diff --git a/MCwrapper/MakeMC.csh b/MCwrapper/MakeMC.csh
index f3b562b9..03710dbd 100755
--- a/MCwrapper/MakeMC.csh
+++ b/MCwrapper/MakeMC.csh
@@ -1,5 +1,5 @@
 #!/bin/csh -f
-
+    
 # SET INPUTS
 setenv ENVIRONMENT $1 
 shift
@@ -82,18 +82,18 @@ echo "detected c-shell"
 #necessary to run swif, uses local directory if swif=0 is used
 if ( "$MCSWIF" == "1" ) then
 # ENVIRONMENT
-echo $ENVIRONMENT
-source $ENVIRONMENT
-echo pwd=$PWD
-mkdir -p $OUTDIR
-mkdir -p $OUTDIR/log
+    echo $ENVIRONMENT
+    source $ENVIRONMENT
+    echo pwd=$PWD
+    mkdir -p $OUTDIR
+    mkdir -p $OUTDIR/log
 endif
 
 if ( "$CUSTOM_GCONTROL" == "0" ) then
-cp $MCWRAPPER_CENTRAL/Gcontrol.in ./temp_Gcontrol.in
-chmod 777 ./temp_Gcontrol.in
+    cp $MCWRAPPER_CENTRAL/Gcontrol.in ./temp_Gcontrol.in
+    chmod 777 ./temp_Gcontrol.in
 else
-cp $CUSTOM_GCONTROL/Gcontrol.in ./temp_Gcontrol.in
+    cp $CUSTOM_GCONTROL/Gcontrol.in ./temp_Gcontrol.in
 endif
 
 @ length_count=`echo $RUN_NUMBER | wc -c` - 1
@@ -153,6 +153,29 @@ if ( ! -d "$OUTDIR/root/" ) then
     mkdir $OUTDIR/root/
 endif
 
+set bkglocstring=""
+if ( "$BKGFOLDSTR" == "DEFAULT" ) then
+		    #find file and run:1
+		    echo "Finding the right file to fold in during MCsmear step"
+		    set runperiod="RunPeriod-2017-01"
+
+		    if ( $RUN_NUMBER > 40000 ) then
+			echo
+			#set runperiod="RunPeriod-2017-10"
+		    endif
+
+		    if ( $RUN_NUMBER < 30000 ) then
+			echo "Warning: random triggers did not exist by this point"
+		    endif
+		    set bkglocstring="/cache/halld/""$runperiod""/sim/random_triggers/""run$formatted_runNumber""_random.hddm"
+		    #set bkglocstring="/w/halld-scifs1a/home/tbritton/converted.hddm"
+		    
+		    if ( ! -f $bkglocstring ) then
+			echo "Could not find mix-in file "$bkglocstring
+			exit
+		    endif
+endif
+
 set gen_pre=""
 
 if ( "$GENR" != "0" ) then
@@ -323,37 +346,15 @@ if ( "$GENR" != "0" ) then
 	    if ( "$BKGFOLDSTR" == "BeamPhotons" || "$BKGFOLDSTR" == "None" ) then
 		echo "running MCsmear without folding in random background"
 		mcsmear -o$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' $STANDARD_NAME'_geant'$GEANTVER'.hddm'
-	    else
-		if ( "$BKGFOLDSTR" == "DEFAULT" ) then
-		    #find file and run:1
-		    echo "Finding the right file to fold in"
-		    set runperiod="RunPeriod-2017-01"
-
-		    if ( $RUN_NUMBER > 40000 ) then
-			echo
-			#set runperiod="RunPeriod-2017-10"
-		    endif
-
-		    if ( $RUN_NUMBER < 30000 ) then
-			echo "Warning: random triggers did not exist by this point"
-		    endif
-		    set bkglocstring="/cache/halld/""$runperiod""/sim/random_triggers/""run$formatted_runNumber""_random.hddm"
-		    #set bkglocstring="/w/halld-scifs1a/home/tbritton/converted.hddm"
-		    
-		    if ( ! -f $bkglocstring ) then
-			echo "Could not find mix-in file "$bkglocstring
-			exit
-		    else
+	    else if ( "$BKGFOLDSTR" == "DEFAULT" )
 			echo "mcsmear -o$STANDARD_NAME"\_"geant$GEANTVER"\_"smeared.hddm $STANDARD_NAME"\_"geant$GEANTVER.hddm $bkglocstring"\:"1"
 			mcsmear -o$STANDARD_NAME\_geant$GEANTVER\_smeared.hddm $STANDARD_NAME\_geant$GEANTVER.hddm $bkglocstring\:1
-		    endif
-		    
 		else
 		    #trust the user and use their string
 		    echo 'mcsmear -o'$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm'' '$STANDARD_NAME'_geant'$GEANTVER'.hddm'' '$BKGFOLDSTR
 		    mcsmear -o$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' $STANDARD_NAME'_geant'$GEANTVER'.hddm' $BKGFOLDSTR
 		endif
-	    endif
+	
 	    #run reconstruction
 	    if ( "$CLEANGENR" == "1" ) then
 		if ( "$GENERATOR" == "genr8" ) then
@@ -369,25 +370,34 @@ if ( "$GENR" != "0" ) then
 	    endif
 	    
