Add documentation after code refactoring and new library mode

[giovannipizzi]

As mentioned in #466, we should add documentation (possibly for different categories of users: users, developers ...) of all the changes happened in #466 and how one can adapt existing code (e.g. for open PRs) or develop new code.

• Documentations for users of the library
• Examples of use of the library in Fortran (and docs on how to use them)
• Examples of use of the library in C (and docs on how to use them)
• Examples of use of the library in Python (and docs on how to use them)
• Examples of use of the library in Julia (possibly adapted from the Python ones with the help of @qiaojunfeng)
• Improve documentation in the library interface source code
• Documentation for new developers (on the wiki)
• Short section on how to migrate from previous code to new code for those who have un-merged changes (on the wiki)