Out of the box, TileMill 0.10.2 can import shapefiles from OpenStreetMaps (OSM), can style layers with CartoCSS, and can output an mbtiles file containing raster tiles (png). TileMill uses mapnik as part of its processing pipeline to go from map-data to rasterized map images (the output).

As of now, April 2017, it is possible to modify Mapnik with a library/plugin to produce Mapnik Vector Tiles (MVT) files instead of raster images. The project is here: mapnik-vector-tile (github).

Can we substitute or augment the "Vanilla" mapnik used in TileMill with the newer version?

Note: A different-but-related question was asked two years ago. It asks if MapNik can output vector tiles. Yes it can, if that library is installed. What I'm asking here, is "given that one can force mapnik to spit out vector tiles, how can I make TileMill call into the modified library?". Is there a way to "shim" mapnik to output MVT tiles?

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