doc: move modules into separate module directories

doc/configuration.rst

doc/index.rst

doc/man/knot.conf.5in

doc/modules.rst

doc/reference.rst

src/knot/modules/dnsproxy/dnsproxy.rst

src/knot/modules/dnstap/dnstap.rst

src/knot/modules/noudp/noudp.rst

src/knot/modules/onlinesign/onlinesign.rst

src/knot/modules/rosedb/rosedb.rst

src/knot/modules/rrl/rrl.rst

src/knot/modules/stats/stats.rst

src/knot/modules/synthrecord/synthrecord.rst

src/knot/modules/whoami/whoami.rst