build: Move 'Makefile' fragments to subdirectories.

This follows a convention used by some other GNU packages like Autoconf,
Bison, Coreutils, and Gnulib.

* doc.am: Rename to ...
* doc/local.mk: ... this.
* emacs.am: Rename to ...
* emacs/local.mk: ... this.
* gnu-system.am: Rename to ...
* gnu/local.mk: ... this.
* daemon.am: Rename to ...
* nix/local.mk: ... this.
* Makefile.am: Adapt to them.
* doc/guix.texi (Porting to a New Platform): Adapt documentation.
* guix/config.scm.in (%state-directory, %config-directory): Adapt comments.
* emacs/guix-config.el.in (guix-config-state-directory): Likewise.