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Also, added a test that a deprecated message will be output.
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* Require the application and environnement in the notes command in order to load the config files
* Adds tests for both register_directories and register_extensions added to a config file
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* It is called with `rails notes`
* It defaults to displaying [OPTIMIZE, FIXME and TODO] annotations
* It accepts custom annotations by using `rails notes -a CUSTOM_ANNOTATION OTHER_ANNOTATION`
* It defaults to look for annotations in [app config db lib test] as dictated by SourceAnnotationExtractor
* It supports ENV["SOURCE_ANNOTATION_DIRECTORIES"] but adds a deprecation warning and recommends using register_directories instead
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