To step over the breakpoints:
- Select
Window > Preferences
from the IDE menu bar.
The
Preferences
dialog box appears.
- Select the
Run/Debug
from the list in the left panel.
The
Run/Debug
page appears in the right panel.
- Check the
Skip breakpoints during `Run to Line' operation
checkbox from the
General Settings for Running and Debugging
list in the right panel.
Figure 1.
Preference Dialog Box

- Start a debugging Session.
- Select the desired source line in the Editor view.
- Right-click and select
Run To Line
from the context menu. Alternatively, press
Ctrl+R
.
Figure 2.
Run to Line Context Menu

With this you do not need to disable your hardware breakpoints in the
Breakpoints
view, and still can do full debugger stepping.