Since upgrading to Unity 5.2 javascript files are not showing in the Monodevelop Solution explorer (see image below). Does anyone know how to resolve this issue?
I had this problem too.
Is the Unity->Preferences->External Tool->External Script Editor set to monodevelop (built-in)?
After I set this, restarted the Unity Editor and double-clicked a UnityScript (i.e. js) file in the Assets pad, I landed in MonoDevelop and suddenly the Assembly-UnityScript and Assembly-UnityScript-firstpass projects were there.