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I've gone ahead and used GNU stow to organise the web site files.
I put a readme on the SF server, which is copied below.
If you need to add static files to the web site then add them to
htdocs_parts/staticweb instead of directly in htdocs. If you create
generated files then create a new directory under htdocs_parts.
Peter
About htdocs & htdocs_parts
---------------------------
The idea is to separate generated content from static content so that,
for example, a stray rsync command with --del enabled doesn't end up
deleting static content by accident.
The htdocs directory contains only symlinks to the real files which
are in htdocs_parts. Each directory in htdocs_parts is a "component" of
the total web site. Currently they are separated as:
staticweb - all the static files on the web site
generatedweb - web site as generated by allegrowww2
a4docs - Allegro 4.2/4.3/4.4 generated docs
a5docs - Allegro 4.9 generated docs
compilefarm - some old compile farm logs
logs - old changelog extracts
mpy-svn-stats - mailing list stats [old?]
Everything inside those directories is combined into htdocs by symlinks
created using GNU Stow.
[snip]