I'm using this flat structure to keep the same hierarchy as we have in
our Eclipse development environment, so I'd prefer to keep it if
possible.

I think I have found the solution though after your comments prompted
(yet another) re-read of the multiproject documentation.

My project.properties in the buildRoot dir also contains an entry for
the docs directory:

maven.docs.dest=F:/path/to/docs

The multiproject documentation says:
"At the completion of the multiproject:site goal, each project's
generated site is copied into the appropriate directory. e.g. if
WebProject1 and JarProject2 are the names of projects processed via
multiproject:site, the project that is executing multiproject:site will
have the generated sites from WebProject1/target/docs and
JarProject2/target/docs copied into target/docs/multiproject/WebProject1
and target/docs/multiproject/JarProject2 respectively. "

As the project.properties for my projectA and projectB did not
explicitly define their own maven.docs.dest I think they were using the
buildRoot's maven.docs.dest path, and because of this I was getting them
copied within each other.

Explicitly setting a unique maven.docs.dest in the project.properties of
each sub-project appears to have fixed this!

Thanks for helping with my question.

Cheers,

Rob. 




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