System level documentation (!13)

# Description

Describes broadly the structure of dragoonfly as well as the utilities we made (such as the CLI).

# Detailed list of changes

Explains:
- Global structure
- What happens inside a node when a command is issued
- Quickly explains interaction with other nodes
- The API / http interface
- The CLI

## Related issues

This MR will:
- close #8 
- close #9 
- close #12