Grunnt: I have that "refresh on access" box ticked, but like a comment on that page wrote: "Although works when you modify file from explorer. it fails to work when files are updated from version control".
HeroesGraveDev: I guess this is what´s bothering me. Why is such a great program like Eclipse problems with something seemingly easy as a refresh function?

Now, this isn´t a huge problem. I´m aware of it and I can work around it but it does disrupts my work flow. Especially 2am and my head is buried in some problem and I get a "file not found". Sometimes that´s just enough to cause an mental meltdown.
