diff --git a/llvm/lib/Transforms/Scaffold/GenQASM.cpp b/llvm/lib/Transforms/Scaffold/GenQASM.cpp
index c7691a0bb..63577f1e8 100644
--- a/llvm/lib/Transforms/Scaffold/GenQASM.cpp
+++ b/llvm/lib/Transforms/Scaffold/GenQASM.cpp
@@ -933,7 +933,6 @@ void GenQASM::genQASM(Function* F)
 	else if(fToPrint.find("Tdag") != string::npos) fToPrint = "Tdag";
 	else if(fToPrint.find("X.") != string::npos) fToPrint = "X";
 	else if(fToPrint.find("Z.") != string::npos) fToPrint = "Z";
-	else if(fToPrint.find("afree") != string::npos) continue; 
 
 	std::replace(fToPrint.begin(), fToPrint.end(), '.', '_');
 	std::replace(fToPrint.begin(), fToPrint.end(), '-', '_');
diff --git a/scaffold.sh b/scaffold.sh
index d5c3ac921..8a58ae8ef 100755
--- a/scaffold.sh
+++ b/scaffold.sh
@@ -2,31 +2,36 @@
 
 ROOT=$(dirname $0)
 
-# Get CTQG path
-export CTQG_PATH=${ROOT}/ctqg/CTQG
-if [ $(echo $PATH | grep ${CTQG_PATH} | wc -l) -eq 0 ]; then
-	export PATH=$PATH:$CTQG_PATH
+# Get RKQC path
+export RKQC_PATH=${ROOT}/rkqc
+if [ $(echo $PATH | grep ${RKQC_PATH} | wc -l) -eq 0 ]; then
+	export PATH=$PATH:$RKQC_PATH
 fi
 
 function show_help {
-    echo "Usage: $0 [-h] [-rqfRTFcpd] [-l #] [-P #] <filename>.scaffold"
+    echo "Usage: $0 [-hv] [-rqfRFcpds] [-L #] <filename>.scaffold"
     echo "    -r   Generate resource estimate (default)"
     echo "    -q   Generate QASM"
     echo "    -f   Generate flattened QASM"
     echo "    -R   Disable rotation decomposition"
     echo "    -T   Disable Toffoli decomposition"    
-	  echo "    -l   Levels of recursion to run (default=1)"
-    echo "    -P   Set precision of rotation decomposition in decimal digits (default=10)"        
+	echo "    -l   Levels of recursion to run (default=1)"
     echo "    -F   Force running all steps"
     echo "    -c   Clean all files (no other actions)"
     echo "    -p   Purge all intermediate files (preserves specified output,"
     echo "         but requires recompilation for any new output)"
     echo "    -d   Dry-run; show all commands to be run, but do not execute"
+    echo "    -s   Generate QX Simulator input file"  
+    echo "    -v   Show current Scaffold version information" 
+}
+
+function show_version {
+    echo "Scaffold - Release 2.0 (July 10, 2016) Beta"
 }
 
 # Parse opts
 OPTIND=1         # Reset in case getopts has been used previously in the shell.
-ctqg=0
+rkqc=0
 clean=0
 dryrun=""
 force=0
@@ -34,22 +39,27 @@ purge=0
 res=0
 rot=1
 toff=1
+flat=0
+qc=0
 targets=""
-precision=4
-while getopts "h?cdfFpqrRT:l:P:" opt; do
+while getopts "h?vcdfsFpqrRTl:" opt; do
     case "$opt" in
     h|\?)
         show_help
         exit 0
         ;;
+    v)
+        show_version
+        exit 0
+        ;;
     c) clean=1
         ;;
 	  d) dryrun="--dry-run"
-		    ;;
+		;;
     F) force=1
         ;;
-    f) targets="${targets} flat"
-        ;;
+    f) flat=1
+		;;
     p) purge=1
         ;;
     q) targets="${targets} qasm"
@@ -60,14 +70,23 @@ while getopts "h?cdfFpqrRT:l:P:" opt; do
         ;;
     T) toff=0
         ;;        
+	s) qc=1
+		;;
     l) targets="${targets} SQCT_LEVELS=${OPTARG}"
         ;;
-    P) precision=${OPTARG}
     esac
 done
 shift $((OPTIND-1))
 [ "$1" = "--" ] && shift
 
+if [ ${flat} -eq 1 ]; then
+	targets="${targets} flat"
+fi
+
+if [ ${qc} -eq 1 ]; then
+	targets="${targets} qc"
+fi
+
 # Put resources at the end so it is easy to read
 if [ ${res} -eq 1 ]; then
     targets="${targets} resources"
@@ -101,17 +120,15 @@ dir="$(dirname ${filename})/"
 file=$(basename ${filename} .scaffold)
 cfile="${file}.*"
 
