It took a while to find how the clear all breakpoints feature (View>>Debug Windows>>Breakpoint[click to show], then right-click in the breakpoint window and select "Delete All"), mainly because I was not actively debugging, so my debug windows were naturally hidden.

There should be some more visible mechanism to clear and/or toggle all breakpoints-- debug menu? project context menu? A Photoshop layer view-style ALT-Click on an existing breakpoint could Toggle all other breakpoints on and off (not really clear them).