diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 655f1e22..dd44795f 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -79,10 +79,10 @@ jobs:
           name: helioscli-artifacts
           path: ./HeliosCLI
       - name: Set execute permissions for test script
-        run: chmod +x ./runtests.sh
+        run: chmod +x ./run_tests.sh
         working-directory: tests
       - name: Run general tests
-        run: ./runtests.sh
+        run: ./run_tests.sh
         working-directory: tests
 
   embedded:
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index aed70e16..f88bbc24 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -37,10 +37,10 @@ jobs:
           name: helioscli-artifacts
           path: ./HeliosCLI
       - name: Set execute permissions for test script
-        run: chmod +x ./runtests.sh
+        run: chmod +x ./run_tests.sh
         working-directory: tests
       - name: Run general tests
-        run: ./runtests.sh
+        run: ./run_tests.sh
         working-directory: tests
 
   embedded:
diff --git a/HeliosCLI/Makefile b/HeliosCLI/Makefile
index e4d245c4..c5cb9cdb 100644
--- a/HeliosCLI/Makefile
+++ b/HeliosCLI/Makefile
@@ -34,6 +34,14 @@ ifneq ($(INCLUDES),)
     CFLAGS+=$(INCLUDES)
 endif
 
+# Architecture passed from parent Makefile (default to x64 if run standalone)
+ARCH ?= x64
+
+# Build and Output directories relative to this Makefile
+BUILD_DIR = $(ARCH)
+OUTPUT_DIR = output
+FINAL_TARGET = $(OUTPUT_DIR)/helios_cli
+
 # local NONSTANDARD libraries to link with
 # these MUST be exact filenames, cannot be -l syntax
 # for example:
@@ -59,13 +67,19 @@ else
         $(shell find . -type f -name '*.cpp')
 endif
 
-# object files are source files with .c replaced with .o
-OBJS=\
-	$(SRC:.cpp=.o) \
+# Separate source files by directory
+HELIOS_SRC = $(shell find ../Helios -type f -name '*.cpp')
+LOCAL_SRC = $(shell find . -type f -name '*.cpp')
 
-# dependency files are source files with .c replaced with .d
-DFILES=\
-	$(SRC:.cpp=.d) \
+# Generate object file paths using BUILD_DIR
+HELIOS_OBJS = $(patsubst ../Helios/%.cpp,$(BUILD_DIR)/Helios/%.o,$(HELIOS_SRC))
+LOCAL_OBJS = $(patsubst ./%.cpp,$(BUILD_DIR)/%.o,$(LOCAL_SRC))
+OBJS = $(HELIOS_OBJS) $(LOCAL_OBJS)
+
+# dependency files
+HELIOS_DFILES = $(patsubst ../Helios/%.cpp,$(BUILD_DIR)/Helios/%.d,$(HELIOS_SRC))
+LOCAL_DFILES = $(patsubst ./%.cpp,$(BUILD_DIR)/%.d,$(LOCAL_SRC))
+DFILES = $(HELIOS_DFILES) $(LOCAL_DFILES)
 
 # target dependencies
 # this includes any script generated c/h files,
@@ -87,12 +101,18 @@ all: $(TARGETS)
 # unit test target
 tests: $(TESTS)
 
-# target for vortex lib
+# target for helios cli
 helios: compute_version $(DEPS)
-	$(CC) $(CFLAGS) $(DEPS) -o $@ $(LLIBS)
+	@mkdir -p $(OUTPUT_DIR)
+	$(CC) $(CFLAGS) $(OBJS) -o $(FINAL_TARGET) $(LLIBS)
 
-# catch-all make target to generate .o and .d files
-%.o: %.cpp
+# Rules for building object files
+$(BUILD_DIR)/Helios/%.o: ../Helios/%.cpp
+	@mkdir -p $(dir $@)
+	$(CC) $(CFLAGS) -MMD -c $< -o $@
+
+$(BUILD_DIR)/%.o: ./%.cpp
+	@mkdir -p $(dir $@)
 	$(CC) $(CFLAGS) -MMD -c $< -o $@
 
 # catch-all for static libraries in the form of:
@@ -107,7 +127,8 @@ FORCE:
 
 # generic clean target
 clean:
-	@$(RM) $(DFILES) $(OBJS) $(TARGETS) $(TESTS)
+	@$(RM) -rf $(BUILD_DIR) $(OUTPUT_DIR)
+	@$(RM) -f $(DFILES) $(OBJS) $(TESTS)
 
 compute_version:
 	$(eval LATEST_TAG ?= $(shell git fetch --depth=1 origin +refs/tags/*:refs/tags/* &> /dev/null && git tag --list | sort -V | tail -n1))
@@ -121,18 +142,43 @@ compute_version:
 	$(eval HELIOS_BUILD_NUMBER := $(if $(HELIOS_BUILD_NUMBER),$(HELIOS_BUILD_NUMBER),0))
 	$(eval HELIOS_VERSION_NUMBER := $(HELIOS_VERSION_MAJOR).$(HELIOS_VERSION_MINOR).$(HELIOS_BUILD_NUMBER))
 
+# generate bmps
+bmps:
+	./PatternGenerator/generate_bmps.sh -c
+
 # generate svg
 svgs: bmps
-	./generate_svgs.sh
+	./PatternGenerator/generate_svgs.sh
 
