small enhancement in robustness of jana config files

MCwrapper/MakeMC.csh

@@ -176,6 +176,14 @@ if ( "$BKGFOLDSTR" == "DEFAULT" ) then
 		    endif
 endif
 
+
+set recon_pre=`echo $CUSTOM_PLUGINS | cut -c1-4`
+set jana_config_file=`echo $CUSTOM_PLUGINS | sed -r 's/^.{5}//'`
+
+if ( -f $jana_config_file ) then
+cp $jana_config_file ./jana_config.cfg
+endif
+
 set gen_pre=""
 
 if ( "$GENR" != "0" ) then
@@ -372,12 +380,11 @@ if ( "$GENR" != "0" ) then
 	    if ( "$RECON" != "0" ) then
 			echo "RUNNING RECONSTRUCTION"
 
-			set	recon_pre=`echo $CUSTOM_PLUGINS | cut -c1-4`
+
 
 			if ( "$recon_pre" == "file" ) then
-				set jana_config_file=`echo $CUSTOM_PLUGINS | sed -r 's/^.{5}//'`
 				echo "using config file: "$jana_config_file
-				hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' --config=$jana_config_file -PNTHREADS=$NUMTHREADS
+				    hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' --config=jana_config.cfg -PNTHREADS=$NUMTHREADS
 			else
 				set pluginlist=("danarest" "monitoring_hists")
 

MCwrapper/MakeMC.sh

@@ -177,6 +177,15 @@ if [[ "$BKGFOLDSTR" == "DEFAULT" ]]; then
 		    fi
 fi
 
+
+recon_pre=`echo $CUSTOM_PLUGINS | cut -c1-4`
+jana_config_file=`echo $CUSTOM_PLUGINS | sed -r 's/^.{5}//'`
+
+if [[ -f $jana_config_file ]]; then
+echo "gathering jana config file"
+cp $jana_config_file ./jana_config.cfg
+fi
+
 gen_pre=""
 
 if [[ "$GENR" != "0" ]]; then
@@ -371,13 +380,10 @@ if [[ "$GENR" != "0" ]]; then
 
 	    if [[ "$RECON" != "0" ]]; then
 		echo "RUNNING RECONSTRUCTION"
-
-		recon_pre=`echo $CUSTOM_PLUGINS | cut -c1-4`
 
 		if [[ "$recon_pre" == "file" ]]; then
-			jana_config_file=`echo $CUSTOM_PLUGINS | sed -r 's/^.{5}//'`
 			echo "using config file: "$jana_config_file
-			hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' --config=$jana_config_file -PNTHREADS=$NUMTHREADS
+			hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' --config=jana_config.cfg -PNTHREADS=$NUMTHREADS
 		else
 
 			declare -a pluginlist=("danarest" "monitoring_hists")