely useful as it jumbles all of the various debugger outputs into one output which quickly becomes large and difficult to read. We must support optionally splitting the output streams by functionality to files.