cmdref: Move html only section inside cmd:def

Fixes missing links in body and `??` in tag/command index.
Update synth.rst to match.

docs/source/using_yosys/synthesis/synth.rst

@@ -42,7 +42,7 @@ The following commands are executed by the `prep` command:
 
 .. literalinclude:: /cmd/prep.rst
    :start-at: begin:
-   :end-before: .. raw:: latex
+   :end-before: .. only:: latex
    :dedent:
 
 :doc:`/getting_started/example_synth` covers most of these commands and what