Ideally, you would export your compressed code somewhere separate from your source code, and probably even give some specifier to let you know it is compressed (source.js => source-min.js). Then, when you search folders you can add an exclude filter
example of path to search, files to search, and files to exclude (min.js)
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I am not sure if you can exclude certain folders with the exclude filter, you would have to play around with it; I haven't tried to define folders in an exclude filter yet, but it might work, but I know you can define wildcards for file names.
I think you might be able to exclude certain folders from a project in general (I have never tried to do this), those exclusions may get picked up my Find (if you can even do this); I don't know though. Maybe some others can chime in here.