Ideally the syntax should be something like: lyx --merge --out=doc3 doc1 doc2, and the result should be a merged document with change tracking so that the user can do all semantic merging. In this mode LyX should not open a window nor require user interaction, as the idea is to use this as a merge strategy for git and the like.
This would be extremely useful for distributed authoring/editing. I'd go farther and ask for a merge tool that can work like traditional version control merge tools, only at the LyX layer, but this seems likely to be very difficult, as opposed to existing change tracking feature. If you wish I can open the feature request. Thanks, Nico --
