Allow modules to be in subdirectories.

And complain when the module name is wrong.
Make separate function for module loading.
Move some code from Parameters to Probability_Model.
Clean up printing of command line.
More cleanup of effects of --show-only.
Work with Parameters in terms of a general Probability_Model.
Make Probability_Model non-virtual.
Don't call create_A_and_T unless given a sequence file.
Add short name for --model.
Allow models w/o alignments.
Allow running models without doing T/A estimation.
Don't forget to discover generic MCMC moves.
Don't mention tree or alignment files for --model case.
Remove some old variables.
Move 500 lines to startup/A-T-model.{H,C}
Move some file-related functions to startup/files.C
Move some code into startup/loggers.{H,C}
Stop exporting some functions.
Move find_exe( ) to startup/files.C
Move streambuf related classes to startup/io.H