 	    if ( "$RECON" != "0" ) then
-		echo "RUNNING RECONSTRUCTION"
-		set pluginlist=("danarest" "monitoring_hists")
+			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
+			else
+				set pluginlist=("danarest" "monitoring_hists")
 	     
-		if ( "$CUSTOM_PLUGINS" != "None" ) then
-		    set pluginlist=( "$pluginlist" "$CUSTOM_PLUGINS" )
-		endif	
+				if ( "$CUSTOM_PLUGINS" != "None" ) then
+			    	set pluginlist=( "$pluginlist" "$CUSTOM_PLUGINS" )
+				endif	
 
-		set PluginStr=""
+				set PluginStr=""
 	       
-		foreach plugin ($pluginlist)
-		set PluginStr="$PluginStr""$plugin"","
-		end
-		
-		set PluginStr=`echo $PluginStr | sed -r 's/.{1}$//'`
-		echo "Running hd_root with:""$PluginStr"
-		echo "hd_root ""$STANDARD_NAME"'_geant'"$GEANTVER"'_smeared.hddm'" -PPLUGINS=""$PluginStr ""-PNTHREADS=""$NUMTHREADS"
-		hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' -PPLUGINS=$PluginStr -PNTHREADS=$NUMTHREADS
-		mv dana_rest.hddm dana_rest_$STANDARD_NAME.hddm
+				foreach plugin ($pluginlist)
+					set PluginStr="$PluginStr""$plugin"","
+				end
 		
+				set PluginStr=`echo $PluginStr | sed -r 's/.{1}$//'`
+				echo "Running hd_root with:""$PluginStr"
+				echo "hd_root ""$STANDARD_NAME"'_geant'"$GEANTVER"'_smeared.hddm'" -PPLUGINS=""$PluginStr ""-PNTHREADS=""$NUMTHREADS"
+				hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' -PPLUGINS=$PluginStr -PNTHREADS=$NUMTHREADS
+				mv dana_rest.hddm dana_rest_$STANDARD_NAME.hddm
+			endif
+
 		if ( "$CLEANGEANT" == "1" ) then
 		    rm *_geant$GEANTVER.hddm
 		    rm control.in
@@ -412,9 +422,10 @@ if ( "$GENR" != "0" ) then
 		foreach rootfile ($rootfiles)
 		    set filename_root=`echo $rootfile | sed -r 's/.{5}$//'`
 		    set filetomv="$rootfile"
-                    mv $filetomv $filename_root\_$STANDARD_NAME.root
-                end
-		mv $PWD/$filename_root\_$STANDARD_NAME.root $OUTDIR/root/
+            mv $filetomv $filename_root\_$STANDARD_NAME.root
+        	mv $PWD/$filename_root\_$STANDARD_NAME.root $OUTDIR/root/
+        end
+		
 
 	    endif
 	endif
@@ -424,6 +435,11 @@ endif
 if ( "$gen_pre" != "file" ) then
 mv $PWD/*.conf $OUTDIR/configurations/
 endif
-mv $PWD/*.hddm $OUTDIR/hddm/
+
+set hddmfiles=`ls | grep .hddm`
+if ( $hddmfiles != "" ) then
+	mv $PWD/*.hddm $OUTDIR/hddm/
+endif
+
 #    mv $PWD/*.root $OUTDIR/root/ #just in case
 echo `date`
diff --git a/MCwrapper/MakeMC.sh b/MCwrapper/MakeMC.sh
index e01c311e..e4ffc6b0 100755
--- a/MCwrapper/MakeMC.sh
+++ b/MCwrapper/MakeMC.sh
@@ -153,6 +153,30 @@ if [[ ! -d "$OUTDIR/root/" ]]; then
     mkdir $OUTDIR/root/
 fi
 
