Make thread control behaviour more intuitive

[rambaut]

BEAGLE 3's CPU kernel is multithreaded. The number of threads produced can be controlled on the command line using the -beagle_thread_count option. The previous -threads controls the number of BEAST threads. The -threads option should be come the priority controlling the overall number of threads.

If only -threads N is specified, given K partitions, then each partition's BEAGLE instance will be created with N/K threads (rounded down?).

If only -beagle_thread_count X is given then each BEAGLE instance has X threads.

If both -threads N and -beagle_thread_count X is specified then there are N threads in the BEAST thread pool and each BEAGLE instance has X threads.

[rambaut]

This just leaves what the default behaviour is. Currently this would result in BEAST using an auto-sizing thread pool with each BEAGLE instances left to create a default number of threads (currently 8?).