diff --git a/resources/sql/autopatches/20161130.search.01.manual.sql b/resources/sql/autopatches/20161130.search.01.manual.sql
new file mode 100644
--- /dev/null
+++ b/resources/sql/autopatches/20161130.search.01.manual.sql
@@ -0,0 +1,6 @@
+CREATE TABLE {$NAMESPACE}_config.config_manualactivity (
+  id INT UNSIGNED NOT NULL AUTO_INCREMENT PRIMARY KEY,
+  activityType VARCHAR(64) NOT NULL COLLATE {$COLLATE_TEXT},
+  parameters LONGTEXT NOT NULL COLLATE {$COLLATE_TEXT},
+  UNIQUE KEY `key_type` (activityType)
+) ENGINE=InnoDB, COLLATE {$COLLATE_TEXT};
diff --git a/resources/sql/autopatches/20161130.search.02.rebuild.php b/resources/sql/autopatches/20161130.search.02.rebuild.php
new file mode 100644
--- /dev/null
+++ b/resources/sql/autopatches/20161130.search.02.rebuild.php
@@ -0,0 +1,26 @@
+<?php
+
+$search_engine = PhabricatorFulltextStorageEngine::loadEngine();
+$use_mysql = ($search_engine instanceof PhabricatorMySQLFulltextStorageEngine);
+
+if ($use_mysql) {
+  $field = new PhabricatorSearchDocumentField();
+  $conn = $field->establishConnection('r');
+
+  // We're only going to require this if the index isn't empty: if you're on a
+  // fresh install, you don't have to do anything.
+  $any_documents = queryfx_one(
+    $conn,
+    'SELECT * FROM %T LIMIT 1',
+    $field->getTableName());
+
+  if ($any_documents) {
+    try {
+      id(new PhabricatorConfigManualActivity())
+        ->setActivityType(PhabricatorConfigManualActivity::TYPE_REINDEX)
+        ->save();
+    } catch (AphrontDuplicateKeyQueryException $ex) {
+      // If we've already noted that this activity is required, just move on.
+    }
+  }
+}
diff --git a/src/__phutil_library_map__.php b/src/__phutil_library_map__.php
--- a/src/__phutil_library_map__.php
+++ b/src/__phutil_library_map__.php
@@ -2272,11 +2272,13 @@
     'PhabricatorConfigListController' => 'applications/config/controller/PhabricatorConfigListController.php',
     'PhabricatorConfigLocalSource' => 'infrastructure/env/PhabricatorConfigLocalSource.php',
     'PhabricatorConfigManagementDeleteWorkflow' => 'applications/config/management/PhabricatorConfigManagementDeleteWorkflow.php',
+    'PhabricatorConfigManagementDoneWorkflow' => 'applications/config/management/PhabricatorConfigManagementDoneWorkflow.php',
     'PhabricatorConfigManagementGetWorkflow' => 'applications/config/management/PhabricatorConfigManagementGetWorkflow.php',
     'PhabricatorConfigManagementListWorkflow' => 'applications/config/management/PhabricatorConfigManagementListWorkflow.php',
     'PhabricatorConfigManagementMigrateWorkflow' => 'applications/config/management/PhabricatorConfigManagementMigrateWorkflow.php',
     'PhabricatorConfigManagementSetWorkflow' => 'applications/config/management/PhabricatorConfigManagementSetWorkflow.php',
     'PhabricatorConfigManagementWorkflow' => 'applications/config/management/PhabricatorConfigManagementWorkflow.php',
+    'PhabricatorConfigManualActivity' => 'applications/config/storage/PhabricatorConfigManualActivity.php',
     'PhabricatorConfigModule' => 'applications/config/module/PhabricatorConfigModule.php',
     'PhabricatorConfigModuleController' => 'applications/config/controller/PhabricatorConfigModuleController.php',
     'PhabricatorConfigOption' => 'applications/config/option/PhabricatorConfigOption.php',
@@ -2896,6 +2898,7 @@
     'PhabricatorManiphestApplication' => 'applications/maniphest/application/PhabricatorManiphestApplication.php',
     'PhabricatorManiphestConfigOptions' => 'applications/maniphest/config/PhabricatorManiphestConfigOptions.php',
     'PhabricatorManiphestTaskTestDataGenerator' => 'applications/maniphest/lipsum/PhabricatorManiphestTaskTestDataGenerator.php',
+    'PhabricatorManualActivitySetupCheck' => 'applications/config/check/PhabricatorManualActivitySetupCheck.php',
     'PhabricatorMarkupCache' => 'applications/cache/storage/PhabricatorMarkupCache.php',
     'PhabricatorMarkupEngine' => 'infrastructure/markup/PhabricatorMarkupEngine.php',
     'PhabricatorMarkupEngineTestCase' => 'infrastructure/markup/__tests__/PhabricatorMarkupEngineTestCase.php',
