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If single sourcing is your goal, for whatever reason, be it staffing, cost,
ease of updating, etc., then FrameMaker plus WebWorks Publisher handles the
task quite nicely. No tweaking at all is needed after you set up WWP
correctly to meet your needs. None.
However, the document you are writing is a single-source document. That is,
the document is not written only for print or only for online help. The
single-source document is a different style than either a print-only or an
online only document. You might call a single-source document a compromise
between online and in-print styles, you might call a single-source document
an evolution of both in-print and online docs. Nonetheless, a single-source
doc is optimized as a single source doc; it is not optimized for in-print or
online alone. What this means is, yes, you can maintain two separate docs,
one for online and one for in-print, and choose to bemoan the fact that
WWP+FrameMaker has not met your desire to single source. I submit, however,
that the software is not restricting you; in fact, you are limiting
FrameMaker + WebWorks publisher can be effectively used for single-sourcing,
if single-sourcing is what you PLAN to do.