coder_upgrade.inc, coder_upgrade.install, coder_upgrade.module, coder_upgrade.main.inc: refactor code to allow execution from a separate process outside of Drupal; coder_upgrade.begin.inc: cache the core theme information in the persistent cache (includes disabled modules).

coder_upgrade.module: improve the menu integration when only Coder Upgrade is enabled, only allow the base files directory to be renamed, enable the submit handler for the settings form; coder_upgrade.main.inc: refactor the coder_upgrade_xxx_path() routines to reflect the coder_upgrade_dir variable.

coder_upgrade.call.inc:#878470: enhance #drupal_set_header_renamed to handle no parameters; coder_upgrade.function.inc: enhance #hook_load_signature to clean the parameter variable; coder_upgrade.list.inc: add routine entry for grammar parser; coder_upgrade.main.inc, coder_upgrade.module: implement settings for preserving array format and debug output by coder upgrade and grammar parser.

coder_upgrade.db.inc: improve sql parsing and conversion to DBTNG syntax; coder_upgrade.begin.inc: refactor call to coder_upgrade_convert_return() and associated callback; coder_upgrade.function.inc: enhance coder_upgrade_convert_op() to use new getParameterVariable() API function, refactor the convert return pattern of routines: coder_upgrade_convert_return(), coder_upgrade_convert_return_loop(), and coder_upgrade_callback_return_caseN(); tests/samples directory: update the input and expected test file: example.module.

coder_upgrade.call.inc, coder_upgrade.main.inc: revise code to reflect change to PGPReader::getFunctionCalls() which now returns a list of nodes; coder_upgrade.call.inc: enhance #comment_node_url, #taxonomy_form_all, and #update_sql to utilize the node now returned by getFunctionCalls().

coder_upgrade.call.inc: #taxonomy_form_all; coder_upgrade.function.inc: #node_form, #drupal_render_children; coder_upgrade.regex.inc: #block_tables_renamed, #fapi_changes.

coder_upgrade.main.inc: enhance cdp() to allow for a description; coder_upgrade.regex.inc: implement #taxonomy_tables; tests/samples directory: update the input and expected test file: example.module.

coder_upgrade.module: enable customization of the module conversion form steps (build, validate and submit); coder_upgrade.main.inc: include function reference in patch file (diff -up)

coder_upgrade.call.inc: Restore missed calls to PGPArray::findValue(); coder_upgrade.test: Refactor setup method to run the theme caching before starting the test method.

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.

coder_upgrade.info, coder_upgrade.main.inc: Reflect the renamed grammar parser module; coder_upgrade.install, coder_upgrade.module: Minor cleanup; coder_upgrade.test, tests directory: Add these files.

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

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.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).

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.

Changes due to revised core api or standards: third person tense in hook_x comments, manually include files again; Change settings menu path; Disable upgrade functionality until grammar parser refactoring is complete.

Separate middle conversion routines into two groups (regex and parser) to utilize the PGP API.
Add handler specification (regex or parser) for the middle changes applied at the file level.
Revise API documentation.

Create log file and patch files; Add links to log file and patch files in user interface; Revise help text; Revise api.php file.