diff --git a/lib/db/upgrade.php b/lib/db/upgrade.php
index 7e6ca5c4af0..912c64521ed 100644
--- a/lib/db/upgrade.php
+++ b/lib/db/upgrade.php
@@ -4916,5 +4916,23 @@ function xmldb_main_upgrade($oldversion) {
         upgrade_main_savepoint(true, 2016020201.00);
     }
 
+    if ($oldversion < 2016021500.00) {
+        $root = $CFG->tempdir . '/download';
+        if (is_dir($root)) {
+            // Fetch each repository type - include all repos, not just enabled.
+            $repositories = $DB->get_records('repository', array(), '', 'type');
+
+            foreach ($repositories as $id => $repository) {
+                $directory = $root . '/repository_' . $repository->type;
+                if (is_dir($directory)) {
+                    fulldelete($directory);
+                }
+            }
+        }
+
+        // Main savepoint reached.
+        upgrade_main_savepoint(true, 2016021500.00);
+    }
+
     return true;
 }
diff --git a/repository/lib.php b/repository/lib.php
index b8c3d20ecc2..1e9bb67053c 100644
--- a/repository/lib.php
+++ b/repository/lib.php
@@ -1663,18 +1663,16 @@ abstract class repository implements cacheable_object {
     }
 
     /**
-     * Decide where to save the file, can be overwriten by subclass
+     * Get a unique file path in which to save the file.
+     *
+     * The filename returned will be removed at the end of the request and
+     * should not be relied upon to exist in subsequent requests.
      *
      * @param string $filename file name
      * @return file path
      */
     public function prepare_file($filename) {
-        global $CFG;
-        $dir = make_temp_directory('download/'.get_class($this).'/');
-        while (empty($filename) || file_exists($dir.$filename)) {
-            $filename = uniqid('', true).'_'.time().'.tmp';
-        }
-        return $dir.$filename;
+        return sprintf('%s/%s', make_request_directory(), $filename);
     }
 
     /**
diff --git a/repository/upgrade.txt b/repository/upgrade.txt
index e47ba3be344..d724dd70295 100644
--- a/repository/upgrade.txt
+++ b/repository/upgrade.txt
@@ -3,6 +3,12 @@ information provided here is intended especially for developers. Full
 details of the repository API are available on Moodle docs:
 http://docs.moodle.org/dev/Repository_API
 
+=== 3.1 ===
+
+* The prepare_file() function will now return a file in a per-request directory which will
+  be automatically cleaned at the end of the request.
+  No modifications should be required as a result of this change.
+
 === 2.8 ===
 
 * Repositories working with Moodle files must replace serialize() with json_encode() in the
diff --git a/version.php b/version.php
index 6b769f9afd2..231fd2404cc 100644
--- a/version.php
+++ b/version.php
@@ -29,7 +29,7 @@
 
 defined('MOODLE_INTERNAL') || die();
 
-$version  = 2016021100.00;              // YYYYMMDD      = weekly release date of this DEV branch.
+$version  = 2016021500.00;              // YYYYMMDD      = weekly release date of this DEV branch.
                                         //         RR    = release increments - 00 in DEV branches.
                                         //           .XX = incremental changes.