Hi Justin, I understand that you are trying to deploy a GUI in M-code using Web App Compiler.
However, the Web App Compiler requires MLAPP files, which are apps build using App Designer. This requirement is noted in the third paragraph of the introduction here: https://www.mathworks.com/help/compiler/web-apps.html
There is currently no way to directly convert M-code to an MLAPP file, but you may be able to reuse some of your code in App Designer as noted in this answer: https://www.mathworks.com/matlabcentral/answers/507366-import-a-m-file-into-app-designer. When you package an app (in a .mlappinstall file), it does not convert it to an MLAPP – it only creates an installer for your users to get the M-code app that you built.
In order to add help files to a App Designer standalone application, required files need to be added in ‘Files required for your application torun’ in following format:
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