diff --git a/tools/bed.sh b/tools/bed.sh
index 12039126c727a54e424422397182fc5459d885f0..6fae5216918dd2b567ecadd5b3160319e4a6c8f5 100755
--- a/tools/bed.sh
+++ b/tools/bed.sh
@@ -21,7 +21,7 @@ fi
 
 #generate the bspri code
 echo "Generating bspri"
-$SECURITY_TRANSFORMS_HOME/tools/spasm/spasm $aspri $bspri $TOP_LEVEL/a.ncexe $TOP_LEVEL/stratafier.o.exe $TOP_LEVEL/libstrata.so.symbols
+$SECURITY_TRANSFORMS_HOME/bin/spasm $aspri $bspri $TOP_LEVEL/a.ncexe $TOP_LEVEL/stratafier.o.exe $TOP_LEVEL/libstrata.so.symbols
 status=$?
 if [ ! $status -eq 0 ]; then
   echo "BED: spasm error -- spasm exited with non-zero status ($status)"
diff --git a/tools/bed_blackbox.sh b/tools/bed_blackbox.sh
index 067603b6b7489cceeaad37655a9c43f55916cf73..e09b4a4cd4b11609eeb63ab5c810c72048d1fd69 100755
--- a/tools/bed_blackbox.sh
+++ b/tools/bed_blackbox.sh
@@ -22,7 +22,7 @@ bspri=$3
 SCRIPT_NAME=$PEASOUP_DIR/manual_test_wrapper
 
 # generate the bspri code
-$SECURITY_TRANSFORMS_HOME/tools/spasm/spasm $aspri $bspri $PEASOUP_DIR/a.ncexe $PEASOUP_DIR/stratafier.o.exe $PEASOUP_DIR/libstrata.so.symbols 
+$SECURITY_TRANSFORMS_HOME/bin/spasm/spasm $aspri $bspri $PEASOUP_DIR/a.ncexe $PEASOUP_DIR/stratafier.o.exe $PEASOUP_DIR/libstrata.so.symbols 
 if [ ! $? -eq 0 ]; then
   echo "BED: spasm error -- exiting"
   exit 1
diff --git a/tools/bed_manual.sh b/tools/bed_manual.sh
index 598f526b6dcee4df869c5a3f0d674f438803cf4c..40e69a8bb523c0a3f82dc8186d26e64e643898d5 100755
--- a/tools/bed_manual.sh
+++ b/tools/bed_manual.sh
@@ -18,7 +18,7 @@ aspri=$2
 bspri=$3
 
 # generate the bspri code
-$SECURITY_TRANSFORMS_HOME/tools/spasm/spasm $aspri $bspri $PEASOUP_DIR/a.ncexe $PEASOUP_DIR/stratafier.o.exe $PEASOUP_DIR/libstrata.so.symbols
+$SECURITY_TRANSFORMS_HOME/bin/spasm $aspri $bspri $PEASOUP_DIR/a.ncexe $PEASOUP_DIR/stratafier.o.exe $PEASOUP_DIR/libstrata.so.symbols
 if [ ! $? -eq 0 ]; then
   echo "BED: spasm error -- exiting"
   exit 1
diff --git a/tools/cover.sh b/tools/cover.sh
index adb610e3a80346c5a912d9cb972d3eb72c8ecfc0..757d1eaad3c016632b3bd27bf4233476bce6a822 100755
--- a/tools/cover.sh
+++ b/tools/cover.sh
@@ -16,7 +16,7 @@ OUTPUT_BLACKLIST_FILE=$6        # output file with list of functions to blacklis
 CANDIDATE_FNS_PRE_LIBC=`dirname $6`/p1.candidates.prelibc
 
