emsdk

Fix the format of the .flake8 file, and exclude the script directory from the py2 linter (#1272)

Flake8's INI config file format requires commas after each line. Because our file didn't have them, the exclude list
wasn't set up correctly, and the --extend-exclude flag wasn't working. This PR fixes the .flake8 file.

Also, update flake8 to the latest version available (because version 3.8 is required to get the --extend-exclude flag)
and use the flag to exclude the files in the scripts/ directory from the python2 linter (since the scripts are python3).