I forgot all about the skip_files in app.yaml and asked my favorite search engine what to do. A number of the top pages returned made it unnecessarily complicated. Just do this to skip directories (.idea and tools in this example):
... skip_files: - ^(.*/)?#.*#$ - ^(.*/)?.*~$ - ^(.*/)?.*\.py[co]$ - ^(.*/)?.*/RCS/.*$ - ^(.*/)?\..*$ - ^\.idea$ - ^tools$ ...
(These are top-level …