Links from CLI point to missing anchors

I got a CLI error pointing me to https://apalache-mc.org/docs/apalache/running.html#supplying-jvm-arguments but this anchor doesn't exist, as it was changed into https://apalache-mc.org/docs/apalache/running.html#13-supplying-jvm-arguments (there's a section number now `#13-*`)

This is probably the same for all other links to anchors.