Honor $(prefix) set in config.mak* when defining ETC_GIT*

Notice that the prefix specified for the build influenced the definitions
of ETC_GITCONFIG and ETC_GITATTRIBUTES only when it was exactly '/usr'.
Kacper Kornet noticed that this was furthermore only the case when the
build was triggered using 'make prefix=/usr', i.e., the prefix was given
on the command line; it did not work when the prefix was specified in
config.mak because this file is included much later in the Makefile.

To fix this, move the conditional after the inclusion of config.mak.

Additionally, it is desirable to specify the etc directory for a build
(for example, a build with prefix /usr/local may still want to have the
system configuration in /etc/gitconfig). For this purpose, promote the
variable 'sysconfdir' from a helper variable to a configuration
variable. The prefix check that was moved must now be wrapped so that it
does not override sysconfdir setting given in config.mak.

Signed-off-by: Johannes Sixt <j6t@kdbg.org>
Signed-off-by: Junio C Hamano <gitster@pobox.com>

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