@@ -7178,11 +7181,13 @@
     'PhabricatorConfigListController' => 'PhabricatorConfigController',
     'PhabricatorConfigLocalSource' => 'PhabricatorConfigProxySource',
     'PhabricatorConfigManagementDeleteWorkflow' => 'PhabricatorConfigManagementWorkflow',
+    'PhabricatorConfigManagementDoneWorkflow' => 'PhabricatorConfigManagementWorkflow',
     'PhabricatorConfigManagementGetWorkflow' => 'PhabricatorConfigManagementWorkflow',
     'PhabricatorConfigManagementListWorkflow' => 'PhabricatorConfigManagementWorkflow',
     'PhabricatorConfigManagementMigrateWorkflow' => 'PhabricatorConfigManagementWorkflow',
     'PhabricatorConfigManagementSetWorkflow' => 'PhabricatorConfigManagementWorkflow',
     'PhabricatorConfigManagementWorkflow' => 'PhabricatorManagementWorkflow',
+    'PhabricatorConfigManualActivity' => 'PhabricatorConfigEntryDAO',
     'PhabricatorConfigModule' => 'Phobject',
     'PhabricatorConfigModuleController' => 'PhabricatorConfigController',
     'PhabricatorConfigOption' => array(
@@ -7877,6 +7882,7 @@
     'PhabricatorManiphestApplication' => 'PhabricatorApplication',
     'PhabricatorManiphestConfigOptions' => 'PhabricatorApplicationConfigOptions',
     'PhabricatorManiphestTaskTestDataGenerator' => 'PhabricatorTestDataGenerator',
+    'PhabricatorManualActivitySetupCheck' => 'PhabricatorSetupCheck',
     'PhabricatorMarkupCache' => 'PhabricatorCacheDAO',
     'PhabricatorMarkupEngine' => 'Phobject',
     'PhabricatorMarkupEngineTestCase' => 'PhabricatorTestCase',
diff --git a/src/applications/config/check/PhabricatorManualActivitySetupCheck.php b/src/applications/config/check/PhabricatorManualActivitySetupCheck.php
new file mode 100644
--- /dev/null
+++ b/src/applications/config/check/PhabricatorManualActivitySetupCheck.php
@@ -0,0 +1,75 @@
+<?php
+
+final class PhabricatorManualActivitySetupCheck
+  extends PhabricatorSetupCheck {
+
+  public function getDefaultGroup() {
+    return self::GROUP_OTHER;
+  }
+
+  protected function executeChecks() {
+    $activities = id(new PhabricatorConfigManualActivity())->loadAll();
+
+    foreach ($activities as $activity) {
+      $type = $activity->getActivityType();
+
+      // For now, there is only one type of manual activity. It's not clear
+      // if we're really going to have too much more of this stuff so this
+      // is a bit under-designed for now.
+
+      $activity_name = pht('Rebuild Search Index');
+      $activity_summary = pht(
+        'The search index algorithm has been updated and the index needs '.
+        'be rebuilt.');
+
+      $message = array();
+
+      $message[] = pht(
+        'The indexing algorithm for the fulltext search index has been '.
+        'updated and the index needs to be rebuilt. Until you rebuild the '.
+        'index, global search (and other fulltext search) will not '.
+        'function correctly.');
+
+      $message[] = pht(
+        'You can rebuild the search index while Phabricator is running.');
+
+      $message[] = pht(
+        'To rebuild the index, run this command:');
+
+      $message[] = phutil_tag(
+        'pre',
+        array(),
+        (string)csprintf(
+          'phabricator/ $ ./bin/search index --all --force --background'));
+
+      $message[] = pht(
+        'You can find more information about rebuilding the search '.
+        'index here: %s',
+        phutil_tag(
+          'a',
+          array(
+            'href' => 'https://phurl.io/u/reindex',
+            'target' => '_blank',
+          ),
+          'https://phurl.io/u/reindex'));
+
+      $message[] = pht(
+        'After rebuilding the index, run this command to clear this setup '.
+        'warning:');
+
+      $message[] = phutil_tag(
+        'pre',
+        array(),
+        (string)csprintf('phabricator/ $ ./bin/config done %R', $type));
+
+      $activity_message = phutil_implode_html("\n\n", $message);
+
+      $this->newIssue('manual.'.$type)
+        ->setName($activity_name)
+        ->setSummary($activity_summary)