 
-$SECURITY_TRANSFORMS_HOME/tools/cover/cover $ORIGINAL_BINARY $ANNOTATION_FILE $EXECUTED_ADDRESS_FILE $OUTPUT_COVERAGE_FILE
+$SECURITY_TRANSFORMS_HOME/bin/cover $ORIGINAL_BINARY $ANNOTATION_FILE $EXECUTED_ADDRESS_FILE $OUTPUT_COVERAGE_FILE
 status=$?
 cp $FILTER_FILE $OUTPUT_BLACKLIST_FILE
 cat $OUTPUT_COVERAGE_FILE | cut -f1 -d" " > $CANDIDATE_FNS_PRE_LIBC
diff --git a/tools/db/pdb_register.sh b/tools/db/pdb_register.sh
index 526d4867dbae60e6d5b11f6e98cc84458833f4e4..898ef3e4d35a9483cbd66df4b5f3d8615a39e1c5 100755
--- a/tools/db/pdb_register.sh
+++ b/tools/db/pdb_register.sh
@@ -136,7 +136,7 @@ update_file_info()
 	create_table ${pn}_address ${pn}_function ${pn}_instruction ${pn}_icfs ${pn}_icfs_map ${pn}_relocs ${pn}_types
 
 	echo Importing $fn.annot into IRDB via meds2pdb 
-	$SECURITY_TRANSFORMS_HOME/tools/meds2pdb/meds2pdb ${fn}.annot ${fn}.infoannot $FILE_ID ${pn}_function ${pn}_instruction ${pn}_address ${pn}_types  $fn ${fn}.STARSxrefs || exit 1
+	$SECURITY_TRANSFORMS_HOME/bin/meds2pdb ${fn}.annot ${fn}.infoannot $FILE_ID ${pn}_function ${pn}_instruction ${pn}_address ${pn}_types  $fn ${fn}.STARSxrefs || exit 1
 }
 
 
diff --git a/tools/do_cinderella.sh b/tools/do_cinderella.sh
index 3c7321582cfb89d4e3105917b69f8dd698fcdf08..f8181bd5721cb0193616cb3e02455d8976d3d3ea 100755
--- a/tools/do_cinderella.sh
+++ b/tools/do_cinderella.sh
@@ -14,22 +14,22 @@ TMP=tmp.$$
 cinderella_malloc="cinderella::malloc"
 
 # infer CGC syscall wrappers
-echo "$SECURITY_TRANSFORMS_HOME/tools/cgclibc/infer_syscall_wrappers.exe $ORIG_VARIANT_ID"
-$SECURITY_TRANSFORMS_HOME/tools/cgclibc/infer_syscall_wrappers.exe $ORIG_VARIANT_ID 
+echo "$SECURITY_TRANSFORMS_HOME/bin/infer_syscall_wrappers.exe $ORIG_VARIANT_ID"
+$SECURITY_TRANSFORMS_HOME/bin/infer_syscall_wrappers.exe $ORIG_VARIANT_ID 
 
 # clone so that we work off a copy
-$SECURITY_TRANSFORMS_HOME/libIRDB/test/clone.exe $ORIG_VARIANT_ID clone.id
+$SECURITY_TRANSFORMS_HOME/bin/clone.exe $ORIG_VARIANT_ID clone.id
 cloneid=`cat clone.id`
 
 # prep the binary for testing
 #     pin all functions
 #     splice-in our testing loop into the target program
-$SECURITY_TRANSFORMS_HOME/tools/cinderella/cinderella_prep.exe $cloneid
+$SECURITY_TRANSFORMS_HOME/bin/cinderella_prep.exe $cloneid
 
 # get list of all functions in binary
 # for stripped binary, this will typically be of the form:
 #    sub_80004fde
-$SECURITY_TRANSFORMS_HOME/tools/cgclibc/display_functions.exe $cloneid | grep "^function" | cut -d' ' -f2 > cinderella.functions.all 
+$SECURITY_TRANSFORMS_HOME/bin/display_functions.exe $cloneid | grep "^function" | cut -d' ' -f2 > cinderella.functions.all 
 
