It's much simpler: Sphinx finds all files in the given directory,
recursively, that have the .rst file extension. And it parses all
of them. There is no need to follow "dependencies" to find more things
to parse: just parse all files you find. Sure, then later you might
be able to give a warning if some documents you rendered were not
included in any toctree's - but you will still render those orphan
documents.

The problem is that a ref called "some-link" is not a document
filename, but it is/was being added into dependencies. The solution
is to track which dependencies are unresolved, and resolve them
later once we can.

Before this commit, if there were 2 :ref: to the same spot, because
"references" were not stored uniquely on Environment, we only resolved
the first, not the second. But, if we simply stored $this->dependencies
as a unique array on Environment, we could have a collision between
a :doc: and a :ref: with the same name. The hack of prefixing the
unresolved dependencies was added to work around this.

For example, if we had :ref:`foo` in subdir/index, then
it would be changed to `subdir/foo` and we wouldn't be
able to resolve the `foo` reference later.