+bkglocstring=""
+if [[ "$BKGFOLDSTR" == "DEFAULT" ]]; then
+		    #find file and run:1
+		    echo "Finding the right file to fold in during MCsmear step"
+		    runperiod="RunPeriod-2017-01"
+
+		    if [[ $RUN_NUMBER > 40000 ]]; then
+			echo
+			#set runperiod="RunPeriod-2017-10"
+		    fi
+
+		    if [[ $RUN_NUMBER < 30000 ]]; then
+			echo "Warning: random triggers did not exist by this point"
+		    fi
+
+		    bkglocstring="/cache/halld/""$runperiod""/sim/random_triggers/""run$formatted_runNumber""_random.hddm"
+		    #set bkglocstring="/w/halld-scifs1a/home/tbritton/converted.hddm"
+		    
+		    if [[ ! -f $bkglocstring ]]; then
+			echo "Could not find mix-in file "$bkglocstring
+			exit
+		    fi
+fi
+
 gen_pre=""
 
 if [[ "$GENR" != "0" ]]; then
@@ -322,36 +346,14 @@ if [[ "$GENR" != "0" ]]; then
 	    if [[ "$BKGFOLDSTR" == "BeamPhotons" || "$BKGFOLDSTR" == "None" ]]; then
 		echo "running MCsmear without folding in random background"
 		mcsmear -o$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' $STANDARD_NAME'_geant'$GEANTVER'.hddm'
-	    else
-		if [[ "$BKGFOLDSTR" == "DEFAULT" ]]; then
-		    #find file and run:1
-		    echo "Finding the right file to fold in"
-		    runperiod="RunPeriod-2017-01"
-		    
-		    if [[ $RUN_NUMBER > 40000 ]]; then
-			echo
-			#runperiod="RunPeriod-2017-10"
-		    fi
-		    
-		    if [[ $RUN_NUMBER < 30000 ]]; then
-			echo "Warning: random triggers did not exist by this point"
-		    fi
-		    bkglocstring="/cache/halld/""$runperiod""/sim/random_triggers/""run$formatted_runNumber""_random.hddm"
-		    #bkglocstring="/w/halld-scifs1a/home/tbritton/converted.hddm"
-		    
-		    if [[ ! -f $bkglocstring ]]; then
-			echo "Could not find mix-in file "$bkglocstring
-			exit
-		    else
+	    elif [[ "$BKGFOLDSTR" == "DEFAULT" ]]; then
 			echo "mcsmear -o$STANDARD_NAME"\_"geant$GEANTVER"\_"smeared.hddm $STANDARD_NAME"\_"geant$GEANTVER.hddm $bkglocstring"\:"1"
 			mcsmear -o$STANDARD_NAME\_geant$GEANTVER\_smeared.hddm $STANDARD_NAME\_geant$GEANTVER.hddm $bkglocstring\:1
-		    fi
-		    
 		else
 		    #trust the user and use their string
 		    echo 'mcsmear -o'$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm'' '$STANDARD_NAME'_geant'$GEANTVER'.hddm'' '$BKGFOLDSTR
 		    mcsmear -o$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' $STANDARD_NAME'_geant'$GEANTVER'.hddm' $BKGFOLDSTR
-		fi
+
 	    fi
 	    #run reconstruction
 	    if [[ "$CLEANGENR" == "1" ]]; then
@@ -369,26 +371,36 @@ if [[ "$GENR" != "0" ]]; then
 	    
 	    if [[ "$RECON" != "0" ]]; then
 		echo "RUNNING RECONSTRUCTION"
-		declare -a pluginlist=("danarest" "monitoring_hists")
-		echo ${pluginlist[@]}
-		echo $CUSTOM_PLUGINS
-                if [[ "$CUSTOM_PLUGINS" != "None" ]]; then
-                    pluginlist=("${pluginlist[@]}" $CUSTOM_PLUGINS)
-                fi
-		echo ${pluginlist[@]}
+		
+		recon_pre=`echo $CUSTOM_PLUGINS | cut -c1-4`
 
-		PluginStr=""
+		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
+		else
 		
-                for plugin in "${pluginlist[@]}"; do
-                    PluginStr="$PluginStr""$plugin"","
-                done
+			declare -a pluginlist=("danarest" "monitoring_hists")
+			echo ${pluginlist[@]}
+			echo $CUSTOM_PLUGINS
+            if [[ "$CUSTOM_PLUGINS" != "None" ]]; then
+				pluginlist=("${pluginlist[@]}" $CUSTOM_PLUGINS)
+            fi
+			echo ${pluginlist[@]}
+
+			PluginStr=""
 		
