• New command line flags -ya and -xa for input/output trajectory arguments (Add stop/start/offset/etc arguments to command line flags #612).
• Add some autodetection to files specified on command line without preceding arguments.
• Address Some tests need to be protected from higher MPI thread counts #599 and Do not allow RMSD of less than 3 atoms #600.

Adds two new command line flags:

	-ya <args>       : * Input trajectory file arguments.
	-xa <args>       : * Output trajectory file arguments.

This allows passing any trajin or trajout arguments to input/output trajectories specified on the command line. If fewer arguments are specified than trajectories, the last specified argument will be used for remaining trajectories. E.g.

cpptraj -p tz2.parm7 -y traj1.nc -y traj2.nc -y traj3.nc -ya "1 last 10"

is equivalent to the input

parm tz2.parm7
trajin traj1.nc 1 last 10
trajin traj2.nc 1 last 10
trajin traj3.nc 1 last 10

There is now some autodetection of files on the command line. Previously the only acceptable invocation with files and without command line flags was

cpptraj <topology> <input>

Now, topology/trajectory files can be specified with any order and cpptraj will detect them; other files are assumed to be cpptraj input.

Instances of "MPI threads" and similar have been changed to "MPI processes" to better distinguish from OpenMP threads. OpenMP-enabled cpptraj will now also print the max number of available OpenMP threads (similar to how number of MPI processes is reported).