better support for LT files not named "system.lt"
When the LT file is not named "system.lt":
- generated "run.in.EXAMPLE" files are renamed to avoid file name collisions (so that users can run moltemplate.sh on multiple LT files in the same directory)
- The "cleanup_moltemplate.sh" script can also handle files with names that do not begin with "system" (by including the "-base" argument).
- The "cleanup_moltemplate.sh" script no longer assumes that the python interpreter is named "python". (It could be named "python" or "python2".)