 # generate pngs
 pngs: bmps
-	./generate_pngs.sh
+	./PatternGenerator/generate_pngs.sh
 
-# generate pngs
-bmps:
-	./generate_bmps.sh -c
+# record tests
+record_tests: all
+	../tests/record_tests.sh
+
+# record test
+record_test: all
+	../tests/record_test.sh
+
+# run tests
+run_tests: all
+	../tests/run_tests.sh
+
+# create_tests
+create_tests: all
+	../tests/create_test.sh
+
+# export tests
+export_tests: all
+	../tests/export_tests.sh
+
+# import tests
+import_tests: all
+	../tests/import_tests.sh
 
+# clean storage
 clean_storage:
 	@echo "Cleaning Helios storage file..."
 	@$(RM) Helios.storage
diff --git a/HeliosCLI/convert_bmp_to_png.py b/HeliosCLI/PatternGenerator/convert_bmp_to_png.py
similarity index 100%
rename from HeliosCLI/convert_bmp_to_png.py
rename to HeliosCLI/PatternGenerator/convert_bmp_to_png.py
diff --git a/HeliosCLI/convert_bmp_to_svg.py b/HeliosCLI/PatternGenerator/convert_bmp_to_svg.py
similarity index 100%
rename from HeliosCLI/convert_bmp_to_svg.py
rename to HeliosCLI/PatternGenerator/convert_bmp_to_svg.py
diff --git a/HeliosCLI/default_patterns/001_Lightside.pattern b/HeliosCLI/PatternGenerator/default_patterns/001_Lightside.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/001_Lightside.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/001_Lightside.pattern
diff --git a/HeliosCLI/default_patterns/002_Sauna.pattern b/HeliosCLI/PatternGenerator/default_patterns/002_Sauna.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/002_Sauna.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/002_Sauna.pattern
diff --git a/HeliosCLI/default_patterns/003_Butterfly.pattern b/HeliosCLI/PatternGenerator/default_patterns/003_Butterfly.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/003_Butterfly.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/003_Butterfly.pattern
diff --git a/HeliosCLI/default_patterns/004_Freezer_Burn.pattern b/HeliosCLI/PatternGenerator/default_patterns/004_Freezer_Burn.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/004_Freezer_Burn.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/004_Freezer_Burn.pattern
diff --git a/HeliosCLI/default_patterns/005_Ice_Blade.pattern b/HeliosCLI/PatternGenerator/default_patterns/005_Ice_Blade.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/005_Ice_Blade.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/005_Ice_Blade.pattern
diff --git a/HeliosCLI/default_patterns/006_Rainbow_Glitter.pattern b/HeliosCLI/PatternGenerator/default_patterns/006_Rainbow_Glitter.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/006_Rainbow_Glitter.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/006_Rainbow_Glitter.pattern
diff --git a/HeliosCLI/default_patterns/007_Ribbon.pattern b/HeliosCLI/PatternGenerator/default_patterns/007_Ribbon.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/007_Ribbon.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/007_Ribbon.pattern
diff --git a/HeliosCLI/default_patterns/008_Ultra_Dops.pattern b/HeliosCLI/PatternGenerator/default_patterns/008_Ultra_Dops.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/008_Ultra_Dops.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/008_Ultra_Dops.pattern
diff --git a/HeliosCLI/default_patterns/009_Dops.pattern b/HeliosCLI/PatternGenerator/default_patterns/009_Dops.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/009_Dops.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/009_Dops.pattern
diff --git a/HeliosCLI/default_patterns/010_Strobe.pattern b/HeliosCLI/PatternGenerator/default_patterns/010_Strobe.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/010_Strobe.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/010_Strobe.pattern
diff --git a/HeliosCLI/default_patterns/011_Hypnostrobe.pattern b/HeliosCLI/PatternGenerator/default_patterns/011_Hypnostrobe.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/011_Hypnostrobe.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/011_Hypnostrobe.pattern
diff --git a/HeliosCLI/default_patterns/012_Strobie.pattern b/HeliosCLI/PatternGenerator/default_patterns/012_Strobie.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/012_Strobie.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/012_Strobie.pattern
diff --git a/HeliosCLI/default_patterns/013_Razor.pattern b/HeliosCLI/PatternGenerator/default_patterns/013_Razor.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/013_Razor.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/013_Razor.pattern
diff --git a/HeliosCLI/default_patterns/014_Flare.pattern b/HeliosCLI/PatternGenerator/default_patterns/014_Flare.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/014_Flare.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/014_Flare.pattern
diff --git a/HeliosCLI/default_patterns/015_Burst.pattern b/HeliosCLI/PatternGenerator/default_patterns/015_Burst.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/015_Burst.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/015_Burst.pattern
diff --git a/HeliosCLI/default_patterns/016_Glow.pattern b/HeliosCLI/PatternGenerator/default_patterns/016_Glow.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/016_Glow.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/016_Glow.pattern
diff --git a/HeliosCLI/default_patterns/017_Flicker.pattern b/HeliosCLI/PatternGenerator/default_patterns/017_Flicker.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/017_Flicker.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/017_Flicker.pattern
diff --git a/HeliosCLI/default_patterns/018_Flash.pattern b/HeliosCLI/PatternGenerator/default_patterns/018_Flash.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/018_Flash.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/018_Flash.pattern
diff --git a/HeliosCLI/default_patterns/019_Morph.pattern b/HeliosCLI/PatternGenerator/default_patterns/019_Morph.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/019_Morph.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/019_Morph.pattern
diff --git a/HeliosCLI/default_patterns/020_Morph_Strobe.pattern b/HeliosCLI/PatternGenerator/default_patterns/020_Morph_Strobe.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/020_Morph_Strobe.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/020_Morph_Strobe.pattern
diff --git a/HeliosCLI/default_patterns/021_Morph_Strobie.pattern b/HeliosCLI/PatternGenerator/default_patterns/021_Morph_Strobie.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/021_Morph_Strobie.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/021_Morph_Strobie.pattern
diff --git a/HeliosCLI/default_patterns/022_Morph_Glow.pattern b/HeliosCLI/PatternGenerator/default_patterns/022_Morph_Glow.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/022_Morph_Glow.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/022_Morph_Glow.pattern
diff --git a/HeliosCLI/default_patterns/023_Dash_Dops.pattern b/HeliosCLI/PatternGenerator/default_patterns/023_Dash_Dops.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/023_Dash_Dops.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/023_Dash_Dops.pattern
diff --git a/HeliosCLI/default_patterns/024_Dash_Dot.pattern b/HeliosCLI/PatternGenerator/default_patterns/024_Dash_Dot.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/024_Dash_Dot.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/024_Dash_Dot.pattern
diff --git a/HeliosCLI/default_patterns/025_Wave_Particle.pattern b/HeliosCLI/PatternGenerator/default_patterns/025_Wave_Particle.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/025_Wave_Particle.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/025_Wave_Particle.pattern
diff --git a/HeliosCLI/default_patterns/026_Lightspeed.pattern b/HeliosCLI/PatternGenerator/default_patterns/026_Lightspeed.pattern
similarity index 100%
rename from HeliosCLI/default_patterns/026_Lightspeed.pattern
rename to HeliosCLI/PatternGenerator/default_patterns/026_Lightspeed.pattern
diff --git a/HeliosCLI/generate_bmps.sh b/HeliosCLI/PatternGenerator/generate_bmps.sh
similarity index 100%
rename from HeliosCLI/generate_bmps.sh
rename to HeliosCLI/PatternGenerator/generate_bmps.sh
diff --git a/HeliosCLI/generate_pngs.sh b/HeliosCLI/PatternGenerator/generate_pngs.sh
similarity index 100%
rename from HeliosCLI/generate_pngs.sh
rename to HeliosCLI/PatternGenerator/generate_pngs.sh
diff --git a/HeliosCLI/generate_svgs.sh b/HeliosCLI/PatternGenerator/generate_svgs.sh
similarity index 100%
rename from HeliosCLI/generate_svgs.sh
rename to HeliosCLI/PatternGenerator/generate_svgs.sh
diff --git a/HeliosEmbedded/Makefile b/HeliosEmbedded/Makefile
index 41308e34..dacd0cda 100644
--- a/HeliosEmbedded/Makefile
+++ b/HeliosEmbedded/Makefile
@@ -141,18 +141,33 @@ CFLAGS+=$(INCLUDES)
 ### SOURCE FILES ######
 #######################
 
