ELPA doesn't "do" anything (it's just a protocol), but as for GNU ELPA
it builds packages in a fairly simplistic way. Given the current
state
of fountain-mode, it should ignore the `docs` subdirectory because it
will decide that fountain-mode is a "simple" package based on the fact
that there's only one .el file (in that case, the package is made of
that .el file and nothing else).
If you want to include more than that single file, you'll probably
want
to set `Package-Type: multi` in the pseudo-headers.
And if instead you want to prevent the `docs` from appearing in the
tarball (say, because you added a second .el file), then you can use
a `.elpaignore` file to say so (see the elpa.git/README file for more
details).