main: Use --limit-files

Earlier --files was being used but that wasn't the correct
option to be used because that replaces the files config value
only in [Default] section. This means that any other
section would clash with it.
Now we use the --limit-files argument which takes a subset
of all files with the glob provided in --limit-files. This ensures
that all sections with this file get executed and no clashes happen.

CoalaThread.py

@@ -62,7 +62,7 @@ def run(self):
  else:
  options.append('--find-config')
 
- options.append('--files=%s' % self.file_name)
+ options.append('--limit-files=%s' % self.file_name)
  options.append('-S=autoapply=false')
  options.extend(self.extra_args)
  command.extend(options)