Refactor code to follow OOP principles

[dharple]

While it's not currently possible to switch to using classes, structs and associated functions can still be grouped together in a way that makes more sense. The current structure is organic, and hard to follow.

General:

• Move functions closer to their represented object (file, translation table, sequence, etc).
• Use typedefs.

Step 1:

• The filter needs to reference a cleaner by an enum instead of a class reference.
• The cleaners need to take options specific to their interface, not a generic, all encompassing "options" struct.

[dharple]

Before I can convert the structs to typedefs, I have to stop using chains to link sequences and filters.

[dharple]

All of the structs have been updated to use typedefs.

Open items:

• Rename the filter methods that load tables to something like table_load_from_filesystem and table_load_builtin.