The few things I don’t like about flatpaks (which become a problem on atomic distros that use almost all flatpak by design):
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Some types of embedded development is essentially impossible with flatpaks. Try getting the J-link software connected with nrftools and then everything linked to VScodium/codeoss
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Digital signing simply doesn’t work, won’t work for the foreseeable future, and is not planned to get working,
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Flatpaks sometimes have bugs for no reasons when their package-manager counterparts don’t (e.g. in KiCAD 8.0, the upper 20% or so of dialog boxes were unclickable with the mouse, but I could select and modify them with the keyboard, only the flatpak version)
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The status on whether it is still being actively developed or not (at least I hear a fair amount of drama surrounding it)
But besides those small things, it seem great to me.
Money and time.
Tons of people build cool projects during their time in university, but the vast vast majority of people don’t because they are eating beans and rice and ramen and pizza and studying, not spending 500€-1000€ on iterative prototyping and the equipment to test everything.