Flag site-specific modules and themes rather than ignore them.

This allows the front-end to be aware of site-specific packages.
We'll then need to ignore them for platform comparison purposes, but
this should otherwise be safe.

platform/provision_drupal.drush.inc

@@ -543,9 +543,9 @@ function provision_drupal_system_map() {
 
   foreach (_provision_system_query("module") as $module) {
     $frags = explode("/", $module->filename);
-    // ignore site-specific modules
+    // flag site-specific modules
     if ($frags[0] == 'sites' && $frags[1] != 'all') {
-      continue;
+      $module->platform = -1;
     }
     $info_file = sprintf("%s/%s.info", dirname($module->filename), $module->name);
     $module->info = provision_parse_info_file($info_file);
@@ -563,9 +563,9 @@ function provision_drupal_system_map() {
   // XXX: mostly a copy-paste from above
   foreach (_provision_system_query("theme") as $theme) {
     $frags = explode("/", $theme->filename);
-    // ignore site-specific themes
+    // flag site-specific themes
     if ($frags[0] == 'sites' && $frags[1] != 'all') {
-      continue;
+      $theme->platform = -1;
     }
     $info_file = sprintf("%s/%s.info", dirname($theme->filename), $theme->name);
     $theme->info = provision_parse_info_file($info_file);