Here is the actual patch to go along with my message from 5 days ago which
included only the full replacement function.

On Mon, May 23, 2016 at 7:11 PM, Robert Weiner <rswgnu@gmail.com> wrote:

> Replacing this function in package.el allows for correct generation of the
> <package>-autoloads.el file for packages that have .el files in multiple
> subdirectories.  The only thing changed is the line with 'apply' in it.  It
> ignores symlinks to directories in case there are any.  It is a simple
> change.  I hope you like it.
>
> This is important for larger packages such as my forthcoming Hyperbole
> package which includes a 2nd directory of code.
>
> *** package-orig.el 2016-05-28 00:54:25.000000000 -0400
> --- package.el 2016-05-28 00:54:25.000000000 -0400
> ***************
> *** 916,928 ****
>            (backup-inhibited t)
>            (version-control 'never))
>       (package-autoload-ensure-default-file generated-autoload-file)
> !     (update-directory-autoloads pkg-dir)
>       (let ((buf (find-buffer-visiting generated-autoload-file)))
>         (when buf (kill-buffer buf)))
>       auto-name))
>
>   (defun package--make-autoloads-and-stuff (pkg-desc pkg-dir)
>    "Generate autoloads, description file, etc.. for PKG-DESC installed at
> PKG-DIR."
>     (package-generate-autoloads (package-desc-name pkg-desc) pkg-dir)
>     (let ((desc-file (expand-file-name (package--description-file pkg-dir)
>                                        pkg-dir)))
> --- 911,927 ----
>            (backup-inhibited t)
>            (version-control 'never))
>       (package-autoload-ensure-default-file generated-autoload-file)
> !     (apply #'update-directory-autoloads pkg-dir
> !     (delq nil (mapcar (lambda (f) (and (file-directory-p f)
> !        (not (file-symlink-p f))
> !        f))
> !       (directory-files pkg-dir t "[a-zA-Z].*" nil))))
>       (let ((buf (find-buffer-visiting generated-autoload-file)))
>         (when buf (kill-buffer buf)))
>       auto-name))
>
>   (defun package--make-autoloads-and-stuff (pkg-desc pkg-dir)
>    "Generate autoloads, description file, etc. for PKG-DESC installed at
> PKG-DIR."
>     (package-generate-autoloads (package-desc-name pkg-desc) pkg-dir)
>     (let ((desc-file (expand-file-name (package--description-file pkg-dir)
>                                        pkg-dir)))
> ***************
>
>