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.

Add documentation examples of using grammar parser API functions; Rename PGPFunctionCall2 to PGPFunctionCall; Upgrade module_invoke with respect to taxonomy_get_tree.