  Free Electron Lasers (FELs) are a solution for providing intense, coherent
and bright radiation in the hard X-ray regime. Due to the low wall-plug
efficiency of FEL facilities, it is crucial and additionally very useful to
develop complete and accurate simulation tools for better optimizing a FEL
interaction. The highly sophisticated dynamics involved in a FEL process was
the main obstacle hindering the development of general simulation tools for
this problem. The software MITHRA tackles this problem by offering a platform
for full-wave simulation of FEL process. The full-wave solver employs a
numerical algorithm based on finite difference time domain/Particle in cell
(FDTD/PIC) in a Lorentz boosted coordinate system. The developed software
offers a suitable tool for the analysis of FEL interactions without considering
any of the usual approximations. This contribution is the complete manual for
the second version of this software, namely MITHRA 2.0, which is released after
extensive efforts on optimizing the software performance and removal of several
bugs in the code.
