Review simulation presets

[mca-sh]

Fixes #104

• Transition rate matrix having non-null diagonal terms and imported from preset files were yielding incorrect state lifetimes used in the generation of state sequences. It is now handles correctly by setting all diagonal term of the matrix to 0 before using it.
• the field nametrans_prob used in preset files was misleading as it intuitively refers to transition probability matrix, what they are not, instead of transition partition probabilities, which they are. It is now replaced by field trans_part.
• State lifetimes could not be imported in preset files. They can now be imported together with the partition probability matrix using the field lifetimes in preset files.