Upgrade versions of dependent packages.

[tpotter7]

Issue #2686: Upgrade versions of dependent packages.

• Had to update millstone, mbtiles, and sqlite3 at the same time since they all have to use the same version of sqlite3 for tilemill.
• Upgraded sphericalmercator to the latest version.
• Also changed sphericalmercator and mbtiles to have an @mapbox scope since those have been moved.
• Also moved the reference to bones and millstone to be a tpotter7 fork so that we can maintain them. It will be better for those to point at timemill-project forks but we need Dane to give us permission for that.
• The files changed other than package* were to update the @mapbox scoping on require statements.

[csytsma]

Can you update to use the new tilemill-project versions of bones and millstone.