It was fixed in R2020a Update 3!
I've reported this issue to MathWorks development teams. Application Compile app R2020a seems not to be able to input a folder in "Files required for your application to run" field.
As far as I know, there are three workaround.
1) Open .prj file which was created in R2019b or earlier
Application Compiler creates .prj file and in this file, all information which is necessary for mcc command is saved. Open this .prj file in R2020a, Application Compiler app will be launched. Addtional folders are contained in "Files required for your application to run" field as well as R2019b.
2) Specify .m files instead of a folder
"Files required for your application to run" field, add all files instead of adding a folder.
3) Use mcc command
Instead of Application Compiler app, you can use mcc command. After creating a standalone app by Application Compiler app, you can find mcc command in "PackagingLog.html" file. "-a inputFolder" option will work in R2020a, so you can compile by mcc command.