+# Architecture passed from parent Makefile (default to avr if run standalone)
+ARCH ?= avr
+
+# Build and Output directories relative to this Makefile
+BUILD_DIR = $(ARCH)
+LOCAL_OUTPUT_DIR = output
+
 # Source files
 ifeq ($(OS),Windows_NT) # Windows
-SRCS = \
-       $(shell find ../Helios -maxdepth 1 -type f -name '\*.cpp') main.cpp
-else # linux
-SRCS = \
-       $(shell find ../Helios -maxdepth 1 -type f -name \*.cpp) main.cpp
+HELIOS_SRCS = \
+       $(shell find ../Helios -maxdepth 1 -type f -name '\*.cpp')
+LOCAL_SRCS = main.cpp
+else # linux/macos
+HELIOS_SRCS = \
+       $(shell find ../Helios -maxdepth 1 -type f -name \*.cpp)
+LOCAL_SRCS = main.cpp
 endif
 
-OBJS = $(SRCS:.cpp=.o)
+# Generate object file paths using BUILD_DIR
+HELIOS_OBJS = $(patsubst ../Helios/%.cpp,$(BUILD_DIR)/Helios/%.o,$(HELIOS_SRCS))
+LOCAL_OBJS = $(patsubst %.cpp,$(BUILD_DIR)/%.o,$(LOCAL_SRCS))
+OBJS = $(HELIOS_OBJS) $(LOCAL_OBJS)
 
-DFILES = $(SRCS:.cpp=.d)
+# Generate dependency file paths
+HELIOS_DFILES = $(patsubst ../Helios/%.cpp,$(BUILD_DIR)/Helios/%.d,$(HELIOS_SRCS))
+LOCAL_DFILES = $(patsubst %.cpp,$(BUILD_DIR)/%.d,$(LOCAL_SRCS))
+DFILES = $(HELIOS_DFILES) $(LOCAL_DFILES)
 
 #######################
 ### BUILD TARGETS #####
@@ -161,30 +176,50 @@ DFILES = $(SRCS:.cpp=.d)
 # Target name
 TARGET = helios
 
