Delete Doxygen blocks duplicated in both .h and .cpp files.
Fix incorrect argument names in \param blocks. Fix filenames
in \file blocks. Fix broken Doxygen syntax (broken numerated
lists containing more than 9 items, invalid HTML tags, broken
links in \ref and malformed math equations). Wrap code blocks
inside \code ... \endcode.

- More flexibility for the user to implement custom checkpointing