A common "gotcha" of re-running `sphinx-autogen`, is that if there are changes it will not remove old files, leading to build errors for files not in a `toctree`
This commit introduces a `--remove-old` option to remove these files.
Note, a key detail here is that we don't want to simply clear the directory before running `sphinx-autogen`,
since this would lead to all files having a new `mtime`,
and then `sphinx-build` would rebuild all of them even if they have not changed.
So we must first collect the list of all correct files, then remove any not in the list.