 # produce a zipr'd version so that we can dynamically test behavior
 echo "cinderella: Produce zipr'ed test version: id: $cloneid"
@@ -64,8 +64,8 @@ do
 	if [ "$positive_id" = "1" ]; then
 		oldfn=`grep $fn cinderella.inferences.positive | cut -f4 -d' '`
 		newfn="cinderella::$fn"
-		echo "$SECURITY_TRANSFORMS_HOME/libIRDB/test/rename_function.exe $ORIG_VARIANT_ID $oldfn $newfn"
-		$SECURITY_TRANSFORMS_HOME/libIRDB/test/rename_function.exe $ORIG_VARIANT_ID $oldfn $newfn
+		echo "$SECURITY_TRANSFORMS_HOME/bin/rename_function.exe $ORIG_VARIANT_ID $oldfn $newfn"
+		$SECURITY_TRANSFORMS_HOME/bin/rename_function.exe $ORIG_VARIANT_ID $oldfn $newfn
 	fi
 done
 rm $TMP
@@ -79,7 +79,7 @@ rm $TMP
 #
 
 echo "CINDERELLA PASS1: simply intersect static + dynamic"
-$SECURITY_TRANSFORMS_HOME/tools/cgclibc/cgclibc.exe $ORIG_VARIANT_ID --positive-inferences cinderella.inferences.positive --negative-inferences cinderella.inferences.negative > cinderella.static.pass1
+$SECURITY_TRANSFORMS_HOME/bin/cgclibc.exe $ORIG_VARIANT_ID --positive-inferences cinderella.inferences.positive --negative-inferences cinderella.inferences.negative > cinderella.static.pass1
 count_malloc=`grep "^static positive malloc" cinderella.static.pass1 | wc -l`
 if [ "$count_malloc" = "0" ]; then
 	echo "No dynamic memory allocation in this program"
@@ -87,7 +87,7 @@ if [ "$count_malloc" = "0" ]; then
 elif [ "$count_malloc" = "1" ]; then
 	oldfn=`grep -i "positive malloc" cinderella.static.pass1 | cut -d' ' -f4` 
 	echo "CINDERELLA PASS1: rename detected malloc fn to cinderella::malloc"
-	$SECURITY_TRANSFORMS_HOME/libIRDB/test/rename_function.exe $ORIG_VARIANT_ID $oldfn $cinderella_malloc
+	$SECURITY_TRANSFORMS_HOME/bin/rename_function.exe $ORIG_VARIANT_ID $oldfn $cinderella_malloc
 	exit 0
 fi
 
@@ -107,14 +107,14 @@ fi
 #
 echo "CINDERELLA PASS2: intersect dynamic and static analyses for malloc / turn on --dominator"
 grep -i "positive malloc" cinderella.static.pass1 > $TMP
-$SECURITY_TRANSFORMS_HOME/tools/cgclibc/cgclibc.exe $ORIG_VARIANT_ID --positive-inferences $TMP --negative-inferences cinderella.inferences.negative --dominator > cinderella.static.pass2
+$SECURITY_TRANSFORMS_HOME/bin/cgclibc.exe $ORIG_VARIANT_ID --positive-inferences $TMP --negative-inferences cinderella.inferences.negative --dominator > cinderella.static.pass2
 count_malloc=`grep "^static positive malloc" cinderella.static.pass2 | wc -l`
 count_free=`grep "^static positive free" cinderella.static.pass2 | wc -l`
 
 if [ "$count_malloc" = "1" ]; then
 	oldfn=`grep -i "positive malloc" cinderella.static.pass2 | cut -d' ' -f4` 
 	echo "CINDERELLA PASS2: rename detected malloc fn to cinderella::malloc"
-	$SECURITY_TRANSFORMS_HOME/libIRDB/test/rename_function.exe $ORIG_VARIANT_ID $oldfn $cinderella_malloc
+	$SECURITY_TRANSFORMS_HOME/bin/rename_function.exe $ORIG_VARIANT_ID $oldfn $cinderella_malloc
 	exit 0
 fi
 