-all: compute_version $(TARGET).hex
+# Define final hex target (still goes to root output)
+ROOT_OUTPUT_DIR = ../output # This needs to stay for the root makefile to copy
+FINAL_HEX_TARGET = $(ROOT_OUTPUT_DIR)/helios_firmware.hex # Keep final target name
+
+# Define targets for intermediate files in local output
+LOCAL_ELF_TARGET = $(LOCAL_OUTPUT_DIR)/$(TARGET).elf
+LOCAL_BIN_TARGET = $(LOCAL_OUTPUT_DIR)/$(TARGET).bin
+LOCAL_EEP_TARGET = $(LOCAL_OUTPUT_DIR)/$(TARGET).eep
+LOCAL_LST_TARGET = $(LOCAL_OUTPUT_DIR)/$(TARGET).lst
+LOCAL_MAP_TARGET = $(LOCAL_OUTPUT_DIR)/$(TARGET).map
+
+all: compute_version $(FINAL_HEX_TARGET)
 	@echo Detected Operating System: $(OS)
-	$(OBJDUMP) --disassemble --source --line-numbers --demangle --section=.text $(TARGET).elf > $(TARGET).lst
-	$(NM) --numeric-sort --line-numbers --demangle --print-size --format=s $(TARGET).elf > $(TARGET).map
+	$(OBJDUMP) --disassemble --source --line-numbers --demangle --section=.text $(LOCAL_ELF_TARGET) > $(LOCAL_LST_TARGET)
+	$(NM) --numeric-sort --line-numbers --demangle --print-size --format=s $(LOCAL_ELF_TARGET) > $(LOCAL_MAP_TARGET)
 	chmod +x avrsize.sh
-	./avrsize.sh $(TARGET).elf
+	./avrsize.sh $(LOCAL_ELF_TARGET)
 	@echo "== Success building Helios v$(HELIOS_VERSION_NUMBER) =="
 
-$(TARGET).hex: $(TARGET).elf
-	$(OBJCOPY) -O binary -R .eeprom $(TARGET).elf $(TARGET).bin
-	$(OBJCOPY) -O ihex -j .eeprom --set-section-flags=.eeprom=alloc,load --no-change-warnings --change-section-lma .eeprom=0 $(TARGET).elf $(TARGET).eep
-	$(OBJCOPY) -O ihex -R .eeprom $< $@
+$(FINAL_HEX_TARGET): $(LOCAL_ELF_TARGET)
+	@mkdir -p $(dir $@)
+	@mkdir -p $(LOCAL_OUTPUT_DIR)
+	$(OBJCOPY) -O binary -R .eeprom $< $(LOCAL_BIN_TARGET)
+	$(OBJCOPY) -O ihex -j .eeprom --set-section-flags=.eeprom=alloc,load --no-change-warnings --change-section-lma .eeprom=0 $< $(LOCAL_EEP_TARGET)
+	$(OBJCOPY) -O ihex -R .eeprom $< ../output/helios_firmware.hex
+	@echo "Created final hex: ../output/helios_firmware.hex"
 
-$(TARGET).elf: compute_version $(OBJS)
+$(LOCAL_ELF_TARGET): compute_version $(OBJS)
+	@mkdir -p $(dir $@)
 	$(LD) $(LDFLAGS) $(OBJS) -o $@
 
-%.o: %.S
-	$(CC) $(ASMFLAGS) -c $< -o $@
+# Rules for building object files
+$(BUILD_DIR)/Helios/%.o: ../Helios/%.cpp
+	@mkdir -p $(dir $@)
+	$(CC) $(CFLAGS) -c $< -o $@
+	$(CC) $(CFLAGS) -MM -MT "$@" -MF "$(BUILD_DIR)/Helios/$*.d" $<
 
-%.o: %.cpp
+$(BUILD_DIR)/%.o: %.cpp
+	@mkdir -p $(dir $@)
 	$(CC) $(CFLAGS) -c $< -o $@
+	$(CC) $(CFLAGS) -MM -MT "$@" -MF "$(BUILD_DIR)/$*.d" $<
 
-upload: set_fuses $(TARGET).hex
-	$(AVRDUDE) $(AVRDUDE_FLAGS) -Uflash:w:$(TARGET).hex:i
+upload: set_fuses $(FINAL_HEX_TARGET)
+	$(AVRDUDE) $(AVRDUDE_FLAGS) -Uflash:w:$(FINAL_HEX_TARGET):i
 
 #######################
 ### LINUX SETUP #######
@@ -284,7 +319,11 @@ extract_hex: helios_firmware.hex
 #####################
 
 clean:
-	rm -f $(OBJS) $(TARGET).elf $(TARGET).hex $(DFILES) $(TARGET).bin $(TARGET).eep $(TARGET).lst $(TARGET).map
+	@echo "Cleaning up HeliosEmbedded..."
+	@$(RM) -rf $(BUILD_DIR) $(LOCAL_OUTPUT_DIR)
+	@$(RM) -f $(OBJS) $(DFILES) # Keep FINAL_HEX_TARGET out of here, root cleans it
+	@$(RM) -f *.d ../Helios/*.d
+	@echo "Cleaned HeliosEmbedded!"
 
 compute_version:
 	$(eval LATEST_TAG ?= $(shell git fetch --depth=1 origin +refs/tags/*:refs/tags/* &> /dev/null && git tag --list | sort -V | tail -n1))
diff --git a/HeliosLib/Makefile b/HeliosLib/Makefile
index 97eacfe6..cf8299dc 100644
--- a/HeliosLib/Makefile
+++ b/HeliosLib/Makefile
@@ -66,25 +66,36 @@ LLIBS=\
 LIBS=\
 	$(LLIBS) \
 
