[API] corrected Eclipse Filesystem IMPL

Some methods may throw RuntimeException. The affected methods will
now throw IOExceptions instead of RuntimeExceptions.

Change-Id: Ia4b51d8f12fea6d4f33f80684315f851312aca92
Reviewed-on: http://saros-build.imp.fu-berlin.de/gerrit/1940
Tested-by: Jenkins CI
Reviewed-by: Stefan Rossbach <srossbach@arcor.de>