// phdana cmd line
Argument usage is like tihs
if there are 2 or more parmas and the 2nd param is -analysis
then 1st param is an alignment file and cmd-line driven pfaat is executed (legacy code)
else if first parameter is -j
then 2nd param is a jar, 3rd is an alignment file IN that jar and 4th is optionally a nhx tree file in that jar
else
first parameter is treated like an alignment file, and an optional 2nd parameter is treated as an nhx tree file
