Cppcheck vs Doxygen

The custom implementation of the C++ parser has at least the deficiency not to support template template arguments. Furthermore its doesn't make much sense to maintain a custom parsing code which is extremely costly. Instead of this one should use a more elaborate existing AST parser which is maintained by a broader community.

Cppcheck is not competitive with other tools like clang static analyzer in order find bugs. E.g. a simple nullpointer access isn't detected by cppcheck if it is function or method return value, whereas clang easily finds such bugs.

As with any static analyzer it is impossible to get it perfect. Each project may produce errors even though the code behaves correctly. This result will vary different between code checks. All static analyzers are striving to achieve zero false positives.

Cppcheck purely checks for bugs in your code as opposed to other stylistic issues. If you wish to perform checks for that as well you will need to add another tool to your reservoir.

Cannot work properly with non-ascii paths on Windows

Doxygen PDF output relies on the now broken LaTeX tabu package which was abandoned over a decade ago by its developer.

For example, if you specify INCLUDE_PATH=incl, it doesn't search other folders included in the incl folder (incl/sub1 or incl/sub2) and there's no option to turn on recursive inclusion.