Add prefectures collection by merging cities

[nobuf]

As us-atlas does, hoping those topojson files would include prefecture boundaries as well. With the below command in build.sh, I noticed that the final output includes many exterior rings unexpectedly.

topomerge prefectures=cities -k 'd.id.slice(0, 2)' -f 'd.id'

Here's a quick demo with the Tokyo shapefile -
https://bl.ocks.org/nobuf/5f2dfb266c909e35b37c95310f06fbcf

#!/usr/bin/env bash
# Choose Tokyo (東京) and download the 2017 data
# http://nlftp.mlit.go.jp/ksj/gml/datalist/KsjTmplt-N03-v2_3.html
unzip -o -j N03-170101_13_GML.zip -d tmp
shp2json -n --encoding sjis tmp/*.shp -o tmp/tokyo.ndjson
geo2topo -n cities=tmp/tokyo.ndjson \
    | toposimplify -p 0.00002 -f \
    > tokyo.json

This is likely due to the original shapefile data but I'm not 100% sure. I'm wondering if there's any workaround.