waf: use wafConfigureFlags for waf flags

This avoids the potential conflict between autoconf flags and the waf
flags. There is some overlap between the two but waf errors when it
doesn’t recognize the flag.

(cherry picked from commit a79a8f29bc509b2d51158846c9562e64e1239b4c)

pkgs/applications/audio/ardour/default.nix

···
     patchShebangs ./tools/
   '';
 
-  configureFlags = [
+  wafConfigureFlags = [
     "--optimize"
     "--docs"
     "--with-backends=jack,alsa,dummy"

pkgs/applications/audio/guitarix/default.nix

···
     zita-resampler curl
   ];
 
-  configureFlags = [
+  wafConfigureFlags = [
     "--shared-lib"
     "--no-desktop-update"
     "--enable-nls"

pkgs/applications/misc/xiphos/default.nix

···
     export SWORD_HOME=${sword};
   '';
 
-  configureFlags= [ "--enable-webkit2" ];
+  wafConfigureFlags = [ "--enable-webkit2" ];
 
   meta = with stdenv.lib; {
     description = "A GTK Bible study tool";

pkgs/development/libraries/audio/lvtk/default.nix

···
     sed -i '/target[ ]*= "ttl2c"/ ilib=["boost_system"],' tools/wscript_build
   '';
 
-  configureFlags = [
+  wafConfigureFlags = [
     "--boost-includes=${boost.dev}/include"
     "--boost-libs=${boost.out}/lib"
   ];

pkgs/development/libraries/ndn-cxx/default.nix

···
   };
   nativeBuildInputs = [ pkgconfig wafHook ];
   buildInputs = [ openssl doxygen boost sqlite python pythonPackages.sphinx];
-  configureFlags = [
+  wafConfigureFlags = [
     "--with-openssl=${openssl.dev}"
     "--boost-includes=${boost.dev}/include"
     "--boost-libs=${boost.out}/lib"

pkgs/development/libraries/science/networking/ns3/default.nix

···
     patchShebangs doc/ns3_html_theme/get_version.sh
   '';
 
-  configureFlags = with stdenv.lib; [
+  wafConfigureFlags = with stdenv.lib; [
       "--enable-modules=${stdenv.lib.concatStringsSep "," modules}"
       "--with-python=${pythonEnv.interpreter}"
   ]

pkgs/development/libraries/talloc/default.nix

···
 
   wafPath = "buildtools/bin/waf";
 
-  configureFlags = [
+  wafConfigureFlags = [
     "--enable-talloc-compat1"
     "--bundled-libraries=NONE"
     "--builtin-libraries=replace"

pkgs/development/libraries/tdb/default.nix

···
 
   wafPath = "buildtools/bin/waf";
 
-  configureFlags = [
+  wafConfigureFlags = [
     "--bundled-libraries=NONE"
     "--builtin-libraries=replace"
   ];

pkgs/development/tools/build-managers/waf/setup-hook.sh

···
         cp @waf@ "$wafPath"
     fi
 
-    if [[ -z "${dontAddPrefix:-}" && -n "$prefix" ]]; then
-        configureFlags="${prefixKey:---prefix=}$prefix $configureFlags"
+    if [ -z "${dontAddPrefix:-}" ] && [ -n "$prefix" ]; then
+        wafConfigureFlags="${prefixKey:---prefix=}$prefix $wafConfigureFlags"
     fi
 
-    local flagsArray=(@crossFlags@);
-    for flag in $configureFlags "${configureFlagsArray[@]}";
-    do
-        if [[
-        # waf does not support these flags, but they are "blindly" added by the
-        # pkgsStatic overlay, for example.
-              $flag != "--enable-static"
-           && $flag != "--disable-static"
-           && $flag != "--enable-shared"
-           && $flag != "--disable-shared"
-        # these flags are added by configurePlatforms but waf just uses them
-        # to bail out in cross compilation cases
-           && $flag != --build=* 
-           && $flag != --host=* 
-           ]];
-        then
-            flagsArray=("${flagsArray[@]}" "$flag");
-        fi;
-    done
-    flagsArray=(
+    local flagsArray=(
+        @crossFlags@
         "${flagsArray[@]}"
+        $wafConfigureFlags "${wafConfigureFlagsArray[@]}"
         ${configureTargets:-configure}
     )
     echoCmd 'configure flags' "${flagsArray[@]}"

pkgs/misc/emulators/wxmupen64plus/default.nix

···
     export CXXFLAGS="-I${libX11.dev}/include/X11 -DLIBDIR=\\\"${mupen64plus}/lib/\\\""
     export LDFLAGS="-lwx_gtk2u_adv-2.9"
 
-    configureFlagsArray+=("--mupenapi=$APIDIR" "--wxconfig=`type -P wx-config`")
+    wafConfigureFlagsArray+=("--mupenapi=$APIDIR" "--wxconfig=`type -P wx-config`")
   '';
 
   NIX_CFLAGS_COMPILE = "-fpermissive";

pkgs/misc/jackaudio/default.nix

···
     export NIX_CFLAGS_COMPILE="-F${CoreFoundation}/Library/Frameworks $NIX_CFLAGS_COMPILE"
   '';
 
-  configureFlags = [
+  wafConfigureFlags = [
     "--classic"
     "--autostart=${if (optDbus != null) then "dbus" else "classic"}"
   ] ++ optional (optDbus != null) "--dbus"

pkgs/tools/graphics/glmark2/default.nix

···
     libjpeg libpng xorg.libxcb libX11 libGL libdrm python27 wayland udev mesa_noglu
   ];
 
-  configureFlags = ["--with-flavors=x11-gl,x11-glesv2,drm-gl,drm-glesv2,wayland-gl,wayland-glesv2"];
+  wafConfigureFlags = ["--with-flavors=x11-gl,x11-glesv2,drm-gl,drm-glesv2,wayland-gl,wayland-glesv2"];
 
   meta = with stdenv.lib; {
     description = "OpenGL (ES) 2.0 benchmark";