So I have just killed the Shaper of Flesh and done the Dockyards quest, is that the end of this expansion?
Malmouth Resistance has one more faction quest after the Blackiron Docks at Honoured (just like the other factions do) but otherwise yes, killing the Shaper of Flesh is the end of the main expansion storyline.
There is also the kraken you can fight as well as the beast rogue like.
The expansion ends there but you can farm up the new nemesis stuff x)