Allow configuring the base temp directory in the JSON configuration file too

There still needs to be a default in the code in case the parameter is
missing from the config file

hive_config.json

@@ -8,7 +8,9 @@
     },
     "Meadow" : {
         "REMARKS" : {
-            "RunWorkerPath" : "The path of runWorker.pl . When null or missing, beekeeper will use $EHIVE_ROOT_DIR or its own path. When RunWorkerPath is '', beekeeper assumes runWorker.pl is in $PATH"
+            "HOWTO"             : "These parameters are optional. When setting them, move them out of the REMARKS section at the same time",
+            "BaseTempDirectory" : "Where to create temporary directories for workers. When null or missing, workers will use /tmp",
+            "RunWorkerPath"     : "The path of runWorker.pl . When null or missing, beekeeper will use $EHIVE_ROOT_DIR or its own path. When RunWorkerPath is '', beekeeper assumes runWorker.pl is in $PATH"
         },
         "CleanupTempDirectoryKilledWorkers" : 0,
         "MaxLimboSeconds"                   : 10,

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -222,7 +222,7 @@ sub create_new_worker {
     }
 
     $worker->set_log_directory_name($hive_log_dir, $worker_log_dir);
-    $worker->set_temp_directory_name( $worker_base_temp_dir );
+    $worker->set_temp_directory_name( $worker_base_temp_dir || $meadow->config_get('BaseTempDirectory') );
 
     $worker->init;
 
@@ -572,6 +572,7 @@ sub check_for_dead_workers {    # scans the whole Valley for lost Workers (but i
 
                     if( ($worker->status ne 'SUBMITTED')                 # There is no worker_temp_directory before specialization
                     and ($worker->meadow_user eq $this_meadow_user) ) {  # if I'm actually allowed to kill the worker...
+                            $worker->set_temp_directory_name( $this_meadow->config_get('BaseTempDirectory') );
                             $this_meadow->cleanup_temp_directory( $worker );
                     }
                 }