Manipulation in cluttered environments like homes requires stable grasps, precise placement and robustness against external contact. We present the Soft-bubble gripper system with a highly compliant gripping surface and dense-geometry visuotactile sensing, capable of multiple kinds of tactile perception. We first present various mechanical design advances and a fabrication technique to deposit custom patterns to the internal surface of the sensor that enable tracking of shearinduced displacement of the manipuland. The depth maps output by the internal imaging sensor are used in an in-hand proximity pose estimation framework -the method better captures distances to corners or edges on the manipuland geometry. We also extend our previous work on tactile classification and integrate the system within a robust manipulation pipeline for cluttered home environments. The capabilities of the proposed system are demonstrated through robust execution multiple real-world manipulation tasks. A video of the system in action can be found here.