Fixed removal of upload temp files

Fixed an issue with an unclosed stream preventing upload temp files from
being removed after use. Also removed the use of FileCleaningTracker and
instead added manual removal of all tempfiles. By doing this the reaper
threads in FileCleaningTracker are avoided and files are removed
directly after use.
Merge pull request #666 from Arcadelia/Temp-file_removal

Fixed removal of upload temp files