Add mapentrysets.xml to Advanced customizations
In Designer -> Manage Format/Target Customizations, add a path to the mapentrysets.xml file.
(Or maybe add a new top-level folder for all Shared formats.)
When working on a project it would be nice to see when this file has been customized.
Adapters (2/20/2013)
In addition to Mike's suggestion about Shared formats, I'd like to be able to see overrides for Adapters. -Lief