+        ->setMessage($activity_message);
+    }
+
+  }
+
+}
diff --git a/src/applications/config/management/PhabricatorConfigManagementDoneWorkflow.php b/src/applications/config/management/PhabricatorConfigManagementDoneWorkflow.php
new file mode 100644
--- /dev/null
+++ b/src/applications/config/management/PhabricatorConfigManagementDoneWorkflow.php
@@ -0,0 +1,54 @@
+<?php
+
+final class PhabricatorConfigManagementDoneWorkflow
+  extends PhabricatorConfigManagementWorkflow {
+
+  protected function didConstruct() {
+    $this
+      ->setName('done')
+      ->setExamples('**done** __activity__')
+      ->setSynopsis(pht('Mark a manual upgrade activity as complete.'))
+      ->setArguments(
+        array(
+          array(
+            'name' => 'activities',
+            'wildcard' => true,
+          ),
+        ));
+  }
+
+  public function execute(PhutilArgumentParser $args) {
+    $activities = $args->getArg('activities');
+    if (!$activities) {
+      throw new PhutilArgumentUsageException(
+        pht('Specify an activity to mark as completed.'));
+    }
+
+    foreach ($activities as $type) {
+      $activity = id(new PhabricatorConfigManualActivity())->loadOneWhere(
+        'activityType = %s',
+        $type);
+      if (!$activity) {
+        throw new PhutilArgumentUsageException(
+          pht(
+            'Activity "%s" is not currently marked as required, so there '.
+            'is no need to complete it.',
+            $type));
+      } else {
+        $activity->delete();
+        echo tsprintf(
+          "%s\n",
+          pht(
+            'Marked activity "%s" as completed.',
+            $type));
+      }
+    }
+
+    echo tsprintf(
+      "%s\n",
+      pht('Done.'));
+
+    return 0;
+  }
+
+}
diff --git a/src/applications/config/storage/PhabricatorConfigManualActivity.php b/src/applications/config/storage/PhabricatorConfigManualActivity.php
new file mode 100644
--- /dev/null
+++ b/src/applications/config/storage/PhabricatorConfigManualActivity.php
@@ -0,0 +1,38 @@
+<?php
+
+final class PhabricatorConfigManualActivity
+  extends PhabricatorConfigEntryDAO {
+
+  protected $activityType;
+  protected $parameters = array();
+
+  const TYPE_REINDEX = 'reindex';
+
+  protected function getConfiguration() {
+    return array(
+      self::CONFIG_TIMESTAMPS => false,
+      self::CONFIG_SERIALIZATION => array(
+        'parameters' => self::SERIALIZATION_JSON,
+      ),
+      self::CONFIG_COLUMN_SCHEMA => array(
+        'activityType' => 'text64',
+      ),
+      self::CONFIG_KEY_SCHEMA => array(
+        'key_type' => array(
+          'columns' => array('activityType'),
+          'unique' => true,
+        ),
+      ),
+    ) + parent::getConfiguration();
+  }
+
+  public function setParameter($key, $value) {
+    $this->parameters[$key] = $value;
+    return $this;
+  }
+
+  public function getParameter($key, $default = null) {
+    return idx($this->parameters, $key, $default);
+  }
+
+}
diff --git a/src/infrastructure/storage/management/workflow/PhabricatorStorageManagementWorkflow.php b/src/infrastructure/storage/management/workflow/PhabricatorStorageManagementWorkflow.php
--- a/src/infrastructure/storage/management/workflow/PhabricatorStorageManagementWorkflow.php
+++ b/src/infrastructure/storage/management/workflow/PhabricatorStorageManagementWorkflow.php
@@ -929,6 +929,7 @@
     }
 
     $applied_map = array();
+    $state_map = array();
     foreach ($api_map as $ref_key => $api) {
       $applied = $api->getAppliedPatches();
 
@@ -946,6 +947,7 @@
       }
 
       $applied = array_fuse($applied);
+      $state_map[$ref_key] = $applied;
 
       if ($apply_only) {
         if (isset($applied[$apply_only])) {
@@ -1097,7 +1099,7 @@
 
           // If we're explicitly reapplying this patch, we don't need to
           // mark it as applied.
-          if (!isset($applied_map[$ref_key][$key])) {
+          if (!isset($state_map[$ref_key][$key])) {
             $api->markPatchApplied($key, ($t_end - $t_begin));
             $applied_map[$ref_key][$key] = true;
           }