Aqua for Command-Line Tools
Why is it that wrapper utilities like this never seem to handle shell quoting properly?
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Because shell quoting sucks and is an utter pain in the ass. - even outside wrapper utilities.
And because there's no well-known readymade function that converts whatever you have into a properly quoted string. Thus everybody tries and most likely fails at first to re-invent the wheel themselves.
No offense, but "Because it's hard" is a lousy reason.
If your goal is to make an easy to use graphical wrapper around command-line functions, then your wrapper should be a well-behaved Macintosh application. That means that things supporting file names and paths with spaces, backslashes, quotes, and all the rest