Encourage the practice of using the Drupal issue node id as patch array key.
Fixed bug where if no-backup option was present, files were never deleted from projects.
Per #801, comment out a Make test until a better host is found, or test gets a Mock.
Fix docblock for php-script command

It contained a @params section which seems to be a copy & paste mistake.
Merge pull request #810 from juampy72/php-script-wrong-docblock

Fix docblock for php-script command
Avoid OO warning.
Support DB prefix in sql sanitize
Remove the pre-outputformats old-fashioned 'format' option from config-list command.

Before this change, the help output was:

 --format                                  Define the output format.
 Known formats are: json, print_r, and export. Available: list, json,
 var_export, yaml. Default is list.

 Now it is:

  --format=<json>                           Select output format.
  Available: list, json, var_export, yaml. Default is list.
TRUE boolean.
Upgrade update_info to a first class engine.
Honour 'add-options-to-command' for engine type options.
Fix management of engine load failure.

Also improve docs and improve readability.
Enable engines to declare dependencies on drupal modules. Remove dependency on update.module in commands that use the update_info engine.
Remove leftover function that we stop using in 2010!.

Refer to commit 8d8433
Fix same OO error in another file.
Add --xh option for xhprof profiling

In order to use this, you have to have the xhprof php extension enabled and have configured two other options: xh-path and xh-link
Add caching to drush_get_commands()

We were calling drush_get_commands() in topic_drush_help_alter() and thats expensive. Noticed  during site-alias command (for example) which needs to call topic_drush_help_alter() once for each loaded alias.
Fix reference in topic_drush_help_alter() param
Fix typo in core-rsync examples
Fix #801. Reenable testMakeSubtree with new url.