The documentation found here is generic and valid for all Crazyflie/Crazyradio versions. If you are looking for details on a specific product then have a look at the projects page for links.
For piloting and using the Crazyflie there's a number of clients available.
Aside from stand-alone clients there's also sets of applications and scripts that works together for using the Crazyflie.
For getting started with development and setting up the environment have a look at the following topics:
The architecture part of the documentation details things that are not User guide or API. It's information that's useful to have to understand how the system and it's parts fit together.
Some parts of the design span multiple firmwares and doesn't below to any one part of the system. Here's a more generic overview of these designs and below there's more detailed information about the specific parts that build them up.
For communicating with the Crazyflie there's a number of APIs available, here's a list:
* PWM to thrust: Thrust and RPM measurements.