I remember that yesterday I wanted to create new C++ Class into my project, but UE4 started compiling it and it was compiling literally over hour and it remained at 79%, so then I quit UE4 (forced it) and went to sleep, now I cannot start engine.
Have you moved the engine from the original location where it was built? (Judging by its location in /opt/unreal-engine it seems so). The metadata stored by UnrealBuildTool contains absolute paths, so this was the reason why the whole engine started to be recompiled after you added a C++ file, and not just your project. Unfortunately breaking the (re)compilation at an arbitrary moment left the engine binaries in half-finished, inconsistent state. You need to recompile the engine again, preferably from scratch, before you can run it.