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Fix sphinx-build out-of-srcdir-build

Ondřej Surý requested to merge fix-out-of-srcdir-sphinx-build into master

This patch mostly replaces relative paths with $(srcdir) and $(builddir) as appropriate in doc/Makefile.am since that breaks when you do out-of-srcdir build:

    autoreconf -fi
    mkdir _build
    cd _build
    ../configure
    make distcheck

Also dropped conf_autoconf in favour of -D variable=@value@ in Makefile.am (that's less prone to break).

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