The patch file is probably the best solution for those with many Mods or other changes who do not want to re-add them back to all the changed files. To use this you will need command line access to a standard UNIX type patch application.
A number of patch files are provided to allow you to upgrade from previous stable releases. Select the correct patch, e.g. if your current version is 2.0.11 you need the phpBB-2.0.11_to_2.0.13.patch. Place the correct patch in the parent directory containing the phpBB 2 core files (i.e. index.php, viewforum.php, etc.). With this done you should run the following command: patch -cl -d [PHPBB DIRECTORY] -p1 < [PATCH NAME] (where PHPBB DIRECTORY is the directory name your phpBB Installation resides in, for example phpBB2, and where PATCH NAME is the relevant filename of the selected patch file). This should complete quickly, hopefully without any HUNK FAILED comments.