Added a new -intro option in the script to include external text/html file in the Introduction section

- Fixed issues with 'foreign keys' and 'unique'

when assigning names to transcript via existing gene name, store under a separate external_db to avoid having the same source on different levels

- Added several options to create a connection to a MySQL database
- Updated the HTML render & javascript + new content to display the examples and the SQL result tables

pass a new reference to files_to_parse array to make sure of any side effects when calling the run method

Introducing a proxy Feature class to allow custom limitation of the boundaries of the feature. This implementation influences the get_all_ methods while leaving the standard methods unaffected.