1. The example Makefile.am code has "lib/" rather than "src/" in the path to the source code, even though it's clearly the package source that is to be analysed, not the gnulib library code.
2. In the generated report, all the filenames have the first character of the path missing ("rc/" rather than "src/" in my case). There seems to be some confusion about --aux-dir. gnulib --help says that its default value is "build-aux", and this is borne out by references to "build-aux" in the example pmccabe2html Makefile.am code, but I just checked by redoing my gnulib setup, and when I don't supply a --aux-dir argument, it is set to the current directory. On further investigation of gnulib-tool, this appears to be because it finds its value of auxdir from reading my configure.ac, which doesn't set a value, and hence defaults to the current directory. It is unclear to me whether this means that autoconf has a different default from gnulib for some reason, but it does suggest that the documentation for gnulib-tool should at least be revised to indicate that the default value for --aux-dir is found by studying configure.ac, with build-aux used as a fallback (if that is indeed the case; by this point I've rather lost the plot trying to understand gnulib-tool, and the gnulib documentation only mentions build-aux). If this is the case, then maybe the gnulib documentation should recommend using "build-aux" via AC_CONFIG_AUX_DIR, or even cause it to be set by gl_EARLY? It certainly seems a better idea to me to keep the auxiliary files out of the project root directory. -- http://rrt.sc3d.org