Add Toml and Json support and more

[flaviojs]

Now IR files and transform files can be Yaml, Toml, or Json.
Yaml is still the default to preserve old behavior.

Basic command tests were added (contains 2 FIXMEs).

Clap arguments were changed:

• new optional format arguments
• easier to understand value names
• require at least one file in commands fmt and check

Closes #96