My suspicion based on what I saw on Friday is that when the application is started through the SDK it is started basically the same way as when you start it with sailfish-qml appname which in turn means it is running without SailJail and also allows the application to “manage” its own files.
When on the other hand the application is started via the menu it gets encapsulated by SailJail and here is what tripped me up -
SailJail pre-creates .local/share/OrgName/AppName .cache/OrgName/AppName and .config/OrgName/AppName
So when I tested with the SDK it just migrated everything fine and nobody was any the wiser, but when I created an RPM and tested on my phone the migration logic which checks for the existence of the new folders as a sign of a previously botched migration and backs off was triggered.
I’m going to change that logic to be ‘check that the target folders are empty’ instead of ‘check the exist’ and I’ll report back.