Merge CLI flags with flags found in config file.

[mikehenrty]

I believe the desired behavior is to merge these flags so that users can specify both CLI flags and a config file simultaneously. As it stands, when a config file is specified, it's flags will replace (and erase) any flags passed through CLI.

Note, I had to upgrade Typescript by a few minor versions because I was getting a TS build error Cannot find name 'Omit'., and I saw that TS 3.0 didn't support it. So I bumped TS to 3.5 and everything seemed to be working. We'll see what travis says.

Fixes #150.