alias inkscape="flatpak run org.inkscape.Inkscape" into your .bashrc.
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Yeah, I tried this, and it works from my session, but I still got the same error from trying to run the program. I figured it was because it is called outside the bash session so the run commands have not been run, but is that perhaps not true?
If that's the case, it's a bit of an ugly hack but you could make a wrapper script placed in /usr/local/bin/inkscape like this:
#!/bin/bash
flatpack run org.inkscape.Inkscape ${*}
(the ${*} will pass along all the arguments that the wrapper script was called with)