-		PluginStr=`echo $PluginStr | sed -r 's/.{1}$//'`
-                echo "Running hd_root with:""$PluginStr"
-		echo "hd_root ""$STANDARD_NAME"'_geant'"$GEANTVER"'_smeared.hddm'" -PPLUGINS=""$PluginStr ""-PNTHREADS=""$NUMTHREADS"
-		hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' -PPLUGINS=$PluginStr -PNTHREADS=$NUMTHREADS
-		mv dana_rest.hddm dana_rest_$STANDARD_NAME.hddm
+            for plugin in "${pluginlist[@]}"; do
+				PluginStr="$PluginStr""$plugin"","
+            done
 		
+			PluginStr=`echo $PluginStr | sed -r 's/.{1}$//'`
+            echo "Running hd_root with:""$PluginStr"
+			echo "hd_root ""$STANDARD_NAME"'_geant'"$GEANTVER"'_smeared.hddm'" -PPLUGINS=""$PluginStr ""-PNTHREADS=""$NUMTHREADS"
+			hd_root ./$STANDARD_NAME'_geant'$GEANTVER'_smeared.hddm' -PPLUGINS=$PluginStr -PNTHREADS=$NUMTHREADS
+			mv dana_rest.hddm dana_rest_$STANDARD_NAME.hddm
+		fi
+
 		if [[ "$CLEANGEANT" == "1" ]]; then
 		    rm *_geant$GEANTVER.hddm
 		    rm control.in
@@ -415,14 +427,17 @@ if [[ "$GENR" != "0" ]]; then
 		filename_root=`echo $rootfile | sed -r 's/.{5}$//'`
 		filetomv="$rootfile"
 		mv $filetomv $filename_root\_$STANDARD_NAME.root
-                done
 		mv $PWD/$filename_root\_$STANDARD_NAME.root $OUTDIR/root/
+        done
 	    fi
 	fi
     fi
 fi
 if [[ "$gen_pre" != "file" ]]; then
-mv $PWD/*.conf $OUTDIR/configurations/
+	mv $PWD/*.conf $OUTDIR/configurations/
+fi
+hddmfiles=$(ls | grep .hddm)
+if [[ $hddmfiles != "" ]]; then
+	mv $PWD/*.hddm $OUTDIR/hddm/
 fi
-mv $PWD/*.hddm $OUTDIR/hddm/
 #mv $PWD/*.root $OUTDIR/root/ #just in case
diff --git a/MCwrapper/examples/MC.config b/MCwrapper/examples/MC.config
index 34b9b99f..22ea962a 100644
--- a/MCwrapper/examples/MC.config
+++ b/MCwrapper/examples/MC.config
@@ -2,25 +2,27 @@
 #CUSTOM_MAKEMC=use-this-script-instead
 #CUSTOM_GCONTROL=use-this-Gcontrol-instead
 #========================================================================
-#TAG=my-custom-prefix-tab
-# OUTPUT DATA LOCATION
+
+#TAG=my-custom-prefix-tag
+
 DATA_OUTPUT_BASE_DIR=OUTPUT-LOCATION#your desired output location
 
 NCORES=4               # Number of CPU threads to use
 
-GENERATOR=generator-to-use
+GENERATOR=generator-to-use #or you may specifile file:/.../file-to-use
 GENERATOR_CONFIG=config file for generator
 
 #common parameters for generators
-eBEAM_ENERGY=12
-COHERENT_PEAK=9
-GEN_MIN_ENERGY=4
-GEN_MAX_ENERGY=12
+#eBEAM_ENERGY=12
+#COHERENT_PEAK=9
+#GEN_MIN_ENERGY=4
+#GEN_MAX_ENERGY=12
 
 GEANT_VERSION=4
 BKG=BeamPhotons #[None, BeamPhotons, DEFAULT, custom bg.hddm:1.8]
 
-#CUSTOM_PLUGINS #optional additional plugins that will be run along side danarest and hd_root.  This should be a comma separated list (e.g. plugin1,plugin2)
+#optional additional plugins that will be run along side danarest and hd_root.  This should be a comma separated list (e.g. plugin1,plugin2)
+#CUSTOM_PLUGINS= #or file:/.../file-to-use which is a configuration file for jana/hd_root 
 #====================================================================================
 
 #EVERYTHING BELOW FOR SWIF ONLY
diff --git a/MCwrapper/gluex_MC.py b/MCwrapper/gluex_MC.py
index 1dad29c5..de700025 100755
--- a/MCwrapper/gluex_MC.py
+++ b/MCwrapper/gluex_MC.py
@@ -103,7 +103,7 @@ def main(argv):
 
         print "*********************************"
         print "Welcome to v1.3.1 of the MCwrapper"
-        print "Thomas Britton 04/14/17"
+        print "Thomas Britton 04/18/17"
         print "*********************************"