Return similarly named, non-submodule modules

In our setuptools integration command, we were attempting to avoid
checking each submodule in the packages list. This was done without
recognizing that two modules may start with the same prefix, e.g.,

- foo
- foo_bar
- foo_biz

In this case, we only ever checked ``foo``. By appending a '.' to the
end of each package name, we avoid this since we only care about
deduplicating submodules, e.g.,

- foo
- foo.sub
- foo.sub.sub

Closes #295

src/flake8/main/setuptools_command.py

@@ -66,7 +66,7 @@ class Flake8(setuptools.Command):
             if package_directory.startswith(seen_package_directories):
                 continue
 
-            seen_package_directories += (package_directory,)
+            seen_package_directories += (package_directory + '.',)
             yield package_directory
 
     def module_files(self):