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macOS app bundle cannot access folders Desktop, Documents, Downloads
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Recent macOS versions have special protection for the folders Desktop, Documents, Downloads. Normally there is a system dialog to ask for extra permissions, but this does not work with the plain shell-script app (e.g. Isabelle2021-RC3).

The same problem occurs for Fontforge, Gimp etc. – see also

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makarius triaged this task as Normal priority.Jan 25 2021, 5:37 PM
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It works by using an x86_64-darwin executable that invokes a shell script: the executable is accepted by Apple "Files and Folders" security, while still being able to launch arm64-darwin Java properly.

See also: