Modify `auto-mode-alist` in `prepare` step

When lazy mode is enabled, altering `auto-mode-alist` in `post-init`
won't work until the mode is enabled a first time. We move all
modifications of `auto-mode-alist` in `prepare`.

I didn't check if the modification of `auto-mode-alist` was still needed (some modes may have been updated for that to be autoloaded). I don't know if there is an easy way to ask el-get to download everything so that I can check something like that.