the public API documentation.
The checks should be self-evident from the source code of the script
-(they are also described in docs/dev-manual/gmxtree.md).
+(they are also described in docs/dev-manual/gmxtree.rst).
All the logic of parsing the Doxygen XML output and creating a GROMACS-specific
representation of the source tree is separated into separate Python modules
(doxygenxml.py and gmxtree.py, respectively). Similarly, logic for handling