+# Architecture passed from parent Makefile (default to x64 if run standalone)
+ARCH ?= x64
+
+# Build and Output directories relative to this Makefile
+BUILD_DIR = $(ARCH)
+OUTPUT_DIR = output
+FINAL_LIB_TARGET = $(OUTPUT_DIR)/helios_lib.a
+FINAL_WASM_TARGET = $(OUTPUT_DIR)/helios_wasm.js
+FINAL_WASM_BIN_TARGET = $(OUTPUT_DIR)/helios_wasm.wasm
+
 # source files
-# local source files first, other sources after
 ifeq ($(OS),Windows_NT)
-    SRC = $(shell find ../Helios/ -type f -name \\*.cpp) HeliosLib.cpp
+    HELIOS_SRC = $(shell find ../Helios/ -type f -name \\*.cpp)
+    LOCAL_SRC = HeliosLib.cpp
 else
-    SRC = $(shell find ../Helios/ -type f -name '*.cpp') HeliosLib.cpp
+    HELIOS_SRC = $(shell find ../Helios/ -type f -name '*.cpp')
+    LOCAL_SRC = HeliosLib.cpp
 endif
 
-# object files are source files with .c replaced with .o
-OBJS=\
-	$(SRC:.cpp=.o) \
+# Generate object file paths using BUILD_DIR
+HELIOS_OBJS = $(patsubst ../Helios/%.cpp,$(BUILD_DIR)/Helios/%.o,$(HELIOS_SRC))
+LOCAL_OBJS = $(patsubst %.cpp,$(BUILD_DIR)/%.o,$(LOCAL_SRC))
+OBJS = $(HELIOS_OBJS) $(LOCAL_OBJS)
 
-# dependency files are source files with .c replaced with .d
-DFILES=\
-	$(SRC:.cpp=.d) \
+# Generate dependency file paths
+HELIOS_DFILES = $(patsubst ../Helios/%.cpp,$(BUILD_DIR)/Helios/%.d,$(HELIOS_SRC))
+LOCAL_DFILES = $(patsubst %.cpp,$(BUILD_DIR)/%.d,$(LOCAL_SRC))
+DFILES = $(HELIOS_DFILES) $(LOCAL_DFILES)
 
 # target dependencies
-# this includes any script generated c/h files,
-# the $(LLIBS) list, and the $(OBJS) list
 DEPS=\
 	$(LLIBS) \
 	$(OBJS) \
@@ -94,10 +105,9 @@ TESTS=\
 
 # target files
 ifdef WASM
-TARGETS=HeliosLib.js \
-	helios.a
+TARGETS=$(FINAL_WASM_TARGET) $(FINAL_LIB_TARGET)
 else
-TARGETS=helios.a
+TARGETS=$(FINAL_LIB_TARGET)
 endif
 
 # Default target for 'make' command
@@ -108,25 +118,45 @@ tests: $(TESTS)
 
 # force sub-build of wasm
 wasm: FORCE
-	env WASM=1 $(MAKE)
+	@if command -v em++; then \
+		echo "WebAssembly compiler found, building WASM..."; \
+		env ARCH=wasm WASM=1 $(MAKE) $(FINAL_WASM_TARGET) $(FINAL_LIB_TARGET); \
+	else \
+		echo "WebAssembly compiler (em++) not found, skipping WASM build."; \
+		mkdir -p $(OUTPUT_DIR); \
+		touch $(FINAL_WASM_TARGET); \
+		touch $(FINAL_WASM_BIN_TARGET); \
+	fi
 
 # target for helios lib
-helios.a: compute_version $(DEPS)
+$(FINAL_LIB_TARGET): compute_version $(DEPS)
+	@mkdir -p $(dir $@)
 	$(AR) $@ $(DEPS)
+	@echo "Created $@"
 
-HeliosLib.js: compute_version $(DEPS)
+# target for HeliosLib.js
+$(FINAL_WASM_TARGET): compute_version $(DEPS)
+	@mkdir -p $(dir $@)
 	$(CC) $(LDFLAGS) $(DEPS) -o $@ $(LLIBS)
 
-# catch-all make target to generate .o and .d files
-%.o: %.cpp
+# Rules for building object files
+$(BUILD_DIR)/Helios/%.o: ../Helios/%.cpp
+	@mkdir -p $(dir $@)
+	$(CC) $(CFLAGS) -MMD -c $< -o $@
+
+$(BUILD_DIR)/%.o: %.cpp
+	@mkdir -p $(dir $@)
 	$(CC) $(CFLAGS) -MMD -c $< -o $@
 
-# Empty rule that forces %.a to run all the time
+# Empty rule that forces .a to run all the time
 FORCE:
 
 # generic clean target
 clean:
-	@$(RM) $(DFILES) $(OBJS) $(TARGETS) $(TESTS) HeliosLib.js HeliosLib.wasm
+	@echo "Cleaning up HeliosLib..."
+	@$(RM) -rf $(BUILD_DIR) $(OUTPUT_DIR)
+	@$(RM) -f $(DFILES) $(OBJS) $(TESTS) HeliosLib.js HeliosLib.wasm # Remove old possible output names
+	@echo "Cleaned HeliosLib!"
 
