Improve cli, output, and tests

[karel-brinda]

• Add a possibility to specify tmp dir (closes Allow to specify pattern for tmp dir #8)
• Don't finish the newick file with a newline (closes Don't finish by endline #28)
• Change the parameter for passing the inference algorithm from -f to -m
• Add a test for upgma (closes Add test for upgma #29 )
• Add support for multiple input fofs (closes Add support for using multiple lists of files as input #30)