Move, rather than copy files staged back to Galaxy via the job files

api. Moving is a rename when the source and destination are on the same
filesystem, which is nearly instantaneous and greatly reduces the
possibility for failure due to mid-copy restarts.

lib/galaxy/webapps/galaxy/api/job_files.py

@@ -97,7 +97,7 @@ class JobFilesAPIController( BaseAPIController ):
             input_file = payload.get( "file",
                                       payload.get( "__file", None ) ).file
         try:
-            shutil.copyfile( input_file.name, path )
+            shutil.move( input_file.name, path )
         finally:
             input_file.close()
         return {"message": "ok"}