It's disabled anyway.

[Unfortunately,] @top_srcdir@ is replaced by the package's top-level
directory relative to the directory of the .in file being processed,
e.g. if you unpack the MPD source to /usr/src/mpd, and build it in the
same directory, @top_srcdir@/src/ in doc/doxygen.conf.in will be re-
placed by "../src/", and, as doxygen is invoked from the top directory,
is will expect the source code in /usr/src/src/, which is obviously
wrong.
To work around this problem, this patch changes @top_srcdir@ to
@abs_top_srcdir@, which expands to the absolute path of the top source
directory[1].

[1] http://www.gnu.org/s/hello/manual/autoconf/Preset-Output-Variables.html

Don't create a modified copy for out-of-tree builds.

This hack creates a copy of doc/doxygen.conf with the INPUT setting
replaced.

Recursive Makefiles are inefficient and error prone (no proper way to
declare dependencies).  Since there's no disadvantage in having one
single Makefile, let's do it.

When configured with --enable-documentation, use doxygen.