Revert "Treat files as external dependencies."

Reverts scala-ide/scala-ide#862

Unfortunately this causes infinite build loops with Auto build. I see the following in the log:

```
EclipseSbtBuildManager - Invalidating /Volumes/Thunderbolt_SSD/dragos/Applications/eclipse-luna/plugins/org.scala-lang.scala-library_2.11.5.v20141126-232057-3ac6eabae6.jar: could not find class scala.Int on the classpath.
EclipseSbtBuildManager - Invalidating /Library/Java/JavaVirtualMachines/1.6.0_32-b05-417.jdk/Contents/Classes/classes.jar: could not find class java.lang.Object on the classpath.
```