Feature: Reworked I/O Transmute model

[jrihon]

👎 Problem definition

The current approach lets ducque read in a file and the cli parsing is far too manual. It doesn't have to be like this.

✅ Proposed Solution

A streamlined and layered (input layer, output layer) approach between the application and the internal functioning.

1. Also, rename the transmute model to something else (like library, to-library, lib-addition, vault, )

These new building blocks are then available for the ducque build command, where you pass the new key.

1. Allow people to store it in a separate directory, or copy it in a separate directory as well. A git pull update should not mean that it deletes all their work
2. The sugar-modified components should always come with a natural base complement. Standard defaults are A, C, G, T, U. This so we can make assumptions on more standard builds.

🛠️ Definition of Done

For this feature to be finished, I expect it to work like ...

• Reworked input
• Reworked output