firefly CLI does not work with flask in remote directory

[agurvich]

--method=flask in a remote directory (i.e. not /path/to/Firefly/src/firefly) probably doesn't work (though i've never tried it, tbh). should figure out what is necessary to get that going (and as a corollary should add --flask_templates= as a CLI option so that remote directories can be generated with the necessary flask files)