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This sort of heavy geometry processing isn't really something that tilemaker does, I'm afraid - you'd typically use PostGIS for this. Martin would be really well suited for serving vector tiles with queries like this.

If you did want to still use tilemaker, you'd typically load the trees into a Postgres database (using osm2pgsql and some custom Lua); cluster them with PostGIS functions; then use pgsql2shp to export the clustered trees to a shapefile which tilemaker could load.

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