--- bundled/cdd/support/configure.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/cdd/support/configure.pl	2023-11-17 10:32:30.035032672 -0700
@@ -56,7 +56,6 @@ sub proceed {
       my $cdd_lib=Polymake::Configure::get_libdir($cdd_path, "cddgmp");
       if (-f "$cdd_lib/libcddgmp.$Config::Config{so}" ) {
          $LDFLAGS = "-L$cdd_lib";
-         $LDFLAGS .= " -Wl,-rpath,$cdd_lib" if $cdd_path ne "/usr";
       }
       if (!$CFLAGS or !$LDFLAGS) {
          die "Invalid installation location of cddlib: header file cdd.h and/or library libcddgmp.$Config::Config{so} not found.\n",
@@ -69,7 +68,6 @@ sub proceed {
       $cdd_path .= "include: $cdd_inc ";
    }
    if (defined ($cdd_lib=$options->{'cdd-lib'})) {
-      $LDFLAGS = "-L$cdd_lib -Wl,-rpath,$cdd_lib";
       $cdd_path .= "lib: $cdd_lib";
    }
 
--- bundled/flint/support/configure.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/flint/support/configure.pl	2023-11-17 10:32:30.036032651 -0700
@@ -23,7 +23,7 @@ sub proceed {
       my $lib=Polymake::Configure::get_libdir($flint_path, "flint");
       if (-f "$inc/flint/flint.h" && -f "$lib/libflint.$Config::Config{so}" ) {
          $cxxflags .= " -I$inc";
-         $ldflags .= " -L$lib -Wl,-rpath,$lib";
+         $ldflags .= " -L$lib";
       } else {
          die "Invalid installation location of flint, header files and/or library not found\n";
       }
--- bundled/libnormaliz/support/configure.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/libnormaliz/support/configure.pl	2023-11-17 10:32:30.036032651 -0700
@@ -48,7 +48,7 @@ sub proceed {
       my $nmz_lib=Polymake::Configure::get_libdir($nmz_path, "normaliz");
       if (-f "$nmz_inc/libnormaliz/libnormaliz.h" && -f "$nmz_lib/libnormaliz.$Config::Config{so}" ) {
          $CXXFLAGS = "-I$nmz_inc";
-         $LDFLAGS = "-L$nmz_lib -Wl,-rpath,$nmz_lib";
+         $LDFLAGS = "-L$nmz_lib";
       } else {
          die "Invalid installation location of libnormaliz header file libnormaliz/libnormaliz.h and/or library libnormaliz.$Config::Config{so} not found\n";
       }
@@ -189,6 +189,7 @@ int main (int argc, char *argv[])
                  Polymake::Configure::v_cmp($Polymake::Configure::CLANGversion, "5.0.0") < 0);
 
    } else {
+      $CXXFLAGS='-I/usr/include/libnormaliz';
       $LIBS="$libs";
       $message = "$nmz_version @ ".($nmz_path//"system")
    }
--- bundled/lrs/support/configure.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/lrs/support/configure.pl	2023-11-17 10:32:30.036032651 -0700
@@ -67,7 +67,7 @@ sub proceed {
       $CFLAGS .= " -DHAVE_LRSDRIVER" if -f "$lrs_inc/lrsdriver.h";
 
       if (-f "$lrs_lib/lib$lrs_libname.$Config::Config{so}" ) {
-         $LDFLAGS = "-L$lrs_lib -Wl,-rpath,$lrs_lib";
+         $LDFLAGS = "-L$lrs_lib";
       } elsif (-f "$lrs_lib/lib$lrs_libname.a" ) {
          $LDFLAGS = "-L$lrs_lib";
       } else {
--- bundled/nauty/apps/graph/src/build_flags.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/nauty/apps/graph/src/build_flags.pl	2023-11-17 10:32:30.036032651 -0700
@@ -1,29 +1,11 @@
 # input for generate_ninja_targets.pl
 
-my $foreign_src = $ConfigFlags{'bundled.nauty.NautySrc'} ne "bundled" && $ConfigFlags{'bundled.nauty.NautySrc'};
-my $nauty_src = $foreign_src ? '${bundled.nauty.NautySrc}' : '${root}/bundled/nauty/external/nauty';
-my $generated_dir = '${buildroot}/staticlib/nauty';
-my @generated_headers = qw( nauty.h naututil.h gtools.h );
-my @generated_in = map { /\.h$/; "$nauty_src/$`-h.in" } @generated_headers;
-my @generated_out = map { "$generated_dir/$_" } @generated_headers;
-my $include_generated = ($foreign_src && grep { -f "$foreign_src/$_" } @generated_headers)
-                        ? join(" ", map { "-include $_" } @generated_out)
-                        : "-I$generated_dir";
-my $nauty_inc = $ConfigFlags{'bundled.nauty.NautySrc'}
-                ? " -I$generated_dir -I$nauty_src"
-                : "";
-
-( 'GraphIso.cc' => $nauty_inc,
-
-  $ConfigFlags{'bundled.nauty.NautySrc'}
-  ? ( GENERATED => {
-        out => "@generated_out", in => "@generated_in",
-        command => "cd $generated_dir; CC=\"\${CC}\" CFLAGS=\"\${CFLAGS}\" $nauty_src/configure --quiet >/dev/null 2>/dev/null; rm -rf makefile nauty; ln -s . nauty",
-      },
-      staticlib => {
-        SOURCEDIR => $nauty_src,
+(
+  $ConfigFlags{'bundled.nauty.UseBundled'}
+  ? ( staticlib => {
+        SOURCEDIR => '${root}/bundled/nauty/external/nauty',
         SOURCES => [ qw(naugraph.c naurng.c nausparse.c nautaux.c nautil.c nautinv.c naututil.c nauty.c rng.c schreier.c) ],
-        CFLAGS => "$include_generated -I$nauty_src",
+        CFLAGS => "-I/usr/include/nauty",
       } )
   : ()
 )
--- bundled/nauty/support/configure.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/nauty/support/configure.pl	2023-11-17 10:32:30.036032651 -0700
@@ -30,8 +30,7 @@ sub usage {
 }
 
 sub check_nauty {
-   my $dir = @_ > 0 ? $_[0] : "bundled/nauty/external/nauty";
-   -e "$dir/nauty-h.in"
+   -e "bundled/nauty/external/nauty/nauty-h.in";
 }
 
 sub proceed {
@@ -54,9 +53,16 @@ sub proceed {
       $LDFLAGS = "-L$nauty_lib";
       undef $NautySrc;
    } elsif (defined ($nauty_src=$options->{"nauty-src"}) && $nauty_src ne "bundled") {
-      check_nauty($nauty_src) or
-         die "Specified nauty source directory invalid, could not find 'nauty-h.in' in $nauty_src.";
-      $NautySrc = "$nauty_src";
+      my $nauty_inc="$nauty_src/include/nauty";
+      my $nauty_lib="@@LIBDIR@@";
+      if (-f "$nauty_inc/nauty.h") {
+         $CXXFLAGS="-I$nauty_inc";
+         $LDFLAGS="-L$nauty_lib";
+         $LIBS="-lnauty";
+         $NautySrc = 0;
+      } else {
+         die "Could not locate a working nauty installation\n";
+      }
    }
 
    if (!$nauty_src && $nauty_path ne "bundled" && $options->{prereq} ne ".none.") {
--- bundled/scip/support/configure.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/scip/support/configure.pl	2023-11-17 10:32:59.874409718 -0700
@@ -42,7 +42,7 @@ sub proceed {
          die "invalid SCIP location $path: header file scip.h not found anywhere below\n";
       }
       my $libdir = Polymake::Configure::get_libdir($path, "scip","so");
-      $LDFLAGS = "-L$libdir -Wl,-rpath,$libdir";
+      $LDFLAGS = "-L$libdir";
    }
 
    $LIBS="-lscip -lz";
--- bundled/singular/support/configure.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/singular/support/configure.pl	2023-11-17 10:32:30.036032651 -0700
@@ -43,7 +43,7 @@ sub singular_config_approach {
    # yes we need it twice ...
    chomp ($singular_prefix = `$singular_config --prefix`);
    chomp $singular_prefix;
-   $LDFLAGS =~ s/-L(\S+)/-L$1 -Wl,-rpath,$1/g;
+   $LDFLAGS =~ s/-L(\S+)/-L$1/g;
    my $libdir = $1;
 
