Hello, Since I updated in 5.3.5f1 Monodevelop can’t see the Unity references as you can see:
The references seems to be in monodevelop as I highlighted in the screenshot.
I tried to reinstall 2 times but that didn’t work.
Monodevelop built in is selected in Unity preferences.
I tried to manually add Monodevelop in preferences with no luck either.
Also my game works fine, no bug reported in Unity, it’s just in Monodevelop.