Packaging an Application with no installer?

You will just have to perform the actions that an Installer EXE for your program would do manually between the snapshots. I.e. make a directory under the correct Program Files directory, place you files in there and then manually make up a shortcut in the Start Menu. The MSIX packaging tool should then do the rest of the work for you, enjoy 🙂

MSIX Packaging Tool is designed to work for converting other setup packages to MSIX, not to create an MSIX from scratch.

For you scenario you can use the Visual Studio Packaging Project template if you are a VS user or you can use other setup authoring tools, like the free Advanced Installer Express edition.

In such tools you will usually create an empty project, add your application binaries then define your application entry points for the MSIX package and any additional configurations you need, like digital signing, etc...

Here is a more detailed answer on Stack Overflow where I cover this topic
https://stackoverflow.com/questions/64702212/how-to-build-an-msix-from-comandline

In essence, I would consider following standard Windows application development guidelines and place the executable and other binaries in a newly created folder under C:\Program Files\**Application Name** and create a shortcut on the Start Menu pointing to this new file location. It will then be picked up by the MSIX Packaging Tool and placed in the default VFS folder which will eventually install it in to the expected Windows Apps Directory when installed.

Might be worth using the new Package Analyzer functionality in the event that any fixups are suggested to support the application working correctly with the aid of PSF Fixups.