Another solution

Eclipse -> Run -> Remove All Breakpoints - for removing all Breakpoints for all Time

Eclipse -> Run -> Skip All Breakpoints - for temporary remove breakpoints

As other users have suggested, to view all breakpoints : Window-> Show View -> Breakpoints.

To delete them, there are three ways:

1. select the breakpoint & click on the cross button displayed in the same view.
2. select the breakpoint, right click & select remove. (You can also temporarily disable it & remove all the breakpoints from this menu.)
3. Go to the breakpoint in your file & double-click it.

Under the Run menu, there's a Skip All Breakpoints checkbox. If you select that, breakpoints won't fire (the actual breakpoint markers in the source have a line drawn through them to indicate they're in skip mode).

Of course, in the default configuration, running the code (rather than debugging it) also seems to ignore breakpoints so you may want to try running it instead of debugging. Note that this is default behaviour under Galileo/Ubuntu - whether that's different under other versions or operating systems is unknown to me.

Steps:

1. Select all the checkboxes (Ctrl + A or Command + A).
2. Right click and choose disable to uncheck all or click Remove all to remove from list.

try to select Debug then group by as I described in below image

Now you can select only the node of your file and disable.

One click disable, one click enable

open debug perspective [right conrer]

go to breakpoints

click clear all breakpoints [double X] or scroll until you find the breakpoint which doesn't want to go away and delete it.

Open the project > select the debugging view >> Somewhere in that view there will be a window titled Breakpoints. From there you can remove the breakpoint you want to get rid of.