diff --git a/fuzzers/041-clk-hrow-pips/Makefile b/fuzzers/041-clk-hrow-pips/Makefile
index 3b9c8eae..5aa5450e 100644
--- a/fuzzers/041-clk-hrow-pips/Makefile
+++ b/fuzzers/041-clk-hrow-pips/Makefile
@@ -30,7 +30,7 @@ build/segbits_clk_hrow.rdb: $(SPECIMENS_OK)
 		$(shell find build -name segdata_clk_hrow_top_r.txt) \
 		$(shell find build -name segdata_clk_hrow_bot_r.txt)
 
-build/segbits_clk_hrow.db: build/segbits_clk_hrow.rdb $(XRAY_FUZZERS_DIR)/piplist/build/clk_hrow_bot_r.txt
+build/segbits_clk_hrow.db: build/segbits_clk_hrow.rdb $(XRAY_FUZZERS_DIR)/piplist/build/clk_hrow/clk_hrow_bot_r.txt
 	${XRAY_DBFIXUP} --db-root build --zero-db bits.dbf \
 		--seg-fn-in build/segbits_clk_hrow.rdb \
 		--seg-fn-out build/segbits_clk_hrow_rc.db
@@ -38,7 +38,7 @@ build/segbits_clk_hrow.db: build/segbits_clk_hrow.rdb $(XRAY_FUZZERS_DIR)/piplis
 	# Convert row/column into PIP definition.
 	python3 merge_clk_entries.py \
 		build/segbits_clk_hrow_rc.db \
-		$(XRAY_FUZZERS_DIR)/piplist/build/clk_hrow_bot_r.txt \
+		$(XRAY_FUZZERS_DIR)/piplist/build/clk_hrow/clk_hrow_bot_r.txt \
 		build/segbits_clk_hrow.db
 
 	# Keep a copy to track iter progress
diff --git a/fuzzers/050-pip-seed/Makefile b/fuzzers/050-pip-seed/Makefile
index 759b49d0..2dc96edd 100644
--- a/fuzzers/050-pip-seed/Makefile
+++ b/fuzzers/050-pip-seed/Makefile
@@ -1,25 +1,20 @@
+MAKETODO_FLAGS=--re ".*" --not-endswith ".VCC_WIRE"
 ifeq ($(QUICK),Y)
 N ?= 1
 SEGMATCH_FLAGS=
 else
+N ?= 48
 # Do relatively large batch to keep parallelism high
 # LCM between 12 (CPUs on my system) and 16, a common CPU count
-N ?= 48
 SEGMATCH_FLAGS=-m 15 -M 45
 endif
-# Driven by int_loop.sh
-ITER := 1
-MAKETODO_FLAGS=--re ".*" --not-endswith ".VCC_WIRE"
-PIPLIST_TCL=$(XRAY_FUZZERS_DIR)/piplist/piplist.tcl
-SPECIMENS := $(addprefix build/$(ITER)/specimen_,$(shell seq -f '%03.0f' $(N)))
-SPECIMENS_OK := $(addsuffix /OK,$(SPECIMENS))
-# Individual fuzzer directory, such as ~/prjxray/fuzzers/010-lutinit
-export FUZDIR=$(shell pwd)
+
+CHECK_ARGS=--max-iters 12 --min-progress 50
+
+include ../pip_loop.mk
 
 # Specimens from current run must complete, but previous iterations may exist
-database: build/database
-
-build/database: build/segbits_int_l.db build/segbits_int_r.db build/mask_clbll_l.db build/mask_clbll_r.db build/mask_clblm_l.db build/mask_clblm_r.db
+database: build/segbits_int_l.db build/segbits_int_r.db build/mask_clbll_l.db build/mask_clbll_r.db build/mask_clblm_l.db build/mask_clblm_r.db
 	# Keep a copy to track iter progress
 	# Also is pre-fixup, which drops and converts
 	cp build/segbits_int_l.db build/$(ITER)/segbits_int_l.db
@@ -27,26 +22,36 @@ build/database: build/segbits_int_l.db build/segbits_int_r.db build/mask_clbll_l
 # May be undersolved
 ifneq ($(QUICK),Y)
 	${XRAY_DBFIXUP} --db-root build --clb-int
+	# https://github.com/SymbiFlow/prjxray/issues/399
+	# Clobber existing .db to eliminate potential conflicts
+	cp ${XRAY_DATABASE_DIR}/${XRAY_DATABASE}/segbits*.db build/database/${XRAY_DATABASE}
+	XRAY_DATABASE_DIR=${FUZDIR}/build/database ${XRAY_MERGEDB} int_l build/segbits_int_l.db
+	XRAY_DATABASE_DIR=${FUZDIR}/build/database ${XRAY_MERGEDB} int_r build/segbits_int_r.db
 endif
-	touch build/database
 