@@ -125,7 +125,7 @@ fi
 if [ "$count_malloc" != "1" ] || [ "$count_free" != "1" ] ; then
 	echo "CINDERELLA PASS3: with restrictions on malloc / turn on --dominator"
 	grep -i "positive malloc" cinderella.static.pass2 > $TMP
-	$SECURITY_TRANSFORMS_HOME/tools/cgclibc/cgclibc.exe $ORIG_VARIANT_ID --positive-inferences $TMP --negative-inferences cinderella.inferences.negative --dominator > cinderella.static.pass3
+	$SECURITY_TRANSFORMS_HOME/bin/cgclibc.exe $ORIG_VARIANT_ID --positive-inferences $TMP --negative-inferences cinderella.inferences.negative --dominator > cinderella.static.pass3
 	count_malloc=`grep "^static positive malloc" cinderella.static.pass3 | wc -l`
 	count_free=`grep "^static positive free" cinderella.static.pass3 | wc -l`
 fi
@@ -135,13 +135,13 @@ echo "CINDERELLA: PASS3: #mallocs: $count_malloc  #frees: $count_free"
 if [ "$count_malloc" = "1" ]; then
 	oldfn=`grep -i "positive malloc" cinderella.static.pass3 | cut -d' ' -f4` 
 	echo "CINDERELLA PASS3: rename detected malloc fn to cinderella::malloc"
-	$SECURITY_TRANSFORMS_HOME/libIRDB/test/rename_function.exe $ORIG_VARIANT_ID $oldfn $cinderella_malloc
+	$SECURITY_TRANSFORMS_HOME/bin/rename_function.exe $ORIG_VARIANT_ID $oldfn $cinderella_malloc
 	exit 0
 fi
 
 echo "CINDERELLA PASS3: with restrictions on malloc / turn on --dominator and --cluster"
 grep -i "positive malloc" cinderella.static.pass3 > $TMP
-$SECURITY_TRANSFORMS_HOME/tools/cgclibc/cgclibc.exe $ORIG_VARIANT_ID --positive-inferences $TMP --negative-inferences cinderella.inferences.negative --dominator --cluster > cinderella.static.pass4
+$SECURITY_TRANSFORMS_HOME/bin/cgclibc.exe $ORIG_VARIANT_ID --positive-inferences $TMP --negative-inferences cinderella.inferences.negative --dominator --cluster > cinderella.static.pass4
 count_malloc=`grep "^static positive malloc" cinderella.static.pass4 | wc -l`
 count_free=`grep "^static positive free" cinderella.static.pass4 | wc -l`
 
@@ -149,7 +149,7 @@ echo "CINDERELLA: PASS4: #mallocs: $count_malloc  #frees: $count_free"
 if [ "$count_malloc" = "1" ]; then
 	oldfn=`grep -i "positive malloc" cinderella.static.pass4 | cut -d' ' -f4` 
 	echo "CINDERELLA PASS4: rename detected malloc fn to cinderella::malloc"
-	$SECURITY_TRANSFORMS_HOME/libIRDB/test/rename_function.exe $ORIG_VARIANT_ID $oldfn $cinderella_malloc
+	$SECURITY_TRANSFORMS_HOME/bin/rename_function.exe $ORIG_VARIANT_ID $oldfn $cinderella_malloc
 	exit 0
 fi
 
diff --git a/tools/do_fptr_shadow.sh b/tools/do_fptr_shadow.sh
index 595df0bd45c603b753ee8f8452fedb5c320145d4..a87e987b7e5566e6fd31263e917bd99c241d667b 100755
--- a/tools/do_fptr_shadow.sh
+++ b/tools/do_fptr_shadow.sh
@@ -14,4 +14,4 @@ FPTR_ANNOT_FILE=a.ncexe.fptrannot
 cp /tmp/$FPTR_ANNOT_FILE .
 
