How to deploy a Win-32 app with Microsoft Intune!

TomWechsler 

I have a question regarding packaging custom apps for Intune deployment.  Your article was superbly written, but just like the MS documentation, it is missing one important area:  Custom settings files.  Many software installations require custom settings (serial numbers, custom settings, JSON configs, etc.).  How do I package those with a deployment?  After days of searching, I found only this mention:

When you're generating an .intunewin file, put any files you need to reference into a subfolder of the setup folder. Then, use a relative path to reference the specific file you need. For example:

Setup source folder: c:\testapp\v1.0
License file: c:\testapp\v1.0\licenses\license.txt

Refer to the license.txt file by using the relative path licenses\license.txt.

(found at https://learn.microsoft.com/en-us/mem/intune/apps/apps-win32-prepare)

I am working on setting up a Cisco AnyConnect VPN client for our users, and testing the waters for my company to understand the process and viability of moving to Intune vs. using our older SCCM methods.  Now that many of our users are no longer working from offices, it would be highly beneficial for us to be able to move this workflow onto Intune and fully automate the process (under SCCM it's partially automated, partially guided by the helpdesk team for each user!).  The key breakthrough would be for me to figure out how to include a couple of JSON files with the .intunewin file in the correct directory, and in theory AnyConnect would then install all the custom VPN configurations on first run by our users.  I'm really struggling with this, but I can't imagine that this isn't a fairly simple (??) step that is just somehow missing from all the documentation.  Any ideas?

Again, thank you for your expert guidance and insights, they are much appreciated.

Kindest regards,
Harro