Prepending custom dirs ($ZPFX/{include,libs}) to CPP..../LDFLAGS with use of config.site file of autotools? - configure

Question

I'm using a $CONFIG_SITE set to $ZPFX/share/config.site file containing:
CPPFLAGS="-I$ZPFX/include $CPPFLAGS"
LDFLAGS="-L$ZPFX/lib $LDFLAGS"
where $ZPFX variable is my custom user prefix, similar to ~/.local.
Now, the problem is that the system iconv.h (under path /usr/include) isn't found because of this, as only the above pre-set (with use of config.site) -I$ZPFX…/-L$ZPFX… are being passed to the test program, as the following lines from config.log are showing:
configure:21831: gcc -o conftest -g -O2 \
-I/home/q/.local/share/zinit/polaris/include \
-L/home/q/.local/share/zinit/polaris/lib \
conftest.c -lxml2 -liconv >&5
/usr/bin/ld: cannot find -liconv
collect2: error: ld returned 1 exit status
($ZPFX is expanded to its value, which is: /home/q/.local/share/zinit/polaris)
The Question: how to append (prepend) any custom ($ZPFX/… in my case) directories to CPPFLAGS/LDFLAGS, preserving their default values? So that my custom libraries are only given higher precedence, and not exclusivity?
What I've tried
As it can be seen, I've tried to prepend to the flags by appending any occurred values at the time of sourcing the config.site file, by "…$CPP…/$LDFLAGS" :
CPPFLAGS="-I$ZPFX/include $CPPFLAGS"
LDFLAGS="-L$ZPFX/lib $LDFLAGS"
However this has no effect.
I'm also waving between not-appending and appending any typically used system-libraries paths: /usr/include and /usr/lib{,64}, however I don't like the idea, because some system might use e.g.: /opt/… for main prefix, making such hack not working at all.

Answer 1

The documentation explains how configure scripts use CONFIG_SITE. The parts most relevant to your question are near the beginning:
If the environment variable CONFIG_SITE is set, configure uses its
value as a space-separated list of shell scripts to read [...].
Otherwise, it reads the shell script prefix/share/config.site if it
exists, then prefix/etc/config.site if it exists. [...]
Site files can be arbitrary shell scripts
You ask:
how to append (prepend) any custom ($ZPFX/… in my case) directories
to CPPFLAGS/LDFLAGS, preserving their default values? So that my
custom libraries are only given higher precedence, and not
exclusivity?
You need to read only a little between the lines to recognize that the mechanism by which configure scripts read site defaults must be via the . command. That the files may contain arbitrary shell code and that they can set shell variables within configure implies that they are going to be parsed and executed as shell code.
The docs also say what configure does by default when you do not provide CONFIG_SITE, so your site config can do that, too, if you wish. And that's what I would do, to start. Specifically, add this at the beginning of $ZPFX/share/config.site:
test -r "${prefix}/share/config.site" && . "${prefix}/share/config.site"
test -r "${prefix}/etc/config.site" && . "${prefix}/etc/config.site"
Now you have the same settings that configure would get when you don't define CONFIG_SITE at all. What remains is to insert your own additional settings, and the code already presented in the question ought to be fine for that:
CPPFLAGS="-I$ZPFX/include $CPPFLAGS"
LDFLAGS="-L$ZPFX/lib $LDFLAGS"
Additionally, you write:
I'm also waving between not-appending and appending any typically used
system-libraries paths: /usr/include and /usr/lib{,64}, however I
don't like the idea, because some system might use e.g.: /opt/… for
main prefix, making such hack not working at all.
I don't like that idea either.
In the first place, /usr/include, /usr/lib, etc. are not just commonly used, they are typical toolchain defaults. You pretty much never need to explicitly specify toolchain defaults, and trying to do so is more likely to cause harm than good. For example, it could cause breakage in cases such as you posit, where the defaults for the toolchain actually being used are different from the usual ones.
But in the second place, your remarks convey an incorrect perspective on what you're doing with site defaults. These are site-specific, which may mean machine specific or may mean more broadly specific to a group or organization, but any way around, you can set only your own site defaults, not those of other sites.
And that leads me to one final point: the site configuration is part of your site, not part of your project. Hopefully this is not a point of confusion for you, but I want to be sure it is clear. You should not be planning to distribute your site configuration file outside your own site, nor to rely on people wanting to build your project at other sites specifically to use a site configuration file to inject build settings.