I made a run through and made two additions as well as several bugfixes that I found.
I added js-beautify to the scripts list in setup.py so it is properly created in /usr/bin when a user runs setup.py install.
I added exception handling if the beautify_file function is passed a file that does not exist or cannot be opened, this also ensures the output file will be properly closed.
The stylistic fixes are, removed 5 trailing semi-colons, fixed a method body where the indent was off by one space, changed the --h option to -h, and changed the getopt error handling to match the rest of the main function.
All the best,
added output file option
fixed file closure
merge cleanup, branch update
catch file does not exist exception, build script update
Merge branches 'master' and 'test'
removed debugging statement