The Exclusions page of the Preferences window includes options to automatically skip breaks when specified apps are frontmost, or just open.
Click the Add (+) button below the list to exclude a new app.
Click the Remove (X) button next to an app to remove the exclusion.
Choose Skip When Frontmost to skip breaks only when the associated app is the active app.
Choose Skip When Open to skip breaks when the associated app is open, not necessarily active.
Also skip breaks during the screensaver: If this box is checked, breaks will be automatically skipped when the screensaver is active.
Also skip breaks during the display sleep: If this box is checked, breaks will be automatically skipped when the display is asleep, another user is active (via Fast User Switching), or when the Mac is asleep.