> cumbersomeness of xml...

Telling the parser to navigate to first element named $ELEMENT, checking a couple of conditions and assigning values in a defensive manner is not cumbersome in my opinion.

I would not call parsing binary formats cumbersome (I'm a demoscene fan, so I aspire to match their elegance and performance in my codebases), but not the pragmatic approach for that particular problem at hand.

So, we arrive to your next question:

> What’s the added value of xml then?

It's various. Let me try to explain.

First of all, it's a self documenting text format. I don't need an extensive documentation for it. I have a spec, but someone opening it in a text editor can see what it is, and understand how it works. When half (or most) of the users of your code are non-CS researchers, that's a huge plus.

Talking about non-CS researchers, these folks will be the ones generating these files from different inputs. Writing an XML in any programming language incl. FORTRAN and MATLAB (not kidding) is 1000 times easier and trivial than writing a binary blob.

Expanding that file format I have developed on XML is extremely easy. You change a version number, and maybe add a couple of paths to your parser, and you're done. If you feel fancy, allow for backwards compatibility, or just throw an error if you don't like the version (this is for non-CS folks mostly. I'm not that cheap). I don't need to work with nasty offsets or slight behavior differences causing to pull my hairs out.

The preservation is much easier. Scientific software rots much quicker than conventional software, so keeping file format readable is better for preservation.

"Sealing" in that project's parlance means "verify and don't touch it again". When you're comparing your results with a ground truth with 32 significant digits, you don't poke here and there leisurely. If it works, you add a disclaimer that the file is "verified at YYYYMMDD", and is closed for modifications, unless necessary. Same principle is also valid for performance reasons.

So, building a complex file format over XML makes sense. It makes the format accessible, cross-platform, easier to preserve and more.