Version control of Mathematica notebooks
Mathematica notebooks are, of course, plaintext files -- it seems reasonable to expect that they should play nice with a version-control system (git in my case, although I doubt the specific system matters). But the fact is that any .nb file is full of cache information, timestamps, and other assorted metadata. Scads of it.
Which means that limited version control is possible -- commits and rollbacks work fine. Merging, though, is a disaster. Mathematica won't open a file with merge markers in it, and a text editor is no way to go through a .nb file.
Has anyone had any luck putting a notebook under version control? How?
It's recommended to disable the file outline cache, which is the metadata you're referring to when you look at the notebook with a text editor. As you discovered, it can cause merge conflicts if multiple parties are editing the same notebook.
This is easily disabled with the Option Inspector. In the Mathematica menu, go to Format → Option Inspector... , in the top-left set the scope dropdown to Selected Notebook and search for FileOutlineCache in the search field. Set the option to False and save your notebook, and you should be all set.
Note that this can make opening notebooks a little slower, but unless the notebook is rather large, you probably won't notice the difference.
There is a nice set of recommendations for how to use Git to do version control with Mathematica at Mathematica Stack Exchange. In short, the philosophy is to minimize use of .nb notebooks, and try to do most of the version control with .m packages (similar to what xuhdev and MMA user say above). This seems quite sensible given the way notebooks are managed.
Not a solution to your merging problem exactly, but this is how we handle notebooks and source control in my team. Basically, we treat Mathematica notebooks the way we'd treat binary files. They're checked-in, but:
We mostly use Mathematica for small proofs, explorations and sidetracks, so the above procedure works fine for us (our main documentation is in LaTeX, which produces friendlier documentation for non-mathematicians/non-programmers)
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