🚀 go-pugleaf

Here's what I use.
I use one directory per manual, with each directory at the same level.
Each book file (one book file per manual) is in its own directory, with its component files. Every book file has the same name (man.book) to make it easier to apply styles - most manuals use the same stylesheet, and the books are differentiated at the system level by the directory names.
All resultant PDF files also have the same name - man.pdf - one PDF file per manual - one PDF file per directory - and are differentiated at the system level by the directory name (again). All links between my manuals therefore have the same relative structure - go up one level, look for the directory name, then look for the file in that directory. This approach has always worked well on my collection of 30 manuals. It also makes it easy to add third-party PDF manuals to the collection - just add another directory with the PDF file in it and set up a link.

There's one other thing which I always mention because in my experience it is usually the culprit whenever documents go offsite and come back with broken links - NEVER use Save As to move a file. And tell your offsite authors to never use Save as.
And then make a big sign to this effect and beat them over the head with it.
The Save As facility will stretch any references (xrefs, graphics), so that they still work from their new non-standard document location. The author who stretched the links won't see any sign that they've done anything wrong because the document will still "look" okay, even though the links now won't work when the document gets back into its old standard location.
It gets worse. Much worse. If you save as to a different disk (or otherwise stretch a link through the root directory) then voila - all pathnames in the links are automatically converted from relative to absolute, and you've just destroyed all document portability between systems.