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I have enabled hidden file visibility on OS X El Capitan 10.11, and the files are semitransparent. Is there a way to make them solid like all other files?
You can use chflags to remove hidden flag from files you need:
chflags nohidden YourFile
Use this command with YourFile replaced with your file to change the file flag to no hidden.
Files and folders with . prefix will remain hidden.