Move routines to new or more appropriate files; revise @file comments; correct typos; delete blank line at top of each file.

Rename files; correct typos; modify help text; update copyright; move coder_upgrade_path(); eliminate include.

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.api.php: update documentation to reflect the node being returned by getFunctionCalls(); coder_upgrade.db.inc: improve sql parsing and conversion to DBTNG syntax.

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

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.