The "doxygen -w html header.html footer.html style.cc options.dox" command is used to create default headers and footers that one can then edit and re-use once actual documentation is generated. If an options file (last argument) is given, my understanding is that this is taken into account when generating the first 3 files.

Since a recent change in doxygen, this no longer reliably works if the options file has entries of the form

HTML_HEADER            = header.html
HTML_FOOTER            = footer.html

If the header/footer.html files do not currently exist, then this leads to an error of the form

error: tag HTML_HEADER: header file `header.html' does not exist

This clearly makes no sense: whether or not the file currently exists, it will be overwritten anyway *because the whole point of the -w command is to create it*. Not requiring these files to exist also happened to be the old behavior of the command.