 compute_version:
 	$(eval LATEST_TAG ?= $(shell git fetch --depth=1 origin +refs/tags/*:refs/tags/* &> /dev/null && git tag --list | sort -V | tail -n1))
diff --git a/Makefile b/Makefile
new file mode 100644
index 00000000..48d17320
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,142 @@
+# Unified Makefile for Helios Engine
+# This Makefile runs commands in subdirectories
+
+# List all make targets which are not filenames
+.PHONY: all clean lib cli embedded tests wasm docs help package setup_root_output
+
+# Directories containing Makefiles
+HELIOS_LIB_DIR = HeliosLib
+HELIOS_CLI_DIR = HeliosCLI
+HELIOS_EMBEDDED_DIR = HeliosEmbedded
+
+# Root output directory for aggregated artifacts
+ROOT_OUTPUT_DIR = output
+
+# Setup root output directory
+setup_root_output:
+	@echo "Setting up root output directory..."
+	@mkdir -p $(ROOT_OUTPUT_DIR)
+
+# Default target - Build the embedded version
+embedded: setup_root_output
+	@echo "Building Helios Embedded..."
+	@$(MAKE) -C $(HELIOS_EMBEDDED_DIR) ARCH=avr
+
+# CLI builds lib implicitly
+cli: setup_root_output
+	@echo "Building Helios CLI..."
+	@$(MAKE) -C $(HELIOS_CLI_DIR) ARCH=x64
+	@cp $(HELIOS_CLI_DIR)/output/helios_cli $(ROOT_OUTPUT_DIR)/
+
+# Build everything (truly "all") - but build them separately
+all:
+	@echo "Building all components..."
+	@$(MAKE) embedded
+	@$(MAKE) cli
+	@$(MAKE) lib
+	@$(MAKE) wasm
+	@echo "All components built successfully"
+
+# Build the Helios library
+lib: setup_root_output
+	@echo "Building Helios library..."
+	@$(MAKE) -C $(HELIOS_LIB_DIR) ARCH=x64
+	@cp $(HELIOS_LIB_DIR)/output/helios_lib.a $(ROOT_OUTPUT_DIR)/
+
+# Build WebAssembly version - HeliosLib will check for compiler availability
+wasm: setup_root_output
+	@echo "Building WebAssembly library..."
+	@$(MAKE) -C $(HELIOS_LIB_DIR) wasm ARCH=wasm
+	@cp -f $(HELIOS_LIB_DIR)/output/helios_wasm.js $(ROOT_OUTPUT_DIR)/ 2>/dev/null || true
+	@cp -f $(HELIOS_LIB_DIR)/output/helios_wasm.wasm $(ROOT_OUTPUT_DIR)/ 2>/dev/null || true
+
+# Upload embedded firmware
+upload:
+	@echo "Uploading firmware to device..."
+	@$(MAKE) -C $(HELIOS_EMBEDDED_DIR) upload
+
+# Generate PNGs for documentation
+svgs:
+	@echo "Generating PNG files..."
+	@$(MAKE) -C $(HELIOS_CLI_DIR) svgs
+	@mkdir -p ./assets
+	@cp $(HELIOS_CLI_DIR)/*.png ./assets/
+
+# Run tests
+run_tests: cli
+	@echo "Running tests for Helios CLI..."
+	@$(MAKE) -C $(HELIOS_CLI_DIR) run_tests
+
+record_tests: cli
+	@echo "Recording tests for Helios CLI..."
+	@$(MAKE) -C $(HELIOS_CLI_DIR) record_tests
+
+create_tests: cli
+	@echo "Creating tests for Helios CLI..."
+	@$(MAKE) -C $(HELIOS_CLI_DIR) create_tests
+
+export_tests: cli
+	@echo "Exporting tests for Helios CLI..."
+	@$(MAKE) -C $(HELIOS_CLI_DIR) export_tests
+
+import_tests: cli
+	@echo "Importing tests for Helios CLI..."
+	@$(MAKE) -C $(HELIOS_CLI_DIR) import_tests
+
+# Clean all build artifacts and storage files
+clean:
+	@echo "Cleaning Helios library..."
+	@$(MAKE) -C $(HELIOS_LIB_DIR) clean
+	@echo "Cleaning Helios CLI..."
+	@$(MAKE) -C $(HELIOS_CLI_DIR) clean
+	@echo "Cleaning Helios Embedded..."
+	@$(MAKE) -C $(HELIOS_EMBEDDED_DIR) clean
+	@echo "Cleaning storage files..."
+	@$(MAKE) -C $(HELIOS_CLI_DIR) clean_storage
+	@echo "Cleaning root directories..."
+	@rm -rf assets helios_package helios_package.zip $(ROOT_OUTPUT_DIR)
+
+# Package all compiled binaries into a zip file
+package:
+	@echo "Packaging Helios binaries..."
+	@$(MAKE) all
+	@mkdir -p helios_package
+	@cp $(ROOT_OUTPUT_DIR)/* helios_package/ 2>/dev/null || true
+	@cp -r assets helios_package/ 2>/dev/null || true
+	@zip -r helios_package.zip helios_package
+	@rm -rf helios_package
+	@echo "Package created: helios_package.zip"
+
+# Help information
+help:
+	@echo "Helios Engine Unified Build System"
+	@echo ""
+	@echo "Available targets:"
+	@echo "  embedded       - default, Build embedded firmware (output in HeliosEmbedded/output & ./output)"
+	@echo "  cli            - Build CLI tool (output in HeliosCLI/output & ./output)"
+	@echo "  all            - Build everything (outputs in component dirs & ./output)"
+	@echo "  lib            - Build library (output in HeliosLib/output & ./output)"
+	@echo "  wasm           - Build WebAssembly (output in HeliosLib/output & ./output)"
+	@echo "  upload         - Upload firmware from HeliosEmbedded/output/helios_firmware.hex"
+	@echo "  run_tests      - Run all tests"
+	@echo "  record_tests   - Record test outputs"
+	@echo "  create_tests   - Create a new test interactively"
+	@echo "  export_tests   - Export tests to CSV"
+	@echo "  import_tests   - Import tests from CSV"
+	@echo "  svgs           - Generate SVG documentation files"
+	@echo "  clean          - Clean all build artifacts, output files, and storage files"
+	@echo "  package        - Build all components and package ./output/* into a zip file"
+	@echo "  help           - Show this help information"
+
+# Important note for component Makefiles:
+# To compile with the correct architecture settings and object file location,
+# the following environment variables need to be used in the component Makefiles:
+#
+# 1. ARCH     - Target architecture (avr, x64, wasm)
+# 2. BUILD_DIR - Location for object files
+#
+# Object files should then be written to $(BUILD_DIR)/*.o instead of
+# in the source directories. Source files in shared directories like
+# ../Helios should create corresponding directories in $(BUILD_DIR).
+#
+# Example: ../Helios/Timer.cpp → $(BUILD_DIR)/Helios/Timer.o
\ No newline at end of file
diff --git a/tests/README.md b/tests/README.md
index 54dcbd67..f12ff3a5 100644
--- a/tests/README.md
+++ b/tests/README.md
@@ -18,17 +18,17 @@ Tests are located in the `tests/` directory and are organized as individual `.te
 To run the tests:
 
