One could easily allow or restrict visibility of almost anything to any program. There were/are some definite usability concerns with how it is done today (the OS was not designed to be friendly, but to try new things) and those could easily be solved. The core of this existed in the Plan9 kernel and the Plan9 kernel is small enough to be understood by one person.
I’m kinda angry that other operating systems don’t do this today. How much malware would be stopped in its tracks and made impotent if every program launched was inherently and natively walled off from everything else by default?
However, I don't know what this metalanguage should be. I don't know how to translate typical comments (or a literate program) into some sort of formal language. I think we have a gap in philosophy (epistemology).
Perhaps you're thinking of mathematics.
If you have to be able to represent arbitrary abstract logical constructs, I don't think you can formalized the whole language ahead of time. I think the best you can do is allow for ad-hoc formalization of notation while trying to keep any newly introduced notation reasonably consitent with previously introduced notation.