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.
Also with the excalidraw plugin, hand drawing images and such is also possible.
It is not as good for flowcharts and diagrams since there are only like 5 non-specified font sizes, but also usable for notes