Cygwin doesn't work at all in Windows AppContainer package isolation; too many voodoo hacks. MSYS2 uses it to this day, and as a result you can't run any MSYS2 binaries in an AppContainer. Had to take a completely different route for Claude Code sandboxing because of this: Claude Code wants Git for Windows, and Git for Windows distributes MSYS2-built binaries of bash.exe and friends. Truly native Windows builds don't do all the unusual compatibility hacks that cygwin1.dll requires; I found non-MSYS2-built binaries of the same programs all ran fine in AppContainer.