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When we save classes in studio or VSCode the files are automatically saved inside cache as well as the dev's local master folder.  This is setup using TortoiseSVN.  Based on Dmitriy's comment I imagine the export as .CLS.xml is setup via this source control setup, TortoiseSVN, instead of the way my individual settings are setup in VSCode.  Here are my settings for reference:

I was able to run the following commands on my local HS 2018 %SYS namespace to create an application:

Set tWebAppName = "/csp/healthshare/samples/myapp"
Set tProperties("NameSpace") = "samples"
Set tProperties("CookiePath") = "/csp/healthshare/samples/myapp/"
Set tProperties("MatchRoles") = "%DB_CACHE:%All"
Set tSC = ##class(Security.Applications).Create(tWebAppName, .tProperties)

The above code works to assign the MatchRoles, but don't know if that answers your question.  I'd suggest running the delete command between attempts via: Set tSC = ##class(Security.Applications).Delete(tWebAppName) until you programmatically get exactly what you are looking to create.

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