Any contributions should make changes to the files in the src directory. Files in the src/_base directory are common to all themes and any files in the src/<theme name> directory are specific to <theme name>.
After the src files are updated, run the command python setup.py gen_themes, which will update the compiled themes in the mkdocs_bootswatch directory. When preparing a patch (pull request), be sure to include the changes in both the src directory and the mkdocs_bootswatch directory.
As explained in an addition to the README: