Fourth attempt at the following. Unreviewed, this was originally reviewed in http://codereview.c...

build/linux/system.gyp

 # Copyright (c) 2011 The Chromium Authors. All rights reserved.
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 
 {
   'conditions': [
     ['sysroot!=""', {
       'variables': {
         'pkg-config': './pkg-config-wrapper "<(sysroot)"',
       },
@@ skipping 13 matching lines @@
         'use_system_ssl%': 1,
       },
     }],
   ],
 
 
   'targets': [
     {
       'target_name': 'gtk',
       'type': 'settings',
+      'toolsets': ['host', 'target'],
       'conditions': [
         ['_toolset=="target"', {
           'direct_dependent_settings': {
             'cflags': [
               '<!@(<(pkg-config) --cflags gtk+-2.0 gthread-2.0)',
             ],
           },
           'link_settings': {
             'ldflags': [
               '<!@(<(pkg-config) --libs-only-L --libs-only-other gtk+-2.0 gthread-2.0)',
             ],
             'libraries': [
               '<!@(<(pkg-config) --libs-only-l gtk+-2.0 gthread-2.0)',
             ],
           },
-      }],
-      [ 'chromeos==1', {
-        'link_settings': {
-          'libraries': [ '-lXtst' ]
-        }
-      }]]
+        }, {
+          'direct_dependent_settings': {
+            'cflags': [
+              '<!@(pkg-config --cflags gtk+-2.0 gthread-2.0)',
+            ],
+          },
+          'link_settings': {
+            'ldflags': [
+              '<!@(pkg-config --libs-only-L --libs-only-other gtk+-2.0 gthread-2.0)',
+            ],
+            'libraries': [
+              '<!@(pkg-config --libs-only-l gtk+-2.0 gthread-2.0)',
+            ],
+          },
+        }],
+        ['chromeos==1', {
+          'link_settings': {
+            'libraries': [ '-lXtst' ]
+          }
+        }],
+      ],
     },
     {
       'target_name': 'gtkprint',
       'type': 'settings',
       'conditions': [
         ['_toolset=="target"', {
           'direct_dependent_settings': {
             'cflags': [
               '<!@(<(pkg-config) --cflags gtk+-unix-print-2.0)',
             ],
           },
           'link_settings': {
             'ldflags': [
               '<!@(<(pkg-config) --libs-only-L --libs-only-other gtk+-unix-print-2.0)',
             ],
             'libraries': [
               '<!@(<(pkg-config) --libs-only-l gtk+-unix-print-2.0)',
             ],
           },
-      }]]
+        }],
+      ],
     },
     {
       'target_name': 'ssl',
       'type': 'settings',
       'conditions': [
         ['_toolset=="target"', {
           'conditions': [
             ['use_openssl==1', {
               'dependencies': [
                 '../../third_party/openssl/openssl.gyp:openssl',
@@ skipping 56 matching lines @@
             ],
           },
           'link_settings': {
             'ldflags': [
               '<!@(<(pkg-config) --libs-only-L --libs-only-other freetype2)',
             ],
             'libraries': [
               '<!@(<(pkg-config) --libs-only-l freetype2)',
             ],
           },
-      }]]
+        }],
+      ],
     },
     {
       'target_name': 'fontconfig',
       'type': 'settings',
       'conditions': [
         ['_toolset=="target"', {
           'direct_dependent_settings': {
             'cflags': [
               '<!@(<(pkg-config) --cflags fontconfig)',
             ],
           },
           'link_settings': {
             'ldflags': [
               '<!@(<(pkg-config) --libs-only-L --libs-only-other fontconfig)',
             ],
             'libraries': [
               '<!@(<(pkg-config) --libs-only-l fontconfig)',
             ],
           },
-      }]]
+        }],
+      ],
     },
     {
       'target_name': 'gdk',
       'type': 'settings',
       'conditions': [
         ['_toolset=="target"', {
           'direct_dependent_settings': {
             'cflags': [
               '<!@(<(pkg-config) --cflags gdk-2.0)',
             ],
           },
           'link_settings': {
             'ldflags': [
               '<!@(<(pkg-config) --libs-only-L --libs-only-other gdk-2.0)',
             ],
             'libraries': [
               '<!@(<(pkg-config) --libs-only-l gdk-2.0)',
             ],
           },
-      }]]
+        }],
+      ],
     },
     {
       'target_name': 'gconf',
       'type': 'settings',
       'conditions': [
         ['use_gconf==1 and _toolset=="target"', {
           'direct_dependent_settings': {
             'cflags': [
               '<!@(<(pkg-config) --cflags gconf-2.0)',
             ],
             'defines': [
               'USE_GCONF',
             ],
           },
           'link_settings': {
             'ldflags': [
               '<!@(<(pkg-config) --libs-only-L --libs-only-other gconf-2.0)',
             ],
             'libraries': [
               '<!@(<(pkg-config) --libs-only-l gconf-2.0)',
             ],
           },
-      }]]
+        }],
+      ],
     },
     {
       'target_name': 'gio',
       'type': 'settings',
       'conditions': [
         ['use_gio==1 and _toolset=="target"', {
           'direct_dependent_settings': {
             'cflags': [
               '<!@(<(pkg-config) --cflags gio-2.0)',
             ],
@@ skipping 14 matching lines @@
               '<!@(<(pkg-config) --libs-only-l gio-2.0)',
             ],
             'conditions': [
               ['linux_link_gsettings==0', {
                 'libraries': [
                   '-ldl',
                 ],
               }],
             ],
           },
-      }]]
+        }],
+      ],
     },
     {
       'target_name': 'x11',
       'type': 'settings',
+      'toolsets': ['host', 'target'],
       'conditions': [
         ['_toolset=="target"', {
           'direct_dependent_settings': {
             'cflags': [
               '<!@(<(pkg-config) --cflags x11)',
             ],
           },
           'link_settings': {
             'ldflags': [
               '<!@(<(pkg-config) --libs-only-L --libs-only-other x11 xi)',
             ],
             'libraries': [
               '<!@(<(pkg-config) --libs-only-l x11 xi)',
             ],
           },
-      }],
+        }, {
+          'direct_dependent_settings': {
+            'cflags': [
+              '<!@(pkg-config --cflags x11)',
+            ],
+          },
+          'link_settings': {
+            'ldflags': [
+              '<!@(pkg-config --libs-only-L --libs-only-other x11 xi)',
+            ],
+            'libraries': [
+              '<!@(pkg-config --libs-only-l x11 xi)',
+            ],
+          },
+        }],
       ],
     },
     {
       'target_name': 'xext',
       'type': 'settings',
       'conditions': [
         ['_toolset=="target"', {
           'direct_dependent_settings': {
             'cflags': [
               '<!@(<(pkg-config) --cflags xext)',
             ],
           },
           'link_settings': {
             'ldflags': [
               '<!@(<(pkg-config) --libs-only-L --libs-only-other xext)',
             ],
             'libraries': [
               '<!@(<(pkg-config) --libs-only-l xext)',
             ],
           },
-      }]]
+        }],
+      ],
     },
     {
       'target_name': 'libgcrypt',
       'type': 'settings',
       'conditions': [
         ['_toolset=="target" and use_cups==1', {
           'direct_dependent_settings': {
             'cflags': [
               '<!@(libgcrypt-config --cflags)',
             ],
           },
           'link_settings': {
             'libraries': [
               '<!@(libgcrypt-config --libs)',
             ],
           },
-      }]]
+        }],
+      ],
     },
     {
       'target_name': 'selinux',
       'type': 'settings',
       'conditions': [
         ['_toolset=="target"', {
           'link_settings': {
             'libraries': [
               '-lselinux',
             ],
           },
-      }]]
+        }],
+      ],
     },
     {
       'target_name': 'gnome_keyring',
       'type': 'settings',
       'conditions': [
         ['use_gnome_keyring==1', {
           'direct_dependent_settings': {
             'cflags': [
               '<!@(<(pkg-config) --cflags gnome-keyring-1)',
             ],
@@ skipping 165 matching lines @@
             ],
             'libraries': [
               '<!@(<(pkg-config) --libs-only-l wayland-client wayland-egl xkbcommon)',
             ],
           },
         }],
       ],
     },
   ],
 }