head back to town after you talk to her and go to the smith, talk to Emily to continue the story.
For future reference, here's a full walkthrough for this update:
Head to the Amazon Village.
Talk to the Matriarch.
Head to the Blacksmith and talk to Emily.
Head to the pub and talk to Claire in the restroom.
In the dungeon pickup the key on the top-right locker in the room with the raft jumping puzzle.
Go through the door in the second room of the dungeon.
Fight the boss and read the papers on the floor for the locker room code, take the key going back.
Switch to night.
Talk to the guard in the pub.
Head to the Café. (I recommend doing the weapon side-quest here)
Talk to the former mayor behind the counter.
Head to the arena (go upstairs, then into the water and jump from the middle tile behind the main square). If the jump indicator isn't showing up, press S or click on the book to refresh it. You can jump without the indicator showing btw.
Head to the left locker room and talk to the princess.
Go to the main desk and talk to the lady in the middle.
Head to the right locker room and talk to the lady.
Beat the boss.
Head to the mountain (update end).
Side-quests:
Weapons quest:
Talk to Claire in the Café.
Go back to the waterways.
North (from the pub): head to the boss room (pick item), the jumping raft room (pick item).
Read the papers in the boss room and open the first locker with the code.
South (from the manhole in town - teacher's home): use key to return to the old water reservatory room and (pick item).
Go back to Claire and give the items.
Go to the blacksmith and talk to Ramdo. Get the materials and make the new Equipment upgrade.
Raphy's scene:
Just go to her shack at night and meet the Apprentice Stats required for the scene to play out.
Veronica's quest:
Talk to Veronica in school (day)
Unlock Hunt 1 in the Amazon Village downstairs room that take you to the mountain part previously inaccessible. Talk to O'ra.
Go to the mountain, head for the room before the mountain boss room (room L iirc).
Shake the red tree and fight the mini-boss.
Go back and talk to Veronica.
Go to the pub (night) and talk to Veronica there - Eric Scene.
After that go to your desk at night to unlock the option.
Mariah's scene:
Keep doing the shower peep scene until you've done it 6 times. (If you got every chapter bonus and dialogue, you should need 2 more).
The MC will fall into the room.
Mariah needs Intimacy 2 and 10+ in Trust/Passion/Lust for the scene to continue.