    # newer versions of singular need -lsingular_resources while older ones needed -lresources
@@ -66,9 +66,6 @@ sub pkg_config_approach {
    chomp ($CXXFLAGS=`$pkg_config --cflags Singular`);
    die "$pkg_config failed: $!" if ($?);
    chomp ($LDFLAGS=`$pkg_config --libs-only-other --libs-only-L Singular`);
-   if (defined ($options->{singular})){
-      $LDFLAGS =~ s/-L(\S+)/-L$1 -Wl,-rpath,$1/g;
-   }
    chomp ($LIBS=`$pkg_config --libs-only-l Singular`);
    return $pc_singular_prefix;
 }
--- bundled/soplex/support/configure.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/soplex/support/configure.pl	2023-11-17 10:33:21.465958942 -0700
@@ -60,7 +60,7 @@ sub proceed {
          $libdir = Polymake::Configure::get_libdir($path, "soplex")
          # (get_libdir has a fallback to $path/lib if nothing was found)
             unless -f "$libdir/libsoplex-pic.a";
-         $LDFLAGS = "-L$libdir -Wl,-rpath,$libdir";
+         $LDFLAGS = "-L$libdir";
       } else {
          $LDFLAGS = $Polymake::Bundled::scip::LDFLAGS;
       }
--- bundled/sympol/apps/polytope/src/build_flags.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/sympol/apps/polytope/src/build_flags.pl	2023-11-17 10:32:30.037032630 -0700
@@ -16,7 +16,7 @@ if ($ConfigFlags{'bundled.sympol.UseBund
                         symmetrygroupconstruction/graphconstructiondefault.cpp symmetrygroupconstruction/matrixconstruction.cpp symmetrygroupconstruction/matrixconstructiondefault.cpp ) ],
        'raycomputationcdd.cpp' => '-DGMPRATIONAL ${bundled.cdd.CFLAGS}',
        'raycomputationlrs.cpp' => '-DGMP -DMA ${bundled.lrs.CFLAGS}',
-       CXXFLAGS => $no_warnings . ($ConfigFlags{ExternalHeaders} =~ /\bpermlib\b/ ? ' -I${root}/include/external/permlib' : ''),
+       CXXFLAGS => $no_warnings . ($ConfigFlags{ExternalHeaders} =~ /\bpermlib\b/ ? ' -I/usr/include/permlib' : ''),
     },
   )
 } else {
--- bundled/sympol/support/configure.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ bundled/sympol/support/configure.pl	2023-11-17 10:32:30.037032630 -0700
@@ -120,6 +120,7 @@ int main() {
       undef $LIBS;
       $CXXFLAGS = '-I${root}/bundled/sympol/external/sympol';
    } else {
+      $CXXFLAGS="-I/usr/include/sympol";
       $LIBS="-lsympol";
    }
 
--- perl/polymake-config.orig	2023-11-06 04:02:24.000000000 -0700
+++ perl/polymake-config	2023-11-17 10:32:30.037032630 -0700
@@ -140,9 +140,6 @@ while (defined ($_=shift)) {
 
    } elsif ($_ eq "--ldflags") {
       my $ldflags=$ConfigFlags{LDFLAGS};
-      if ($ldflags !~ /(?:^|\s)-L$ConfigFlags{InstallLib}(?:\s|$)/) {
-         $ldflags="-L$ConfigFlags{InstallLib} $ldflags";
-      }
       my $add_rpath=1;
 
       # collect standard library paths of the C++ compiler and exclude them from the result
@@ -164,9 +161,6 @@ while (defined ($_=shift)) {
          $ldflags = "$ConfigFlags{ARCHFLAGS} $ldflags -flat_namespace";
       } else {
          $ldflags .= " -Wl,-E";
-         if ($add_rpath) {
-            $ldflags .= " -Wl,-rpath,$ConfigFlags{InstallLib}";
-         }
       }
       $ldflags =~ s/^\s+//; $ldflags =~ s/\s+$//; $ldflags =~ s/\s{2,}/ /g;
 
--- support/configure.pl.orig	2023-11-06 04:02:24.000000000 -0700
+++ support/configure.pl	2023-11-17 10:32:30.037032630 -0700
@@ -498,7 +498,7 @@ sub parse_command_line {
       }
    }
 
-   $CXXOPT   =$vars{CXXOPT}   // "-O3";
+   $CXXOPT   =$vars{CXXOPT}   // "-O2";
    $CXXDEBUG =$vars{CXXDEBUG} // "-g";
    $CFLAGS   =$vars{CFLAGS}   // "";
    $CXXFLAGS =$vars{CXXFLAGS} // $CFLAGS;
@@ -725,7 +725,7 @@ sub determine_cxx_library {
       }
       $CFLAGS   .= " -I$options{toolchain}/include";
       $CXXFLAGS .= " -I$options{toolchain}/include";
-      $LDFLAGS  .= " -L$libdir -Wl,-rpath,$libdir";
+      $LDFLAGS  .= " -L$libdir";
    }
 
    if ($options{libcxx} eq ".true.") {
@@ -1127,10 +1127,6 @@ sub locate_gmp_and_mpfr_libraries {
       $CXXFLAGS .= " -I$GMP/include";
       my $libdir=get_libdir($GMP, "gmp");
       $LDFLAGS .= " -L$libdir";
-      if (!$FinkBase) {
-         # non-standard location
-         $LDFLAGS .= " -Wl,-rpath,$libdir";
-      }
    }
 
    my $MPFR=$options{mpfr};
@@ -1139,10 +1135,6 @@ sub locate_gmp_and_mpfr_libraries {
       $CXXFLAGS .= " -I$MPFR/include";
       my $libdir=get_libdir($MPFR, "mpfr");
       $LDFLAGS .= " -L$libdir";
-      if (!$FinkBase) {
-         # non-standard location
-         $LDFLAGS .= " -Wl,-rpath,$libdir";
-      }
    } elsif ($FinkBase) {
       $MPFR=$FinkBase;
    }