coder_upgrade.main.inc: #245471 (comment #7): remove base directory path from...

coder_upgrade.main.inc: #245471 (comment #7): remove base directory path from patch file in coder_upgrade_make_patch_file(); inc, install, help.inc, main.inc, module, test: refactor file_directory_path() references to coder_upgrade_directory_path(); coder_upgrade.run.php: add php memory and time limits.