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For Impasse flags there are two modes - the default mode only stops them from claiming territory within its area of effect. The second mode (activated by left-clicking the flag) will prevent workers from passing, so use this to stop them from fortifying walls.

"Workers wont claim a shrine if there is sacred ground next to it."

Have you claimed the ground directly adjacent to the shrine?

Mine is showing as 100% for the main campaign - you're probably just missing a few. Most likely would be Shaboozey (hidden achievement for losing level 1) and Stay a While and Listen (lots of waiting around in your Home Realm).

Noticed some other weird stuff that happens when defeating Korvek on this level if you don't leave him for last. After destroying his Dungeon Cores, his workers don't die, his traps and doors remain intact and it isn't possible to claim the Cores.

To make an alternate version you can use the "import" function.

I can't say whether it's the exact same issue, but occasionally when loading any level in the map editor (not just MPD), it will sometimes drop one or two Impenetrable Rock blocks at seemingly random positions on the map.

No, I have the New Year Goodness achievement and it's still only showing the Crucible as 1/3 complete.

Same problem here. I've got 100% of the achievements in the game and it still only shows 1/3 complete for the Crucible.

Fair enough. A bit of a weird decision if it was intended though, as like I said the dwarves don't show up until later - there don't actually appear to be ANY Sappers, Wardens, Vanguards, Firebreathers or any other dwarven units on this level and they're not mentioned in dialogue/narration. Plus, sticking with the basic Empire theme would tie this level together better visually with the previous two thematically similar "destroy the Inhibitor" levels.