At least a couple of them are unambiguously programs (despite being defined in config formats). And many of the others are configs which allow program formats,

At least a couple of them are unambiguously programs (despite being defined in config formats). And many of the others are configs which allow program formats, which could hypothetically do arbitrary program things as well. There are other top level files which I’d want to include if I were the one designing this, many of which are just text/reference, all of which are inherently meta content relative to their containing project. It may well even be worth nesting sub-category directories below .meta, eg .meta/config or even .meta/config/{checks,env,…}. I’m sure some would consider any/all of this overkill, but the current status quo of top-level junk is certainly no better than a tree with well defined and well named branches.