I think those would work, although IIRC msix requires some extra security things that may be a hassle, though your mention of the MS Store signature does make me think that would suffice.
This worked flawlessly for me. I’m still on Qt 6.8.1 so I had to use my own build to get this to work, but it was as simple as using this command:
windeployqt --release C:\Users\Brock\Desktop\avogadro_qt6\prefix\bin\
No messing around required, it just worked after that.
Dark mode is gorgeous.
Awesome 
I’ll tweak the Qt6 Windows build tomorrow so it’s usable and then figure out Windows installers. (The new build script also includes pixi for setting up Python and plugins.)
Amazing, great work @brockdyer03!
@ghutchis re the installer format, see my previous comment in How to determine "stub" python on Mac and Windows - #6 by matterhorn103. Basically, to submit to the MS Store it is far easier if it’s an MSIX anyway (and possibly a requirement?), it’s a hard requirement for installation via winget, and it’s in general the modern and preferred format.
Yeah, my question was more “we’ve been providing .exe installers for Windows – if we switch to providing .msix files to download, will that work for users?”
I see a variety of options online for using Cmake to produce msix so I’ll tinker around.
Well if I’m correctly reading between the lines and you’re wondering whether users would be happy to install from the MS store, then I want to clarify that an MSIX doesn’t oblige use of the store!
As far as I understand it, double-clicking an MSIX also launches installation just like an EXE, so users can download and install it just like they currently do. Difference is just that there’s no old-school installation wizard, the installation gets handled by the system software installer.
So an MSIX shouldn’t inhibit any current workflows, it just enables new ones. It’s also much easier to deploy an MSIX remotely, because installation is non-interactive. In fact, in a Windows domain environment you can can only deploy software to PCs via the domain if it is packaged as an MSIX, so when I was an IT admin in my research group in order to get Avogadro to everyone we actually had to create an MSIX wrapper for it anyway using a freeware tool. 
