coder_upgrade.begin.inc: New file to handle module preprocessing;...

coder_upgrade.begin.inc: New file to handle module preprocessing; coder_upgrade.function.inc: Restore hook_install_alter, implement new coder_upgrade_convert_return and use with #theme_alter; coder_upgrade.module: Enhance coder_upgrade_module_list to use with theme registry caching; coder_upgrade.install.inc: #728252: Array error when checking for @file in install files; coder_upgrade.api.php: Update documentation.