Well I guess I will give up but will just explain the intention
one more time, just so you don't think I'm completely nuts!
Step-1. I am developing a set of interlinked documents entirely
in md and previewing them in Marked. This works nicely. It requires
all the pages being .md files, otherwise you jump to browser when
you click on a link rather than staying in Marked. (BTW, this is
also how I keep notes, using markdown as a kind of desktop
Step-2. When that structure is ready, I want to add top matter
and batch-convert all the md files to html files, and the md
references to html references. Then I have the same
linked-structure working as a set of browser-viewable web pages
rather than a set of Marked-viewable md pages.
Now of course I can link to the html in the first place, and
convert the .md files to .html files one by one as I make them, and
preview in the browser all the time. But then I lose the ability to
preview everything in Marked first, which I like a lot.
You are right of course that MMD can't guess your intention, but
that's what switches are for, so you can tell a command your
intention. I can do it by hand with a bit of sed or something I
guess, so that's probably what I will do.