Changed references to `--additional_file_patterns` to be `--additional-file-patterns` to make it consistent with other flags.

Adds tests for `.include_routes?`, `.include_models?`, `.skip_on_migration?`. Also moves the `TRUE_RE` under the `Annotate::Constants` namespace.

Prior to this change, `Annotate.include_models?` returned the inverse of `Annotate.include_routes?`. This made it so annotating models and routes was not possible to do together.

This PR adds an explicit `--models` flag and also adds it the option to `lib/generators/annotate/templates/auto_annotate_models.rake` with the default being set to `false`. 

Fixes #563 and undoes the bug introduced in #485.

In looking into #563, I realized there are gaps in test coverage. For example, `bin/annotate` doesn't have any tests. 

Tidying the spec directory to make it easier to add tests in future work.