Allow remotely executed tools to write version files to the temp directory.

Like with discovered datasets - such use of this directory should be phased out in favor of the job's working directory of a job relative to it.

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

@@ -118,9 +118,16 @@ class JobFilesAPIController( BaseAPIController ):
         https://gist.github.com/jmchilton/9103619.)
         """
         in_work_dir = self.__in_working_directory( job, path, trans.app )
-        if not in_work_dir and not self.__is_output_dataset_path( job, path ):
+        allow_temp_dir_file = self.__is_allowed_temp_dir_file( trans.app, job, path )
+        if not in_work_dir and not allow_temp_dir_file and not self.__is_output_dataset_path( job, path ):
             raise exceptions.ItemAccessibilityException("Job is not authorized to write to supplied path.")
 
+    def __is_allowed_temp_dir_file( self, app, job, path ):
+        # grrr.. need to get away from new_file_path - these should be written
+        # to job working directory like metadata files.
+        in_temp_dir = util.in_directory( path, app.config.new_file_path )
+        return in_temp_dir and os.path.split( path )[ -1 ].startswith( "GALAXY_VERSION_")
+
     def __is_output_dataset_path( self, job, path ):
         """ Check if is an output path for this job or a file in the an
         output's extra files path.