 build/segbits_int_l.db: $(SPECIMENS_OK)
-	${XRAY_SEGMATCH} $(SEGMATCH_FLAGS) -o build/segbits_int_l.db $(shell find build -name segdata_int_l.txt |sort)
+	${XRAY_SEGMATCH} $(SEGMATCH_FLAGS) -o build/segbits_int_l.db \
+		$(shell find build -name segdata_int_l.txt |sort)
 
 build/segbits_int_r.db: $(SPECIMENS_OK)
-	${XRAY_SEGMATCH} $(SEGMATCH_FLAGS) -o build/segbits_int_r.db $(shell find build -name segdata_int_r.txt |sort)
+	${XRAY_SEGMATCH} $(SEGMATCH_FLAGS) -o build/segbits_int_r.db \
+		$(shell find build -name segdata_int_r.txt |sort)
 
 build/mask_clbll_l.db: $(SPECIMENS_OK)
-	${XRAY_MASKMERGE} build/mask_clbll_l.db $(shell find build -name segdata_int_l.txt |sort)
+	${XRAY_MASKMERGE} build/mask_clbll_l.db \
+		$(shell find build -name segdata_int_l.txt |sort)
 
 build/mask_clbll_r.db: $(SPECIMENS_OK)
-	${XRAY_MASKMERGE} build/mask_clbll_r.db $(shell find build -name segdata_int_r.txt |sort)
+	${XRAY_MASKMERGE} build/mask_clbll_r.db \
+		$(shell find build -name segdata_int_r.txt |sort)
 
 build/mask_clblm_l.db: $(SPECIMENS_OK)
-	${XRAY_MASKMERGE} build/mask_clblm_l.db $(shell find build -name segdata_int_l.txt |sort)
+	${XRAY_MASKMERGE} build/mask_clblm_l.db \
+		$(shell find build -name segdata_int_l.txt |sort)
 
 build/mask_clblm_r.db: $(SPECIMENS_OK)
-	${XRAY_MASKMERGE} build/mask_clblm_r.db $(shell find build -name segdata_int_r.txt |sort)
+	${XRAY_MASKMERGE} build/mask_clblm_r.db \
+		$(shell find build -name segdata_int_r.txt |sort)
 
 pushdb:
 	${XRAY_MERGEDB} int_l build/segbits_int_l.db
@@ -55,47 +60,3 @@ pushdb:
 	${XRAY_MERGEDB} mask_clbll_r build/mask_clbll_r.db
 	${XRAY_MERGEDB} mask_clblm_l build/mask_clblm_l.db
 	${XRAY_MERGEDB} mask_clblm_r build/mask_clblm_r.db
-
-$(SPECIMENS_OK): build/todo.txt
-	mkdir -p build/$(ITER)
-	bash generate.sh $(subst /OK,,$@)
-	touch $@
-
-$(XRAY_FUZZERS_DIR)/piplist/build/pips_int_l.txt: $(XRAY_FUZZERS_DIR)/piplist/piplist.tcl
-	mkdir -p $(XRAY_FUZZERS_DIR)/piplist/build
-	cd $(XRAY_FUZZERS_DIR)/piplist/build && ${XRAY_VIVADO} -mode batch -source $(PIPLIST_TCL)
-
-build/todo.txt: $(XRAY_FUZZERS_DIR)/piplist/build/pips_int_l.txt $(XRAY_DIR)/fuzzers/int_maketodo.py
-# Doesn't pushdb until very end. Compare against db so far
-	mkdir -p build/$(ITER)
-	python3 $(XRAY_DIR)/fuzzers/int_maketodo.py --db-dir build $(MAKETODO_FLAGS) |sort >build/todo_all.txt
-	cat build/todo_all.txt | sort -R > build/todo.txt.tmp
-	mv build/todo.txt.tmp build/todo.txt
-	# Per iter files
-	mkdir -p build/$(ITER)
-	cp build/todo_all.txt build/todo.txt build/$(ITER)/
-	# All in one dir for easier trending
-	mkdir -p build/todo
-	cp build/todo_all.txt build/todo/$(ITER)_all.txt
-
-# XXX: conider moving to script
-run:
-	$(MAKE) clean
-	# Because 056 cannot solve IMUX and LOGIC_OUTS, force zero entries for the
-	# LOGIC_OUTS or IMUX entries.
-	XRAY_DIR=${XRAY_DIR} MAKE="$(MAKE)" QUICK=$(QUICK) $(XRAY_DIR)/fuzzers/int_loop.sh \
-		--check-args "--max-iters 12 --min-progress 50"
-	touch run.ok
-
-clean:
-	rm -rf build run.ok todo
-
-# Remove iteration specific files, but keep piplist.tcl output
-cleaniter:
-	rm -rf build/$(ITER) build/todo.txt
-
-# Remove piplist build files in piplist directory
-cleanpiplist:
-	rm -rf $(XRAY_FUZZERS_DIR)/piplist/build
-
-.PHONY: database pushdb run clean cleaniter cleanpiplist
diff --git a/fuzzers/int_maketodo.py b/fuzzers/int_maketodo.py
index 8ed0774a..55e37aa8 100644
--- a/fuzzers/int_maketodo.py
+++ b/fuzzers/int_maketodo.py
@@ -100,7 +100,8 @@ def run(
             os.getenv("XRAY_DATABASE_DIR"), os.getenv("XRAY_DATABASE"))
 