-if [ $(egrep '^ctqg.*{\s*' ${filename} | wc -l) -gt 0 ]; then
-	ctqg=1
+if [ $(egrep '^rkqc.*{\s*' ${filename} | wc -l) -gt 0 ]; then
+	rkqc=1
 	toff=1
-	#dir=""
 fi
 
 if [ ${clean} -eq 1 ]; then
 	make -f $ROOT/scaffold/Scaffold.makefile ${dryrun} ROOT=$ROOT DIRNAME=${dir} FILENAME=${filename} FILE=${file} CFILE=${cfile} clean
     exit
 fi
-make -f $ROOT/scaffold/Scaffold.makefile ${dryrun} ROOT=$ROOT DIRNAME=${dir} FILENAME=${filename} FILE=${file} CFILE=${cfile} TOFF=${toff} CTQG=${ctqg} ROTATIONS=${rot} PRECISION=${precision} ${targets}
+make -f $ROOT/scaffold/Scaffold.makefile ${dryrun} ROOT=$ROOT DIRNAME=${dir} FILENAME=${filename} FILE=${file} CFILE=${cfile} TOFF=${toff} RKQC=${rkqc} ROTATIONS=${rot} ${targets}
 
 exit 0
-
diff --git a/scaffold/Scaffold.makefile b/scaffold/Scaffold.makefile
index 1687aaf0b..482fd15ad 100644
--- a/scaffold/Scaffold.makefile
+++ b/scaffold/Scaffold.makefile
@@ -3,20 +3,17 @@ PERL=/usr/bin/perl
 PYTHON=/usr/bin/python
 
 ROOT=".."
-DIRNAME=""
 FILENAME=""
 FILE=""
 CFILE=""
-TOFF=0
-CTQG=0
-ROTATIONS=0
+DIRNAME=""
 
 BUILD=$(ROOT)/build/Release+Asserts
 
 SQCTPATH=$(ROOT)/Rotations/sqct/rotZ
 GRIDSYNTHPATH=$(ROOT)/Rotations/gridsynth/gridsynth
 ROTATIONPATH=$(GRIDSYNTHPATH) # select rotation decomposition tool
-PRECISION=""
+SCRIPTSPATH=$(ROOT)/scripts/ # select rotation decomposition tool
 
 CC=$(BUILD)/bin/clang
 OPT=$(BUILD)/bin/opt
@@ -32,11 +29,14 @@ SCAFFOLD_LIB=$(ROOT)/build/Release+Asserts/lib/Scaffold.dylib
 endif
 
 
+RKQC=0
+ROTATIONS=0
+TOFF=0
+
 ################################
 # Resource Count Estimation
 ################################
 resources: $(FILE).resources
-	@cat $(FILE).resources
 
 ################################
 # Flat QASM generation
@@ -48,30 +48,24 @@ flat: $(FILE).qasmf
 ################################
 qasm: $(FILE).qasmh
 
-.PHONY: res_count qasm flat
+################################
+# QX Simulator generation
+################################
+qc: $(FILE).qc
+
+.PHONY: resources qasm flat qc
 
 ################################
 # Intermediate targets
 ################################
-# Pre-process CTQG
+# Compile Scaffold to LLVM bytecode
+
 $(FILE)_merged.scaffold: $(FILENAME)
-	@if [ $(CTQG) -eq 1 ]; then \
-		echo "[Scaffold.makefile] Extracting CTQG from Scaffold ..."; \
-		$(PERL) $(ROOT)/ctqg/trans/pre_process.pl $(FILENAME); \
-		echo "[Scaffold.makefile] Compiling CTQG ..."; \
-		$(ROOT)/ctqg/CTQG/ctqg $(CFILE).ctqg; \
-		echo "[Scaffold.makefile] Merging CTQG output back into Scaffold ..."; \
-    $(PERL) $(ROOT)/ctqg/trans/trans.pl $(CFILE).qasm > trans.qasm; \
-    mv trans.qasm $(CFILE).qasm; \
-		$(PERL) $(ROOT)/ctqg/trans/merge.pl $(CFILE).qasm; \
-	else \
-		cp $(FILENAME) $(FILE)_merged.scaffold; \
-	fi
+	@cp $(FILENAME) $(FILE)_merged.scaffold
 
-# Compile Scaffold to LLVM bytecode
 $(FILE).ll: $(FILE)_merged.scaffold
-	@echo "[Scaffold.makefile] Compiling $(FILE)_merged.scaffold ..."
-	@$(CC) $(FILE)_merged.scaffold $(CC_FLAGS) -o $(FILE).ll
+	@echo "[Scaffold.makefile] Compiling $(FILE).scaffold ..."
+	@$(CC) $(FILE)_merged.scaffold $(CC_FLAGS) -o $(FILE).ll 
 