 # weave-in calls to callback handlers for shadowing
-$SECURITY_TRANSFORMS_HOME/tools/fptr_shadow/fptr_shadow64.exe $CLONE_ID
+$SECURITY_TRANSFORMS_HOME/bin/fptr_shadow64.exe $CLONE_ID
diff --git a/tools/do_integertransform.sh b/tools/do_integertransform.sh
index 8bd7513d98530a61fbd8204d4c2723a1d89e0edf..ddfb8bd21b7c72d8db755f1caf8db1fd39b4aeff 100755
--- a/tools/do_integertransform.sh
+++ b/tools/do_integertransform.sh
@@ -90,5 +90,5 @@ if [ $? -eq 0 ]; then
 	$PEASOUP_HOME/tools/update_env_var.sh STRATA_MAX_WARNINGS 0
 fi
 
-echo "intxform: cmd: timeout $TIMEOUT $SECURITY_TRANSFORMS_HOME/tools/transforms/integertransformdriver.exe $CLONE_ID $LIBC_FILTER $INTEGER_WARNINGS_FILE $OPTIONS"
-timeout $TIMEOUT $SECURITY_TRANSFORMS_HOME/tools/transforms/integertransformdriver.exe $CLONE_ID $LIBC_FILTER $INTEGER_WARNINGS_FILE $OPTIONS
+echo "intxform: cmd: timeout $TIMEOUT $SECURITY_TRANSFORMS_HOME/bin/integertransformdriver.exe $CLONE_ID $LIBC_FILTER $INTEGER_WARNINGS_FILE $OPTIONS"
+timeout $TIMEOUT $SECURITY_TRANSFORMS_HOME/bin/integertransformdriver.exe $CLONE_ID $LIBC_FILTER $INTEGER_WARNINGS_FILE $OPTIONS
diff --git a/tools/do_p1transform.sh b/tools/do_p1transform.sh
index 90630ffc53f11761c3e8f8ad13366e08e30ee21d..e322f44f163d30a13f3c28cee2b0e7e31abb74d5 100755
--- a/tools/do_p1transform.sh
+++ b/tools/do_p1transform.sh
@@ -39,7 +39,7 @@ BLACK_LIST=$P1_DIR/p1.filtered_out        # list of functions to blacklist
 COVERAGE_FILE=$P1_DIR/p1.coverage
 P1THRESHOLD=0.75
 
-PN_BINARY=$SECURITY_TRANSFORMS_HOME/tools/transforms/p1transform.exe
+PN_BINARY=$SECURITY_TRANSFORMS_HOME/bin/p1transform.exe
 
 echo "P1: transforming binary: cloneid=$CLONE_ID bed_script=$BED_SCRIPT timeout_value=$TIMEOUT_VALUE options=$PN_OPTIONS"
 
@@ -271,10 +271,10 @@ mv tmp $EXECUTED_ADDRESSES_FINAL
 sort $EXECUTED_ADDRESSES_FINAL | uniq > tmp
 mv tmp $EXECUTED_ADDRESSES_CONCOLIC
 
-echo "$SECURITY_TRANSFORMS_HOME/tools/cover/cover $CLONE_ID $EXECUTED_ADDRESSES_FINAL $COVERAGE_FILE"
+echo "$SECURITY_TRANSFORMS_HOME/bin/cover $CLONE_ID $EXECUTED_ADDRESSES_FINAL $COVERAGE_FILE"
 # produce coverage file
 #$PEASOUP_HOME/tools/cover.sh $ORIGINAL_BINARY $MEDS_ANNOTATION_FILE $EXECUTED_ADDRESSES_FINAL $LIBC_FILTER $COVERAGE_FILE $BLACK_LIST
-$SECURITY_TRANSFORMS_HOME/tools/cover/cover $CLONE_ID $EXECUTED_ADDRESSES_FINAL $COVERAGE_FILE
+$SECURITY_TRANSFORMS_HOME/bin/cover $CLONE_ID $EXECUTED_ADDRESSES_FINAL $COVERAGE_FILE
 