     if pip_dir is None:
-        pip_dir = "%s/piplist/build" % (os.getenv("XRAY_FUZZERS_DIR"))
+        pip_dir = "%s/piplist/build/%s" % (
+            os.getenv("XRAY_FUZZERS_DIR"), pip_type)
 
     assert intre, "RE is required"
 
diff --git a/fuzzers/pip_loop.mk b/fuzzers/pip_loop.mk
index 6fad6d66..bd9d8b82 100644
--- a/fuzzers/pip_loop.mk
+++ b/fuzzers/pip_loop.mk
@@ -20,7 +20,7 @@ SPECIMENS_DEPS ?=
 
 # See int_loop_check.py
 # rempips took 35 iters once, so set 50 as a good start point
-CHECK_ARGS := --zero-entries --timeout-iters 50
+CHECK_ARGS ?= --zero-entries --timeout-iters 50
 SPECIMENS := $(addprefix build/$(ITER)/specimen_,$(shell seq -f '%03.0f' $(N)))
 SPECIMENS_OK := $(addsuffix /OK,$(SPECIMENS))
 # Individual fuzzer directory, such as ~/prjxray/fuzzers/010-lutinit
@@ -30,15 +30,19 @@ all: database
 
 $(SPECIMENS_OK): build/todo.txt $(SPECIMENS_DEPS)
 	mkdir -p build/$(ITER)
-	bash ${XRAY_DIR}/utils/top_generate.sh $(subst /OK,,$@)
+	if [ -f ${FUZDIR}/generate.sh ] ; then \
+			bash ${FUZDIR}/generate.sh $(subst /OK,,$@) ; \
+		else \
+			bash ${XRAY_DIR}/utils/top_generate.sh $(subst /OK,,$@) ; \
+		fi
 	touch $@
 
-$(XRAY_FUZZERS_DIR)/piplist/build/$(A_PIPLIST): $(PIPLIST_TCL)
-	mkdir -p $(XRAY_FUZZERS_DIR)/piplist/build
-	cd $(XRAY_FUZZERS_DIR)/piplist/build && ${XRAY_VIVADO} -mode batch -source $(PIPLIST_TCL)
+$(XRAY_FUZZERS_DIR)/piplist/build/$(PIP_TYPE)/$(A_PIPLIST): $(PIPLIST_TCL)
+	mkdir -p $(XRAY_FUZZERS_DIR)/piplist/build/$(PIP_TYPE)
+	cd $(XRAY_FUZZERS_DIR)/piplist/build/$(PIP_TYPE) && ${XRAY_VIVADO} -mode batch -source $(PIPLIST_TCL)
 
 # Used 1) to see if we are done 2) pips to try in generate.tcl
-build/todo.txt: $(XRAY_FUZZERS_DIR)/piplist/build/$(A_PIPLIST) $(XRAY_DIR)/fuzzers/int_maketodo.py build/database/seeded
+build/todo.txt: $(XRAY_FUZZERS_DIR)/piplist/build/$(PIP_TYPE)/$(A_PIPLIST) $(XRAY_DIR)/fuzzers/int_maketodo.py build/database/seeded
 	XRAY_DATABASE_DIR=${FUZDIR}/build/database \
 		python3 $(XRAY_DIR)/fuzzers/int_maketodo.py \
 		$(MAKETODO_FLAGS) |sort >build/todo_all.txt