I previously used Tes4Gecko to merge esp to master, which avoided all of the issues that currently arise, such as form errors that make save games impossible to go back to custom world locations.

Are there any such tools in development?

Gecko is, if I recall correctly. Dunno when it'll be ready for a public release though.

I hope so, Gecko was the god send of Oblivion for me, one click merge to this, merge with that etc. If anyone knows more of Gecko for Skyrim please shout up. I am struggling with version control for merging esp to master.