The suggestion in the thread to "support defining this in package.json" (https://github.com/nodejs/tooling/issues/79#issuecomment-664...) reminded me of autoconf. It also has the issue of lots of auxiliary files in the project root (but worse since they're not hidden files), and the solution there is that you can add "AC_CONFIG_AUX_DIR(aux)" to the configure.ac to make it look for these auxiliary files in the "aux" subdirectory instead of the project root (for instance, "aux/config.guess" instead of "config.guess").