 $(FILE)1.ll: $(FILE).ll
 	@echo "[Scaffold.makefile] Transforming cbits ..."
@@ -117,40 +111,53 @@ $(FILE)7.ll: $(FILE)6.ll
 		cp $(FILE)6.ll $(FILE)7.ll; \
 	elif [ $(ROTATIONS) -eq 1 ]; then \
 		echo "[Scaffold.makefile] Decomposing Rotations ..."; \
-		if [ ! -e /tmp/epsilon-net.0.bin ]; then echo "Generating decomposition databases"; fi; \
+		if [ ! -e /tmp/epsilon-net.0.bin ]; then echo "Generating decomposition databases; this may take up to an hour"; fi; \
 		export ROTATIONPATH=$(ROTATIONPATH); \
-    export PRECISION=$(PRECISION); \
 		$(OPT) -S -load $(SCAFFOLD_LIB) -Rotations $(FILE)6.ll -o $(FILE)7.ll > /dev/null; \
 	else \
 		cp $(FILE)6.ll $(FILE)7.ll; \
 	fi
 
 # Remove any code that is useless after optimizations
-$(FILE)10.ll: $(FILE)7.ll
+$(FILE)8.ll: $(FILE)7.ll
 	@echo "[Scaffold.makefile] Internalizing and Removing Unused Functions ..."
-	@$(OPT) -S $(FILE)7.ll -internalize -globaldce -deadargelim -o $(FILE)10.ll > /dev/null
+	@$(OPT) -S $(FILE)7.ll -internalize -globaldce -deadargelim -o $(FILE)8.ll > /dev/null
+
+# Compile RKQC 
+$(FILE)9.ll: $(FILE)8.ll
+	@if [ $(RKQC) -eq 1 ]; then \
+        echo "[Scaffold.makefile] Compiling RKQC Functions ..."; \
+        $(OPT) -S -load $(SCAFFOLD_LIB) -GenRKQC $(FILE)8.ll -o $(FILE)9.ll > /dev/null 2> $(FILE).errs; \
+	else \
+		mv $(FILE)8.ll $(FILE)9.ll; \
+    fi
 
 # Perform Toffoli decomposition if TOFF is 1
-$(FILE)11.ll: $(FILE)10.ll
+$(FILE)11.ll: $(FILE)9.ll
 	@if [ $(TOFF) -eq 1 ]; then \
     echo "[Scaffold.makefile] Toffoli Decomposition ..."; \
-		$(OPT) -S -load $(SCAFFOLD_LIB) -ToffoliReplace $(FILE)10.ll -o $(FILE)11.ll > /dev/null; \
+		$(OPT) -S -load $(SCAFFOLD_LIB) -ToffoliReplace $(FILE)9.ll -o $(FILE)11.ll > /dev/null; \
 	else \
-		cp $(FILE)10.ll $(FILE)11.ll; \
+		cp $(FILE)9.ll $(FILE)11.ll; \
 	fi
 
+# Insert reverse functions if REVERSE is 1
+$(FILE)12.ll: $(FILE)11.ll
+	@echo "[Scaffold.makefile] Inserting Reverse Functions..."
+	@$(OPT) -S -load $(SCAFFOLD_LIB) -FunctionReverse $(FILE)11.ll -o $(FILE)12.ll > /dev/null
+
 # Generate resource counts from final LLVM output
-$(FILE).resources: $(FILE)11.ll
+$(FILE).resources: $(FILE)12.ll
 	@echo "[Scaffold.makefile] Generating resource count ..."    
-	@$(OPT) -load $(SCAFFOLD_LIB) -ResourceCount $(FILE)11.ll 2> $(FILE).resources > /dev/null
+	@$(OPT) -load $(SCAFFOLD_LIB) -ResourceCount $(FILE)12.ll 2> $(FILE).resources > /dev/null
 	@echo "[Scaffold.makefile] Resources written to $(FILE).resources ..."  
 
-# Generate hierarchical QASM
-$(FILE).qasmh: $(FILE)11.ll
+$(FILE).qasmh: $(FILE)12.ll
 	@echo "[Scaffold.makefile] Generating hierarchical QASM ..."  
-	@$(OPT) -load $(SCAFFOLD_LIB) -gen-qasm $(FILE)11.ll 2> $(FILE).qasmh > /dev/null
+	@$(OPT) -load $(SCAFFOLD_LIB) -gen-qasm $(FILE)12.ll 2> $(FILE).qasmh > /dev/null
 	@echo "[Scaffold.makefile] Hierarchical QASM written to $(FILE).qasmh ..."  
 
