I'm running Sublime Text 3 (build 3083).
After adding the Python Breakpoints package I found that if you set a breakpoint (using the combination Ctrl+Shift+b) and you then remove the created line (where the BP is) by deleting it instead of toggling it (using the combination Ctrl+Shift+b again), an icon is left in the gutter. See:
I've tried setting the package option gutter_icon": ""
(ie: no icon), disabling the package, and even removing the package altogether. After restarting Sublime, the left over icons are still there.
I've asked the creator of the package who told me this is an issue with ST, not with the package itself.
How can I remove these icons?
Apparently the information that there should be icons in the gutter persists somewhere in Sublime, even after closing it.
The solution was (found with help from plugin's creator) to close each file where this issue was occurring, and then re-opening them.
Not restarting Sublime, but closing-reopening the file itself.