I'm wondering whether questions such as these should be considered appropriate on this site:
They seem like questions which are relevant to physicists (or some subset of physicists) but are really about computing rather than physics. In my view, just because the specific programs or file formats in question are typically used by physicists, it doesn't mean the question is necessarily appropriate here. Sometimes Super User might be a better fit.
What do you think?
As discussed in Noldorin's answer and Tobias's comment, we seem to be taking the position that questions about the interpretation or justification of an algorithm or its results, or about physically motivated algorithm design, are okay, but questions about how to accomplish <task> in <program> (or <programming language>) should generally go to Super User (or Stack Overflow, respectively).