Only sync the relevant sites directory.

file/file.drush.inc

@@ -454,8 +454,13 @@ class provisionService_file extends provisionService {
 
   /**
    * If necessary, sync files out to a remote server.
+   *
+   * @param $path
+   *   Full path to sync.
+   * @param $exclude_sites
+   *   Exclude sites/*, except sites/*.
    */
-  function sync($path = NULL) {
+  function sync($path = NULL, $exclude_sites = FALSE) {
     if (is_null($path)) {
       $path = $this->config_path;
     }

file/remote/remote_service.inc

 <?php
 
+require_once DRUSH_BASE_PATH . '/commands/core/rsync.core.inc';
+
 class provisionService_file_remote extends provisionService_file {
   function init() {
     $this->config_path = $this->config_path . '--' . $this->remote_host;
     parent::init();
   }
 
-  function sync($path = NULL) {
+  function sync($path = NULL, $exclude_sites = FALSE) {
     if (is_null($path)) {
       $path = $this->config_path;
     }
-    if (drush_shell_exec('rsync -azC --delete %s/ %s@%s:%s', $path, $this->script_user, $this->remote_host, $path)) {
+
+    $options = array(
+      'delete' => TRUE,
+      'exclude-sites' => $exclude_sites,
+    );
+    if (drush_core_call_rsync(escapeshellarg($path . '/'), escapeshellarg($this->script_user . '@' . $this->remote_host . ':' . $path), $options)) {
       drush_log(dt('@path has been synced to remote server.', array('@path' => $path)));
     }
     else {

platform/provision_drupal.drush.inc

@@ -171,6 +171,13 @@ function _provision_drupal_site_installed() {
   return FALSE;
 }
 
+function provision_drupal_sync_site() {
+  d()->service('file')->sync(d()->root, TRUE);
+  if (d()->type === 'site') {
+    d()->service('file')->sync(d()->root . '/sites/' . d()->uri);
+  }
+}
+
 /**
  * Generate a settings file for the site.
  *
@@ -183,7 +190,7 @@ function _provision_drupal_site_installed() {
 function _provision_drupal_create_settings_file() {
   $config = new provisionConfig_drupal_settings(d()->name);
   $config->write();
-  d()->service('file')->sync(d()->root);
+  provision_drupal_sync_site();
 }
 
 class provisionConfig_drupal_settings extends provisionConfig {

provision.inc

@@ -43,7 +43,7 @@ function provision_save_site_data() {
   if (!drush_get_error()) {
     $config = new provisionConfig_drushrc_site(d()->name);
     $config->write();
-    d()->service('file')->sync(d()->root);
+    provision_drupal_sync_site();
   }
 }
 
@@ -55,7 +55,7 @@ function provision_save_platform_data() {
   if (!drush_get_error()) {
     $config = new provisionConfig_drushrc_platform(d()->name);
     $config->write();
-    d()->service('file')->sync(d()->root);
+    provision_drupal_sync_site();
   }
 }