default diffusion constants should be in layout, not parameters

[jeremymchacon]

Hey,

I think something that would improve intuition about where certain parameters are would be to remove default diffusion constants from the parameters files and instead have them as part of the layout. Especially because if we ever have non-default values (e.g. specific to only one metabolite), these specifics are defined in the layout. Therefore, it makes sense to have the default there.

Alternatively, we could "hide" these defaults in the python and matlab toolboxes, so that from a user's perspective it all appears to happen in the layout even if that is not true in the written comets files. I'd prefer the first option though. Thoughts?