 #just in case something went wrong, touch the coverage file. An empty coverage file is permissible, but a missing one will cause PN to crash
 
diff --git a/tools/do_rss.sh b/tools/do_rss.sh
index 22b9bb8b2cd3ee57df5aee2340ebdabd80a95eec..d83bc9391b81677404e6142e50a2b28ce851dbfa 100755
--- a/tools/do_rss.sh
+++ b/tools/do_rss.sh
@@ -8,7 +8,7 @@
 #
 # $PEASOUP_HOME/tools/update_env_var.sh STRATA_SHADOW_STACK 1
 
-$SECURITY_TRANSFORMS_HOME/tools/ret_shadow_stack/ret_shadow_stack.exe $*
+$SECURITY_TRANSFORMS_HOME/bin/ret_shadow_stack.exe $*
 
 
 
diff --git a/tools/intxform_detect_benign_fp.sh b/tools/intxform_detect_benign_fp.sh
index ac23960be76850e3ec53695fadd894c14395610a..b45fd7b213785cf5af7e5cd9eba59f0f80b6c747 100755
--- a/tools/intxform_detect_benign_fp.sh
+++ b/tools/intxform_detect_benign_fp.sh
@@ -37,16 +37,16 @@ else
 fi
 
 echo "intxform(detect-benign-fp): Clone program"
-$SECURITY_TRANSFORMS_HOME/libIRDB/test/clone.exe $CLONE_ID clone.id
+$SECURITY_TRANSFORMS_HOME/bin/clone.exe $CLONE_ID clone.id
 tempcloneid=`cat clone.id`
 
 echo "intxform(detect-benign-fp): Integer transform on cloned copy"
-$SECURITY_TRANSFORMS_HOME/tools/transforms/integertransformdriver.exe $tempcloneid $LIBC_FILTER $INTEGER_WARNINGS_FILE --warning
+$SECURITY_TRANSFORMS_HOME/bin/integertransformdriver.exe $tempcloneid $LIBC_FILTER $INTEGER_WARNINGS_FILE --warning
 
 # generate aspri, and assemble it to bspri
 echo "intxform(detect-benign-fp): Generate temporary aspri --> bspri for integer transform"
-$SECURITY_TRANSFORMS_HOME/libIRDB/test/generate_spri.exe $($PEASOUP_HOME/tools/is_so.sh a.ncexe) $tempcloneid $INTEGER_ASPRI
-$SECURITY_TRANSFORMS_HOME/tools/spasm/spasm $INTEGER_ASPRI $INTEGER_BSPRI a.ncexe stratafier.o.exe libstrata.so.symbols
+$SECURITY_TRANSFORMS_HOME/bin/generate_spri.exe $($PEASOUP_HOME/tools/is_so.sh a.ncexe) $tempcloneid $INTEGER_ASPRI
+$SECURITY_TRANSFORMS_HOME/bin/spasm $INTEGER_ASPRI $INTEGER_BSPRI a.ncexe stratafier.o.exe libstrata.so.symbols
 
 # generate script to run instrumented binary
 DETECTOR_BINARY=benignfp.detector
diff --git a/tools/manual_coverage_wrapper.sh b/tools/manual_coverage_wrapper.sh
index c96480cb58808522966d48e5b972c7b42689e69f..392197b51ac7670d050eb0c57c85c4d6acff63ef 100755
--- a/tools/manual_coverage_wrapper.sh
+++ b/tools/manual_coverage_wrapper.sh
@@ -14,7 +14,7 @@ TIMEOUT_VALUE=600
 PIN_BENCH=`pwd`/pin_bench
 COVERAGE_RESULTS_DIR=`pwd`/manual_coverage_results/
 ACCUMULATED_COVERAGE_FILE=$COVERAGE_RESULTS_DIR/manual_coverage_results.out
-COVER_SCRIPT=$SECURITY_TRANSFORMS_HOME/tools/cover/cover
+COVER_SCRIPT=$SECURITY_TRANSFORMS_HOME/bin/cover
 
 echo "manual coverage script"
 
diff --git a/tools/p1xform_v2.sh b/tools/p1xform_v2.sh
index fc88f3967e53701c91dfc202fbfa8c6fa7bc20b5..196bfb86d1213e1ad1d7ff18d5199f6e15b7fefb 100755
--- a/tools/p1xform_v2.sh
+++ b/tools/p1xform_v2.sh
@@ -14,7 +14,7 @@ bspri=$3
 P1_DIR=p1.xform/$fname
 