 1. Navigate to the `tests/` directory.
-2. Run the `runtests.sh` script:
+2. Run the `run_tests.sh` script:
 
 ```bash
-./runtests.sh
+./run_tests.sh
 ```
 
 This script will execute all available tests and report the results.
 
 ### Test Options
 
-The `runtests.sh` script supports several options:
+The `run_tests.sh` script supports several options:
 
 - `-v`: Verbose mode. Provides more detailed output during test execution.
 - `-n`: No-make mode. Skips rebuilding the Helios executable before running tests.
@@ -39,7 +39,7 @@ The `runtests.sh` script supports several options:
 Example usage:
 
 ```bash
-./runtests.sh -v -t=5
+./run_tests.sh -v -t=5
 ```
 
 This command runs test number 5 in verbose mode.
@@ -139,7 +139,7 @@ By following these guidelines, you can create a robust test suite that helps mai
 The project includes scripts for recording and replaying test scenarios:
 
 - `record_test.sh`: Records a single test case.
-- `recordtests.sh`: Records multiple test cases.
+- `record_tests.sh`: Records multiple test cases.
 
 #### Recording a Single Test
 
@@ -156,13 +156,13 @@ This script will prompt you to enter test commands, a description, and any neces
 To record multiple tests:
 
 1. Navigate to the `tests/` directory.
-2. Run the `recordtests.sh` script:
+2. Run the `record_tests.sh` script:
 
 ```bash
-./recordtests.sh [options]
+./record_tests.sh [options]
 ```
 
-The `recordtests.sh` script supports the following options:
+The `record_tests.sh` script supports the following options:
 
 - `-q`: Quiet mode. Reduces output verbosity.
 - `-v`: Validate mode. Performs additional validation checks.
@@ -171,21 +171,21 @@ The `recordtests.sh` script supports the following options:
 Example usage:
 
 ```bash
-./recordtests.sh -v -t=10
+./record_tests.sh -v -t=10
 ```
 
 This command records test number 5 in quiet and validate mode.
 
 This command will record test number 10 with validation enabled.
 
-When running `recordtests.sh`:
+When running `record_tests.sh`:
 
 1. The script will prompt you to enter test commands for each test case.
 2. After entering the commands, you'll be asked to provide a brief description of the test.
 3. You can specify any necessary arguments for the test.
 4. The script will generate a new `.test` file for each recorded test in the `tests/` directory.
 
-Using `recordtests.sh` is particularly useful when you need to create multiple related tests or when you want to quickly generate a series of test cases for a new feature or bug fix.
+Using `record_tests.sh` is particularly useful when you need to create multiple related tests or when you want to quickly generate a series of test cases for a new feature or bug fix.
 
 ### Exporting and Importing Tests
 
diff --git a/tests/create_test.sh b/tests/create_test.sh
index 981286f3..a88c6913 100755
--- a/tests/create_test.sh
+++ b/tests/create_test.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-HELIOS="../HeliosCLI/helios"
+HELIOS="./output/helios_cli"
 OUTPUT_FILE="recorded_input.txt"
 
 # Color definitions
@@ -61,7 +61,8 @@ function insert_w10_w100() {
   echo "300w${output_string}300wq"
 }
 
-TESTDIR=tests
+# Test directory relative to CWD (HeliosCLI)
+TESTDIR=../tests/tests
 
 mkdir -p $TESTDIR
 
@@ -142,14 +143,14 @@ while true; do
   # replace spaces with underscores
   TEST_NAME="${TEST_NAME// /_}"
 
