Hi,

Thanks for asking.  It's a difficult area.

    I'm not sure if such documentation would be considered a "manual" and if
    GNU FDL would be needed for it to be hosted on Savannah, or could it be
    licensed under GNU AGPL3 or later.

I'm not sure if there's an explicit policy about autogenerated
documentation.

    If FDL is needed, is there a GPL exception which could be used for the
    code with comments included into the documentation, or should I write
    a completely separated FDL-licensed manual instead?

To avoid doubling the documentation burden, and yet allowing sharing the
documentation with other FDL-using manuals (the goal for savannah), I
recommend dual-licensing under both FDLv1.3+ and AGPLv3+.

To do this, given that the doc sources are entwined with the source
code, the easiest way I know of is to make a separate statement in the
README (or some such) that the documentation parts of the sources are
licensed under the GFDL.  And the regular GFDL notice should be included
in the generated documentation.

Hope this helps,
Karl

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