Our cli.el ended up in the profile used at runtime. Although we could
have fixed overwriting a user's cli.el by appending to it, that still
would have leaked our build commands into the build.
This approach should be equivalent and reduces our profile modifications
to replacing packages.el (which is kind of the point) and prepending to
init.el (unfortunate, but seemingly necessary).
Removes the need to build a stage1 DOOMDIR, we can just use the user's
DOOMDIR directly.
The same approach should work for the next stage, removing the need to
leave our cli.el in the final DOOMDIR.