it to minor

various files: replace calls to pgp_log_memory_use() with coder_upgrade_memory_print(); coder_upgrade.module: #982380: correct coder_upgrade_parameters_save() to use module directory instead of files directory, enhance coder_upgrade_conversions_apply() to capture errors and return code; coder_upgrade.main.inc: refactor print routines to use coder_upgrade_path_print(); coder_upgrade.run.php: enhance documentation; coder_upgrade.test: refactor getInfo() routines; tests/samples directory: update the input and expected test file: example.module.

#976940: eliminate php warnings related to files not present: core.coder_review_ignores.txt and info file.

coder_upgrade.main.inc: #245471 (comment #7): remove base directory path from patch file in coder_upgrade_make_patch_file(); inc, install, help.inc, main.inc, module, test: refactor file_directory_path() references to coder_upgrade_directory_path(); coder_upgrade.run.php: add php memory and time limits.

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.db.inc: enhance error handling by checking for conditions not being found in a select query; coder_upgrade.call.inc, coder_upgrade.function.inc: enhance #theme_changes to check number of parameters to theme_xxx() and hook_theme entry; coder_upgrade.function.inc: enhance #theme_changes when setting theme key to 'render element' also change value from an associative array to a string.

coder_upgrade.install: hook_uninstall(): delete recently added settings variables, hook_requirements(): use get_t().

coder_upgrade.function.inc: refactor #hook_permission to hook_upgrade_hook_perm_alter(), refactor #descriptions_permissions to use the convert_return() pattern (use cases 1 and 2), refactor doc_comment checking in coder_upgrade_convert_update_N() to revert to that in hook_upgrade_hook_alter(); tests/samples directory: update the input and expected test file: example.module.

coder_upgrade.inc: define file_directory_path() in response to its removal from core; coder_upgrade.db.inc, coder_upgrade.function.inc: coding style fixes.

coder_upgrade.function.inc: enhance #hook_filter_info (including a missed parser API change that broke the entire routine), #install-schema, #hook-user-changes, #hook_load_signature, and #theme_changes.

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.