I want all the stuff - tools, projects, documents - pertaining to a single project to be close together: in the same directory or neighboring directories. But I do not want to duplicate stuff. When things are shared among projects, I move the two projects together and create a shared file. I call this object-oriented filing system and it is not at all easy.
The filing by project allows me to find quickly everything pertaining to a project, to combine various projects into larger ones, and to collaborate with others on specific projects without burdening them with unnecessary software.
I have a collection of directories that contain my various research projects in from of a reproducible document. A nice portfolio. The object-oriented filing allows me to combine projects into books (possibly with overlapping chapters).