Stone Tool

If you want to remove Atlan Stones from your weapon or your Shadowhunter Armor, you'll need a Stone Tool.  To pick this item up, you'll need to head to the Artifex Vault, just northwest of the northern Dires land bridge.  This used to be an easy trip, but with the remapped spawns, you can encounter anything from Tumerok Overlords to Grievvers of various shapes and sizes during the brief run.  The fastest way is to head to Glendon Woods, run due south to the North Dires portal (21.N, 53.8E, 12+ restricted).  This drops you within a short run of the vault (26.5N, 45.8W, no restrictions).  The foyer is safe, so you can hit the portal directly.  Alternately, you can run to 24.5N 8.1E.

The dungeon itself is filled entirely with tumeroks, including Warriors, Officers, Gladiators, High Priests, and High Tumeroks.  Since tumeroks are equally resistant to all elements, pick your most potent weapon for this fight. Tumeroks are also potent mages for their level, so you'll want to use as many protects as you can cast or wear.  You'll enter the dungeon at the top of a large ramp.  There's plenty of space to buff here.

When you're ready, head down the ramp and you'll encounter several warriors surrounding a pit, which has a few officers at the bottom.  Clear the warriors then head down into the pit.  Head to your right and you'll see a hallway.  Take this down until you come to a T intersection.  The majority of your party should head to the right, through a gallery of officers and a high priest.  Strafe as you run to avoid spells and arrows.  You will come to a door, which you can open.  Get inside, safe from the tummies, and then press the lever inside.  This will open a door back at the T intersection.  The remaining person will then need to go through the door and pull another lever.  This lever opens a door back past the gallery.  The whole group now needs to head through.  You'll want to head straight until you come to a room with a sofa overlooking a large room with barrels in the middle of it.

Here comes the tricky jumping.  You first need to jump from the sofa to the barrel across from you.  This requires a mid-power jump, but varies depending on your jump skill.  If you fall, there is a corridor to the right of the sofa room.  Follow it back to the sofa room to try again.  Once you make the jump, you'll need to head right from barrel to barrel.  This can be done either by using tap jumps or by shift jumps, depending on your style.  Be aware that the jump to the last barrel is bigger than the others, so a tap jump will probably not work successfully.  A full powered shift jump is your best bet here.  If you fall on this jump, you will not be able to take the corridor back to the sofa room and will have to take the exit portal in the pit you landed in.  Hopefully, you were fast enough so the dungeon is still clear and you can run back and try again.  After you cross the barrels, you will come to a very deep pit.

There are small platforms along the walls going down.  Unless you have good life protects and jumping skill, you will want to avoid falling the whole way down.  Do not try to jump to platforms diagonally across from you.  These are very hard to hit.  It is far easier to jump directly across to platforms on the other side of the wall.  This will require 3 jumps, preferably tap jumps to minimize damage.  Once you land at the bottom, you will need to press a button to open the door in front of you.  Do this quickly, as there will be several High Tumeroks raining war magic down on you.  

From this point on, you will be fighting Gladiators exclusively.  As you proceed, you will come across a door you cannot open on your right-hand side.  Leave one party member here.  The next hallway on the right will curve and lead to a door which you can open.  If your party has lockpick, you can opt to go straight instead of taking this right turn.  Have one member of your party open the door and run into another gallery room.  There will be many Gladiators shooting arrows at you from above.  There is also a lever for you to pull here.  This triggers the door where you left a member behind to open.  Inside that room, there is another lever which opens the final door in the Gallery room.  Have your party run into the last room, where you will find the tool and a bit of lore.  

Congrats, you can now change stones.  Be aware that it is possible to break both the tool and your stones, so try not to use either too much.  The timer on the tool is 1 day and you may have more than one tool if you desire.