This hidden preference will be implemented in FoxTrot Pro version 8 (the beta version will be announced soon). We won't surcharge the user interface with this.
You can use Prefs Editor to change these hidden preferences without using Terminal.app.
This setting will apply both for folders and files, and you can add multiple regular expressions if you have different patterns to skip.
The setting is ignored for folders that you directly add to the indexed locations; i.e. if you skip all folders named "cache", but explicitly add a specific "cache" folder to the indexed location, this one will be indexed.
A few examples:
To skip any folder whose name is exactly "cache" or "meta" (case sensitive), use one of these commands:
defaults write com.ctmdev.FoxTrotShared SkipPathRegex -string '/(cache|meta)$'
defaults write com.ctmdev.FoxTrotShared SkipPathRegex -array -string '/cache$' -string '/meta$'
defaults write com.ctmdev.FoxTrotShared SkipPathRegex -string '\.repo/(.*/)?(cache|meta)$'
defaults write com.ctmdev.FoxTrotShared SkipPathRegex -array -string '\.repo/(.*/)?cache$' -string '\.repo/(.*/)?meta$'
] 
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