autoconf-generated configure scripts substitute strings like @var@ in files
like for the value of output variables set in the configure script. Most of
the time, these will only be used in lines like

var = @var@

in Makefile.in. The Makefile.in may have many of these lines. In fact,
automake scans configure.ac for use of the AC_SUBST macro and automatically
adds such lines to the generated Makefile.in.

It can be confusing to try to understand what it means for variables to
copied from one level of the build system to another. If a user writes
Makefile.in by hand, they will have to write out all these lines manually.
Also, it's hard to read Makefile.in's because of such lines.

My suggestion would provide a simpler way which would work for most use
cases. It would be to generate a file (called, say, "config.mk") which
contained all these assignments automatically. I.e., config.mk would
contain lines like

CC = cc
CXX = g++

and so on. Then in the Makefile, have a line "include config.mk". The
output variables would be referred to in the Makefile as ordinary
environment variable (e.g. $(CC)).

This could be done with a macro like AC_CONFIG_INCLUDE(config.mk) in
configure.ac.

As well as being simpler (only having a Makefile instead of a Makefile and
Makefile.in, and only having one type of variable instead of two (@var@ and
$(var)), this would let the user browse through config.mk to see exactly
what configure decided. At the moment, you would have to read config.status
to do this, which is not easy.

It may be advisable to also produce a config.mk.in file showing what
variables are set. Then a user on a system where configure doesn't work
would know what they had to set manually. (This is the same rationale for
having a config.h.in.)

There is a possible problem with the user running make before they run
configure. In a lot of cases, the user doesn't care about the difference
between make and configure, and wants to use the default configure options.
Then a default config.mk could be included with a a rule to rebuilding
itself by running configure. (GNU make would then read the produced
config.mk in again.) Alternatively, the program developer could decide for
make to spit out a message saying "Please run configure first." if they
want to make running configure manually compulsory.
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