 #generate the bspri code
-$SECURITY_TRANSFORMS_HOME/tools/spasm/spasm $aspri $bspri $TOP_LEVEL/a.ncexe $TOP_LEVEL/stratafier.o.exe $TOP_LEVEL/libstrata.so.symbols
+$SECURITY_TRANSFORMS_HOME/bin/spasm $aspri $bspri $TOP_LEVEL/a.ncexe $TOP_LEVEL/stratafier.o.exe $TOP_LEVEL/libstrata.so.symbols
 
 if [ $? -ne 0 ]; then
 	echo "Spasm failure in performing validation"
diff --git a/tools/ps_analyze.sh b/tools/ps_analyze.sh
index 295178c3d3eea39732e4235647ee6380168452fb..2266a3ec602da4ba72a09e8be5733cd5b1098b53 100755
--- a/tools/ps_analyze.sh
+++ b/tools/ps_analyze.sh
@@ -799,12 +799,12 @@ if [ $record_stats -eq 1 ]; then
 fi
 
 # build basic IR
-perform_step fill_in_cfg mandatory $SECURITY_TRANSFORMS_HOME/libIRDB/test/fill_in_cfg.exe $varid	
-perform_step fill_in_safefr mandatory $SECURITY_TRANSFORMS_HOME/tools/safefr/fill_in_safefr.exe $varid 
-perform_step fill_in_indtargs mandatory $SECURITY_TRANSFORMS_HOME/libIRDB/test/fill_in_indtargs.exe $varid 
+perform_step fill_in_cfg mandatory $SECURITY_TRANSFORMS_HOME/bin/fill_in_cfg.exe $varid	
+perform_step fill_in_safefr mandatory $SECURITY_TRANSFORMS_HOME/bin/fill_in_safefr.exe $varid 
+perform_step fill_in_indtargs mandatory $SECURITY_TRANSFORMS_HOME/bin/fill_in_indtargs.exe $varid 
 
 # finally create a clone so we can do some transforms 
-perform_step clone mandatory $SECURITY_TRANSFORMS_HOME/libIRDB/test/clone.exe $varid clone.id
+perform_step clone mandatory $SECURITY_TRANSFORMS_HOME/bin/clone.exe $varid clone.id
 is_step_on clone
 if [ $? = 1 ]; then
 	cloneid=`cat clone.id`
@@ -817,9 +817,9 @@ if [ $? = 1 ]; then
 fi
 
 # do the basic tranforms we're performing for peasoup 
-perform_step fix_calls mandatory $SECURITY_TRANSFORMS_HOME/libIRDB/test/fix_calls.exe $cloneid	
+perform_step fix_calls mandatory $SECURITY_TRANSFORMS_HOME/bin/fix_calls.exe $cloneid	
 # look for strings in the binary 
-perform_step find_strings none $SECURITY_TRANSFORMS_HOME/libIRDB/test/find_strings.exe $cloneid
+perform_step find_strings none $SECURITY_TRANSFORMS_HOME/bin/find_strings.exe $cloneid
 
 #
 # analyze binary for string signatures
@@ -906,7 +906,7 @@ perform_step cinderella clone,fill_in_indtargs,fill_in_cfg $PEASOUP_HOME/tools/d
 #
 # For CGC, pad malloc
 #
-perform_step cgc_hlx cinderella $SECURITY_TRANSFORMS_HOME/tools/cgc_hlx/cgc_hlx.exe --varid=$cloneid $step_options_cgc_hlx
+perform_step cgc_hlx cinderella $SECURITY_TRANSFORMS_HOME/bin/cgc_hlx.exe --varid=$cloneid $step_options_cgc_hlx
 
