First convert to sqlite
$ time ogr2ogr -f SQLite out.db 1447454472-debug.geojson
real 2m31.904s
user 1m37.525s
sys 0m48.042s
Checks number of features
$ sqlite3 out.db "Select count(*) from ogrgeojson"
3199531
Run dedupe
$ time ogr2ogr -f SQlite dedupe.db out.db -sql "Select * from ogrgeojson group by from_node,to_node" -dialect SQLITE
real 0m16.296s
user 0m13.737s
sys 0m1.240s
Yay, less features
$ sqlite3 dedupe.db "Select count(*) from 'select'"
1754049
Convert back to a format we can upload to mapbox.com
$ time ogr2ogr new.shp dedupe.db
Warning 6: Field timestamp create as date field, though DateTime requested.
real 0m17.298s
user 0m13.988s
sys 0m1.113s
$ $ zip -r -9 upload.zip new.*
adding: new.dbf (deflated 89%)
adding: new.prj (deflated 15%)
adding: new.shp (deflated 81%)
adding: new.shx (deflated 72%)
Then upload upload.zip
to https://www.mapbox.com/studio/data