Above: The green boxes represent Clue Bottles. The black box represents the Safe.
Just south of the hideout, you'll find your first Clue Bottle atop a light pole.
Head to the hideout roof and walk the rope that heads southwest. You'll find a Clue Bottle at the end.
Return to the hideout roof and head north to spot another bottle.
Cross the rope at the northern end of the roof for another.
Look east from the end of the rope to spot a springy pole where another Clue Bottle awaits.
Drop to the ground and follow the street as it heads north. You'll spot a bottle bobbing on a springy branch.
South of the branch, some poles jut out of the water. A Clue Bottle bobs above one.
Head into the nearby tunnel and make a left at the fork. Another bottle awaits on a pole in the water.
Near Clue Bottle #7 is a series of bamboo shoots and rocks you can use to reach a high ledge. Do so and cross the rope up here to find another bottle.
Follow the ledge to find another hovering on a springy branch.
South of the branch, another Clue Bottle bobs on a rooftop spire.
Drop to ground level and head northwest. A Clue Bottle sits on a pole in the stream here.
Follow the street south the geisha house. Another bottle rests on the fountain in front of the bright building.
Another Clue Bottle hides behind the geisha house.
East of the geisha house is a springy branch that extends toward a bridge. A Clue Bottle bobs on it.
Cross that bridge and hop onto the roof to the north. A Clue Bottle floats above an awning up here.
Cross the rope at the northwest end of the roof to find another bottle.
To the northeast is a bridge lined by ropes. Hop onto the southernmost rope to find another Clue Bottle.