diff --git a/fpga/constraints/debug2.xdc b/fpga/constraints/debug2.xdc
index 69d295f8..0acdcf6e 100644
--- a/fpga/constraints/debug2.xdc
+++ b/fpga/constraints/debug2.xdc
@@ -87,7 +87,7 @@ connect_debug_port u_ila_0/probe15 [get_nets [list {wallypipelinedsoc/core/priv.
 create_debug_port u_ila_0 probe
 set_property port_width 64 [get_debug_ports u_ila_0/probe16]
 set_property PROBE_TYPE DATA_AND_TRIGGER [get_debug_ports u_ila_0/probe16]
-connect_debug_port u_ila_0/probe16 [get_nets [list {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[0]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[1]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[2]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[3]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[4]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[5]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[6]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[7]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[8]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[9]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[10]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[11]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[12]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[13]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[14]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[15]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[16]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[17]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[18]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[19]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[20]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[21]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[22]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[23]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[24]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[25]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[26]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[27]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[28]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[29]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[30]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[31]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[32]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[33]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[34]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[35]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[36]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[37]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[38]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[39]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[40]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[41]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[42]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[43]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[44]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[45]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[46]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[47]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[48]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[49]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[50]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[51]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[52]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[53]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[54]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[55]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[56]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[57]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[58]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[59]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[60]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[61]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[62]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/csrs.SCAUSE_REGW[63]} ]]
+connect_debug_port u_ila_0/probe16 [get_nets [list {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[0]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[1]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[2]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[3]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[4]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[5]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[6]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[7]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[8]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[9]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[10]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[11]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[12]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[13]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[14]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[15]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[16]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[17]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[18]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[19]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[20]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[21]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[22]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[23]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[24]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[25]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[26]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[27]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[28]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[29]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[30]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[31]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[32]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[33]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[34]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[35]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[36]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[37]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[38]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[39]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[40]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[41]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[42]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[43]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[44]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[45]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[46]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[47]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[48]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[49]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[50]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[51]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[52]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[53]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[54]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[55]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[56]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[57]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[58]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[59]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[60]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[61]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[62]} {wallypipelinedsoc/core/priv.priv/csr/csrs.csrs/SCAUSE_REGW[63]} ]]
 
 
 create_debug_port u_ila_0 probe
diff --git a/fpga/generator/Makefile b/fpga/generator/Makefile
index 82c5a2ca..3ab35b34 100644
--- a/fpga/generator/Makefile
+++ b/fpga/generator/Makefile
@@ -26,6 +26,7 @@ SDC:
 	tar xzf ../src/sdc.tar.gz -C ../src
 
 PreProcessFiles:
+	rm -rf ../src/CopiedFiles_do_not_add_to_repo/
 	cp -r ../../pipelined/src/ ../src/CopiedFiles_do_not_add_to_repo/
 	./insert_debug_comment.sh
 
diff --git a/fpga/generator/insert_debug_comment.sh b/fpga/generator/insert_debug_comment.sh
index 5e85d17b..66c232e1 100755
--- a/fpga/generator/insert_debug_comment.sh
+++ b/fpga/generator/insert_debug_comment.sh
@@ -26,14 +26,13 @@
 
 # This script copies wally's pipelined#src to fpga#src#CopiedFiles_do_not_add_to_repo
 # Then it processes them to add mark_debug on signals needed by the FPGA's ILA.
-copiedDir="..#src#CopiedFiles_do_not_add_to_repo"
+copiedDir="../src/CopiedFiles_do_not_add_to_repo"
 while read line; do
     readarray -d ":" -t StrArray <<< "$line"
-    file="${copiedDir}#${StrArray[0]}"
-    #signal=`echo "${StrArray[1]}" | awk '{$1=$1};1'`
+    file="${copiedDir}/${StrArray[0]}"
     signal=`echo "${StrArray[1]}" | awk '{$1=$1};1'`
     readarray -d " " -t SigArray <<< $signal
     sigType=`echo "${SigArray[0]}" | awk '{$1=$1};1'`
     sigName=`echo "${SigArray[1]}" | awk '{$1=$1};1'`
-    find $copiedDir -wholename $file | xargs sed -i "s#\(.*${sigType}.*${sigName}\)#(\* mark_debug = \"true\" \*)\1#g" 
-done < ..#constraints#marked_debug.txt
+    find $copiedDir -wholename $file | xargs sed -i "s/\(.*${sigType}.*${sigName}\)/(\* mark_debug = \"true\" \*)\1/g" 
+done < ../constraints/marked_debug.txt
diff --git a/fpga/generator/wally.tcl b/fpga/generator/wally.tcl
index b2597f60..45444d57 100644
--- a/fpga/generator/wally.tcl
+++ b/fpga/generator/wally.tcl
@@ -15,7 +15,7 @@ read_ip IP/xlnx_axi_clock_converter.srcs/sources_1/ip/xlnx_axi_clock_converter/x
 read_ip IP/xlnx_ddr4.srcs/sources_1/ip/xlnx_ddr4/xlnx_ddr4.xci
 
 
-read_verilog -sv [glob -type f ../../pipelined/src/*/*.sv ../../pipelined/src/*/*/*.sv]
+read_verilog -sv [glob -type f ../src/CopiedFiles_do_not_add_to_repo/*/*.sv ../src/CopiedFiles_do_not_add_to_repo/*/*/*.sv]
 read_verilog  {../src/fpgaTop.v}
 read_verilog -sv  [glob -type f ../src/sdc/*.sv]