I also uninstalled and installed the whole engine. Here is the whole outputlog:
MainFrameActions: Packaging (Windows (64-bit)): UE4Editor-Cmd: [2016.08.27-16.17.37:585][ 0]LogSavePackage:Display: Finished SavePackage F:/Johann programmiert/BeispielProjekt 4.12/Saved/Cooked/WindowsNoEditor/Engine/Content/EngineMaterials/DefaultPhysicalMaterial.uasset
MainFrameActions: Packaging (Windows (64-bit)): UE4Editor-Cmd: [2016.08.27-16.17.37:586][ 0]LogCook:Display: Cooking /Engine/EngineFonts/RobotoTiny -> F:/Johann programmiert/BeispielProjekt 4.12/Saved/Cooked/WindowsNoEditor/Engine/Content/EngineFonts/RobotoTiny.uasset
MainFrameActions: Packaging (Windows (64-bit)): CommandUtils.Run: Run: Took 59,3814255s to run UE4Editor-Cmd.exe, ExitCode=3
MainFrameActions: Packaging (Windows (64-bit)): Project.Cook: Cook failed. Deleting cooked data.
MainFrameActions: Packaging (Windows (64-bit)): Program.Main: ERROR: AutomationTool terminated with exception: System.IO.IOException: The file or directory is corrupted and unreadable.
MainFrameActions: Packaging (Windows (64-bit)): at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
MainFrameActions: Packaging (Windows (64-bit)): at System.IO.FileSystemEnumerableIterator`1.CommonInit()
MainFrameActions: Packaging (Windows (64-bit)): at System.IO.FileSystemEnumerableIterator`1..ctor(String path, String originalUserPath, String searchPattern, SearchOption searchOption, SearchResultHandler`1 resultHandler, Boolean checkHost)
MainFrameActions: Packaging (Windows (64-bit)): at System.IO.Directory.EnumerateFiles(String path)
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.InternalUtils.RecursivelyDeleteDirectory(String Path, Boolean bQuiet)
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.InternalUtils.RecursivelyDeleteDirectory(String Path, Boolean bQuiet)
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.InternalUtils.RecursivelyDeleteDirectory(String Path, Boolean bQuiet)
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.InternalUtils.RecursivelyDeleteDirectory(String Path, Boolean bQuiet)
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.CommandUtils.DeleteDirectory(Boolean bQuiet, String[] Directories)
MainFrameActions: Packaging (Windows (64-bit)): at Project.Cook(ProjectParams Params)
MainFrameActions: Packaging (Windows (64-bit)): at BuildCookRun.DoBuildCookRun(ProjectParams Params)
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.BuildCommand.Execute()
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.Automation.Execute(List`1 CommandsToExecute, CaselessDictionary`1 Commands)
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.Automation.Process(String[] CommandLine)
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.Program.MainProc(Object Param)
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.InternalUtils.RunSingleInstance(Func`2 Main, Object Param)
MainFrameActions: Packaging (Windows (64-bit)): at AutomationTool.Program.Main()
MainFrameActions: Packaging (Windows (64-bit)): Program.Main: AutomationTool exiting with ExitCode=1 (Error_Unknown)
MainFrameActions: Packaging (Windows (64-bit)): Domain_ProcessExit
MainFrameActions: Packaging (Windows (64-bit)): copying UAT log files...
MainFrameActions: Packaging (Windows (64-bit)): BUILD FAILED
PackagingResults:Error: Error Unknown Error
If you need the whole log, you can write it down.