root directory looks like an absolute mess

20 directories
Just the number is a lot to browse.
Most of them containing a single config file, a few just are empty (with a nice .gitignore file).
Just pack all the config files into a single etc folder.

Duplicate directory name (I mean, bin and js/bin, and scripts ... manual test and testsuite)
src/site ??? src is usually where i would expect sources ...

Marmotinni, mustella ???

In my opinion, this is repulsive to any contributor.
It doesn't look like an open source project, more like a student pet project.

Start by inventorying the root directories and the specific pairs and locations mentioned: bin, js/bin, scripts, manual test, testsuite, src/site, Marmotinni, and mustella. Determine which directories contain configuration files, which are empty, and whether moving or renaming them would preserve the project's existing layout and tests; done requires an agreed, consistent root structure.

Written by the indexing model from the issue text.