+
 # Translate hierarchical QASM back to C++ for flattening
 $(FILE)_qasm.scaffold: $(FILE).qasmh
 	@echo "[Scaffold.makefile] Generating flattened QASM ..."
@@ -164,15 +171,19 @@ $(FILE)_qasm: $(FILE)_qasm.scaffold
 $(FILE).qasmf: $(FILE)_qasm
 	@./$(FILE)_qasm > $(FILE).tmp
 	@cat fdecl.out $(FILE).tmp > $(FILE).qasmf
-	@echo "[Scaffold.makefile] Flat QASM written to $(FILE).qasmf ..."    
+	@echo "[Scaffold.makefile] Flat QASM written to $(FILE).qasmf ..."
+
+$(FILE).qc: $(FILE).qasmf
+	@echo "[Scaffold.makefile] Transforming flat QASM to QX Simulator input ..."
+	@$(SHELL) $(ROOT)/scripts/qasmf2qc.sh $(FILE).qasmf
+	@echo "[Scaffold.makefile] QX Simulator input written to $(FILE).qc ..." 
 
 # purge cleans temp files
 purge:
-	@rm -f $(FILE)_merged.scaffold $(FILE)_noctqg.scaffold $(FILE).ll $(FILE)1.ll $(FILE)1a.ll $(FILE)1b.ll $(FILE)2.ll $(FILE)3.ll $(FILE)4.ll $(FILE)5.ll $(FILE)5a.ll $(FILE)6.ll $(FILE)6tmp.ll $(FILE)7.ll $(FILE)8.ll $(FILE)9.ll $(FILE)10.ll $(FILE)11.ll $(FILE)tmp.ll $(FILE)_qasm $(FILE)_qasm.scaffold fdecl.out $(CFILE).ctqg $(CFILE).c $(CFILE).signals $(FILE).tmp sim_$(CFILE) $(FILE).*.qasm
+	@rm -f $(FILE)_merged.scaffold $(FILE)_no.scaffold $(FILE).ll $(FILE)1.ll $(FILE)1a.ll $(FILE)1b.ll $(FILE)2.ll $(FILE)3.ll $(FILE)4.ll $(FILE)5.ll $(FILE)5a.ll $(FILE)6.ll $(FILE)6tmp.ll $(FILE)7.ll $(FILE)8.ll $(FILE)9.ll $(FILE)10.ll $(FILE)11.ll $(FILE)12.ll $(FILE)tmp.ll $(FILE)_qasm $(FILE)_qasm.scaffold fdecl.out $(CFILE).ctqg $(CFILE).c $(CFILE).signals $(FILE).tmp sim_$(CFILE) $(FILE).*.qasm 
 
 # clean removes all completed files
 clean: purge
-	@rm -f $(FILE).resources $(FILE).qasmh $(FILE).qasmf
+	@rm -f $(FILE).resources $(FILE).qasmh $(FILE).qasmf $(FILE).qc
 
 .PHONY: clean purge
-
diff --git a/scaffold/flatten-qasm.py b/scaffold/flatten-qasm.py
index 9d4485a91..cf52c37c6 100644
--- a/scaffold/flatten-qasm.py
+++ b/scaffold/flatten-qasm.py
@@ -12,6 +12,7 @@ def process_qasm(fname):
     qgates_4 = ['PrepX','PrepZ']
     qgates_5 = ['MeasX','MeasZ']
     qgates_6 = ['Rz']
+    qgates_7 = ['afree']
     
 
     gateNames = {
@@ -30,7 +31,8 @@ def process_qasm(fname):
         'Rz':'Rz',
         'CNOT':'CNOT', #'CX',
         'Toffoli':'Tof',
-        'Fredkin':'Fredkin'
+        'Fredkin':'Fredkin',
+        'afree':'afree'
         }
     
     pattern_qbit_decl = re.compile(r"\s*\bqbit\b\s+(?P<qbit_var>\w+)\s*\[\s*(?P<array_size>\d+)\s*\]\s*;")
@@ -97,6 +99,13 @@ def process_qasm(fname):
         instFnName = 'qg_'+q
         fstr = 'void '+instFnName+'(char* a, double b){ printf("' +gateNames[q] +' %s,%f\\n",a,b); }\n'
         fout.write(fstr)
+    
+    for q in qgates_7:
+        instFnName = q
+        fstr = 'void '+instFnName+'(char** a, int b ){ for(int i = 0; i < b; i++){ printf("' +gateNames[q] +' %s\\n",(*a)); a++; }}\n'
+                
+        fout.write(fstr)
+
 
     fout.write('\n')