main.inc: Refactor debug and log print to automatically call $object->print_r(), Add calls to pgp_log_memory_use.

call.inc: implement #node_type_base (function call portion), update #theme_changes for parser changes.

call.inc: implement #absolute_includes, #preg_match, #file_scan_directory_nomask, #file_scan_directory_property_names, #file_scan_directory_array_itize, #drupal_valid_path, implement hook_upgrade_call_alter for db_... function calls and #absolute_includes

coder_upgrade.api.inc: Update API documentation for new alter hooks; coder_upgrade.main.inc: Add hook_upgrade_hook_alter, use old directory name in hook_upgrade_end_alter if files are being replaced.

coder_upgrade.module: Add setting to run against core modules; coder_upgrade.list.inc, coder_upgrade.main.inc, coder_upgrade.module, coder_upgrade.end.inc, coder_upgrade.install.inc, coder_upgrade.regex.inc: Refactor the API to be totally hook based using drupal_alter; coder_upgrade.call.inc, coder_upgrade.function.inc: Remove first parameter from search function calls.

coder_upgrade.install.inc: Add this file, implement #afile, #info_core_7; coder_upgrade.list.inc: Allow for array of files to be associated with a routine, add entries for install_file and info_file routines; coder_upgrade.db.inc: Add this file, start on #dbtng for non-select queries.

coder_upgrade.api.inc: Update API documentation for new alter hooks; other non-conversion files: Update copyright years.

coder_upgrade.list.inc, coder_upgrade.main.inc: Include files from new 'file' parameter; coder_upgrade.other.inc: Refactor function and function call routines to use drupal_alter; coder_upgrade.call.inc, coder_upgrade.function.inc, coder_upgrade.regex.inc: Add these files; coder_upgrade.call.inc: drupal_add_css, drupal_add_js, drupal_set_html_head, filter_formats: revised.

#688424 by chx: coder_upgrade.main.inc: Replace require_once statements with call to module_load_include (that includes DRUPAL_ROOT).

coder_upgrade.other.inc: Grammar Parser changes: T_RETURN statements changed from array to PGPExpression, body statements changed from PGPList to PGPBody.

Refactor: move functions from main to list, module to main; improve on setting module name; change debug echo to print; use second person tense in document comments.

Refactor upgrade routines for drupal_http_request, format_plural, module_invoke, t, taxonomy_get_tree and theme function calls.