Index: connection.php
===================================================================
--- connection.php	(revision 1450)
+++ connection.php	(working copy)
@@ -104,10 +104,8 @@
 		}
 
 		// Merge the queries into allqueries; pragmas MUST go first
-		$allqueries = array_merge($pqueries, $indexqueries, $iqueries);
+		$allqueries = array_merge($pqueries, $iqueries);
 
-
-
 		$tables= $this->get_column( "SELECT name FROM sqlite_master WHERE type = 'table';" );
 
 		foreach ( $cqueries as $tablename => $query ) {
@@ -126,6 +124,8 @@
 				$allqueries[]= $query;
 			}
 		}
+		
+		$allqueries = array_merge($allqueries, $indexqueries);
 
 		if ( $execute ) {
 			foreach ( $allqueries as $query ) {
Index: schema.sql
===================================================================
--- schema.sql	(revision 1450)
+++ schema.sql	(working copy)
@@ -144,14 +144,14 @@
   id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   name VARCHAR(255) NOT NULL
 );
-CREATE UNIQUE INDEX name ON {$prefix}groups(name);
+CREATE UNIQUE INDEX group_name ON {$prefix}groups(name);
 
 CREATE TABLE {$prefix}permissions (
   id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   name VARCHAR(255) NOT NULL,
   description VARCHAR(255)
 );
-CREATE UNIQUE INDEX name ON {$prefix}permissions(name);
+CREATE UNIQUE INDEX permissions_name ON {$prefix}permissions(name);
 
 CREATE TABLE {$prefix}users_groups (
   id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,