flake8 exclude list does not work

flake8 runs on files even if they are in the exclude list.

To reproduce:
1. Create a file called `.svn`.
2. Open it in Atom.
3. Change the grammar to MagicPython.
4. Type `1 + `.
5. Open the Linter pane and notice flake8 has raised W291 and E999.

Reproduce the issue in Atom by creating a `.svn` file, selecting MagicPython, typing `1 + `, and checking the Linter pane. Start by tracing how flake8 receives the exclude list; done means files listed there are not linted and the W291 and E999 messages no longer appear.

Written by the indexing model from the issue text.