Refactor entities and update interfaces

[clane9]

• type optional entities in BIDSEntities as Optional[...]
• Integrate unsupported/extension entities as an extra_entities dict field
• add from_path(), to_path(), to_dict(), with_update() methods to BIDSEntities
• support "no value" entities in path generation.
• update README
• update example
• use a column multi index in output table
• Refactor main command-line and python interfaces