The current HTML doc (UsersGuideHTML, ReferenceManualHTML, ThornDocHTML and ArrangementDocHTML) generating code contains a call to the script
ConvertFigures which blindly converts all pdf found in the doc directory to eps files with the same basename creating a mess as well as potentially overwriting exiting files with the same name. Similarly htlatex will convert those eps files to png files again potentially creating a mess and overwriting existing files.
Finally, at least, UsersGuideHTML and ReferenceManualHTML run htlatex in the source code repository’s doc directory creating all of LaTeX’ and htlatex’ temporary files in there.
None of these files are removed by a
make foo-clean or even
make foo-realclean creating issues when trying for a “clean” documentation build.