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sincewe have the baselayer switcher available when defining TMS layers. this enables to define a layer as either baselayer or overlay layer.
when i use the overlay functionality with a custom MBTiles tilemill export with zoom levels 0-8 there is a problem that the map won't work for certain zoom levels. for zoom levels great than 4, the zoom-level part of the tile image links being generated will be set to -1 instead of the correct value from 5-8:
as tmcw stated in the #mapbox irc channel there seems to be some PHP number conversion problem in D7 but we couldn't really figure out how exactly that's being caused...