fix files in console-and-shells folder

- completion-shell : theme => template
- i18n-shell : app => src
- upgrade-shell : for cakephp 2, so use old notations for app (no src)
Explaing the use of upgrade tool for 1.3 to 2.0 in 3.0 docs doesn't make sense. The page should only have 2.x to 3.0 upgrading info using https://github.com/cakephp/upgrade which is a standalone tool.