 #
 # Function pointer shadowing
@@ -940,19 +940,19 @@ if [[ "$TWITCHER_HOME" != "" && -d "$TWITCHER_HOME" ]]; then
 fi
 
 # input filtering
-perform_step input_filtering clone,fill_in_indtargs,fill_in_cfg $SECURITY_TRANSFORMS_HOME/tools/watch_syscall/watch_syscall.exe  --varid $cloneid --do_input_filtering $step_options_input_filtering
+perform_step input_filtering clone,fill_in_indtargs,fill_in_cfg $SECURITY_TRANSFORMS_HOME/bin/watch_syscall.exe  --varid $cloneid --do_input_filtering $step_options_input_filtering
 
 # watch syscalls
-perform_step watch_allocate clone,fill_in_indtargs,fill_in_cfg,pdb_register $SECURITY_TRANSFORMS_HOME/tools/watch_syscall/watch_syscall.exe  --varid $cloneid --do_sandboxing $step_options_watch_allocate
+perform_step watch_allocate clone,fill_in_indtargs,fill_in_cfg,pdb_register $SECURITY_TRANSFORMS_HOME/bin/watch_syscall.exe  --varid $cloneid --do_sandboxing $step_options_watch_allocate
 
 # only do ILR for main objects that aren't relocatable.  reloc. objects 
 # are still buggy for ILR
 if [ $($PEASOUP_HOME/tools/is_so.sh a.ncexe) = 0 ]; then
-	perform_step ilr none $SECURITY_TRANSFORMS_HOME/libIRDB/test/ilr.exe $cloneid 
+	perform_step ilr none $SECURITY_TRANSFORMS_HOME/bin/ilr.exe $cloneid 
 fi
 
-perform_step selective_cfi none $SECURITY_TRANSFORMS_HOME/tools/selective_cfi/selective_cfi.exe $cloneid 
-perform_step simple_cdi none $SECURITY_TRANSFORMS_HOME/tools/simple_cdi/simple_cdi.exe $cloneid 
+perform_step selective_cfi none $SECURITY_TRANSFORMS_HOME/bin/selective_cfi.exe $cloneid 
+perform_step simple_cdi none $SECURITY_TRANSFORMS_HOME/bin/simple_cdi.exe $cloneid 
 
 # do plugins directory
 for i in $SECURITY_TRANSFORMS_HOME/plugins_install/*.exe $SECURITY_TRANSFORMS_HOME/plugins_install/*.sh;
@@ -965,14 +965,14 @@ do
 done
 
 # generate aspri, and assemble it to bspri
-perform_step generate_spri mandatory $SECURITY_TRANSFORMS_HOME/libIRDB/test/generate_spri.exe $($PEASOUP_HOME/tools/is_so.sh a.ncexe) $cloneid a.irdb.aspri
+perform_step generate_spri mandatory $SECURITY_TRANSFORMS_HOME/bin/generate_spri.exe $($PEASOUP_HOME/tools/is_so.sh a.ncexe) $cloneid a.irdb.aspri
 
 # hack to work with cgc file size restrictions.
 stratafier_file=`ls -1 *nostrip 2>/dev/null |head -1` 
 if [ "X$stratafier_file" = "X" ]; then 
 	stratafier_file=stratafier.o.exe
 fi
-perform_step spasm mandatory $SECURITY_TRANSFORMS_HOME/tools/spasm/spasm a.irdb.aspri a.irdb.bspri a.ncexe $stratafier_file libstrata.so.symbols 
+perform_step spasm mandatory $SECURITY_TRANSFORMS_HOME/bin/spasm a.irdb.aspri a.irdb.bspri a.ncexe $stratafier_file libstrata.so.symbols 
 
 perform_step fast_spri spasm $PEASOUP_HOME/tools/fast_spri.sh a.irdb.bspri a.irdb.fbspri