A fundamental problem when writing a book and stand-alone chapters arises with cross-referencing. In a book file it makes sense to refer to an equation in any chapter, say (4.23), while in a stand-alone chapter references to equations or sections in other stand-alone documents will not work. That is, LaTeX has a native mechanism for this, the xr package, where one can register a set of .aux files for other LaTeX documents and refer directly to these labels and get them right. It is then possible to write something like
see (\eqref{sec:results:u:eq}) in \cite{Hansen_2011b}
and get it out as
see (2.37) in [12]
provided our .tex file contains \externaldocument{myother} and the label sec:results:u:eq is defined in myother.aux. DocOnce has generalized this feature so it works for non-LaTeX formats as well. It is called generalized cross-references. You can then write such references across chapters and get all labels right whether you produce the entire book or individual chapters.
Here is an example on a generalized reference to an equation in another chapter:
The world's most famous equation is ref[(ref{fake:Emc2})][in
cite{Langtangen_dobook_fake}][
as found in the document "Some document":
"http://hplgit.gthub.io/setup4book-doconce/doc/pub/fake"
cite{Langtangen_dobook_fake}].
This sentence is rendered as follows in the present format (sphinx):
The world’s most famous equation is as found in the document Some document [Ref4].
More detailed information about generalized cross-references is found in the DocOnce manual. In particular, one has to insert # Externaldocuments: commands in all main_*.do.txt files that includes files with generalized references.