We will consider adding a hidden preference (accessible via Terminal.app) for this in the future. This will probably be a global (i.e. not per-index) setting, with a regular expression.
For example, if you want to skip all folders named "cache" or "meta", the command line to set this hidden preference would be something like:
defaults write com.ctmdev.FoxTrotShared SkipFoldersRegex '/(cache|meta)$'
Or if you want to skip these folders only when located at any depth inside another folder whose name ends with ".repo", the command line would be:
defaults write com.ctmdev.FoxTrotShared SkipFoldersRegex '\.repo/(.*/)?(cache|meta)$'
Would this work for you?