fix typos, named correct arguments of function calls, etc.

With the new structure, /ref bibliography doesn't work any more
on the mainpage. However, this solution only circumvents the problem.

added dois/urls so that doxygen can generate hyperlinks to the publications

[cleanup] Harmonize logical operators

See merge request !346

Replace and by &&, not by !, or by ||

Feature/allow adl for std mathfunctions

Closes #328

See merge request !364

[bin/postprocessing] Add script to calculate l2error

See merge request !322