I'm not seeing any build.gradle files so you wouldn't need to change namespace in those.
It looks like there's a build config file you might need to change but I'm unsure.
Ultimately you can pop open android studio and hit Ctrl+shift+R and replace all com.android.deskclock
with org.lineageos.deskclock
- that might be easiest. I'd do a Ctrl+shift+F for org.lineageos.deskclock
first to be sure I don't have any clashing namespace but I think you're good.