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I changed the startup script to convert my provider chest in passive provider chests, as I didn't want my storage to fill up with junk

after start the conversion happened, but logistic bots insist in moving stuff from the chest to the storage area

save at https://www.dropbox.com/s/r4xwbamh924stdh/0.zip

Hmmm this is a problem with the migrations. The thing is that the migration only changes the name of the entity (from provider chest to passive provider chest, because they are of the same type), but it doesn't migrate the properties properly. For instance the chest will stay in internal lists for the logistic systems. We will have a look at this for 0.9.5 as this is a general problem and could cause confusion also for modders.

For now you cannot use migration to passive provider chest (the migration to active provider chest works fine because it is the same type of object). Either you can rebuild the entities manually or write a lua code in your control.lua that will iterate through all the entities in the given bounding box and if they are active provider chests it will destroy them and build a passive provider chest instead.

So I fixed it for 0.9.5, so the migration will update the inclusion of the chest in the structures correctly, so it will do what would one expect.
We will release minimod containing this migration with 0.9.5, so anyone can activate it if they want to.