-  # cd to test dir
-  cd $TESTDIR
-
-  # Create the test file with an incremented prefix number
+  # Determine test file path relative to CWD (HeliosCLI)
   PREFIX=0
   MAX_PREFIX=0
-  for file in [0-9][0-9][0-9][0-9]*.test; do
+  for file in $TESTDIR/[0-9][0-9][0-9][0-9]*.test; do
+    # Check if file exists
+    [ -e "$file" ] || continue
     PREFIX_NUM="${file%%_*}"
+    PREFIX_NUM="${PREFIX_NUM##*/}"
     if [[ "$PREFIX_NUM" =~ ^[0-9]+$ ]]; then
       if ((10#$PREFIX_NUM > 10#$MAX_PREFIX)); then
         MAX_PREFIX=$PREFIX_NUM
@@ -160,7 +161,7 @@ while true; do
   if [ "$TODO" != "" ]; then
     NEXT_PREFIX=$TODO
   fi
-  TEST_FILE="$(printf "%04d" $NEXT_PREFIX)_${TEST_NAME}.test"
+  TEST_FILE="$TESTDIR/$(printf "%04d" $NEXT_PREFIX)_${TEST_NAME}.test"
 
   # Write the test information to the test file
   echo "Input=${NEW_INPUT}" > "$TEST_FILE"
@@ -168,15 +169,12 @@ while true; do
   echo "Args=${ARGS}" >> "$TEST_FILE"
   echo "--------------------------------------------------------------------------------" >> "$TEST_FILE"
 
-  # generate the history for the test and append it to the test file
-  echo "${NEW_INPUT}" | ../$HELIOS $ARGS --hex --no-timestep >> "$TEST_FILE"
+  # generate the history for the test and append it to the test file (run Helios from CWD: HeliosCLI)
+  echo "${NEW_INPUT}" | $HELIOS $ARGS --hex --no-timestep >> "$TEST_FILE"
 
   # strip any \r in case this was run on windows
   sed -i 's/\r//g' $TEST_FILE
 
-  # cd back
-  cd -
-
   # done
   echo "Test file created: ${TEST_FILE}"
 
diff --git a/tests/export_tests.sh b/tests/export_tests.sh
index 14f85c1b..d87e690c 100755
--- a/tests/export_tests.sh
+++ b/tests/export_tests.sh
@@ -1,9 +1,9 @@
 #!/bin/bash
 
-# Directory containing test files
-TEST_DIR="./tests"
+# Directory containing test files relative to CWD (HeliosCLI)
+TEST_DIR="../tests/tests"
 
-# Output CSV file
+# Output CSV file relative to CWD (HeliosCLI)
 OUTPUT_CSV="output.csv"
 
 # Write header to the CSV file
diff --git a/tests/import_tests.sh b/tests/import_tests.sh
index fc51a9ac..863e1f4f 100755
--- a/tests/import_tests.sh
+++ b/tests/import_tests.sh
@@ -1,4 +1,8 @@
 #!/bin/bash
+
+# Helios path relative to HeliosCLI CWD
+HELIOS="./output/helios_cli"
+
 parse_csv() {
   tail -n +2 "$1" | while IFS=, read -r input brief file_name
 do
@@ -19,30 +23,29 @@ create_test() {
     # Format the file name with prefix and replace spaces with underscores
     local test_file="$(printf "%04d" $next_prefix)_${file_name// /_}.test"
 
-    # Create test file
-    cd $TESTDIR
-
-    echo "Input=${input}" > "$test_file"
-    echo "Brief=${brief}" >> "$test_file"
-    echo "Args="
-    echo "--------------------------------------------------------------------------------" >> "$test_file"
+    # Create test file inside TESTDIR (relative to CWD: HeliosCLI)
+    # No need to cd, paths are relative
+    echo "Input=${input}" > "$TESTDIR/$test_file"
+    echo "Brief=${brief}" >> "$TESTDIR/$test_file"
+    echo "Args=" >> "$TESTDIR/$test_file"
+    echo "--------------------------------------------------------------------------------" >> "$TESTDIR/$test_file"
 
-    # Append history to the test file
-    echo "$input" | $HELIOS --hex --no-timestep >> "$test_file"
+    # Append history to the test file (run Helios from CWD: HeliosCLI)
+    echo "$input" | $HELIOS --hex --no-timestep >> "$TESTDIR/$test_file"
 
     # Strip any \r in case this was run on windows
-    sed -i 's/\r//g' $test_file
+    sed -i 's/\r//g' "$TESTDIR/$test_file"
 
-    # Return to previous directory
-    cd -
-
-    echo "Test file created: ${test_file}"
+    echo "Test file created: $TESTDIR/${test_file}"
 }
 
 # Function to get the next available prefix number
 get_next_prefix() {
     local max_prefix=0
+    # Look for files in TESTDIR (relative to CWD: HeliosCLI)
     for file in $TESTDIR/[0-9][0-9][0-9][0-9]*.test; do
+        # Check if file exists to avoid errors on empty dir
+        [ -e "$file" ] || continue
         local prefix_num="${file%%_*}"
         prefix_num="${prefix_num##*/}"
         prefix_num="${prefix_num%%.*}"
@@ -63,13 +66,10 @@ fi
 
 CSV_FILE="$1"
 
-# Set the directory for test files
-TESTDIR="tests"
+# Set the directory for test files relative to CWD (HeliosCLI)
+TESTDIR="../tests/tests"
 mkdir -p $TESTDIR
 
-# Helios command path
-HELIOS="../HeliosCLI/helios"
-
 # Check if the CSV file exists
 if [ ! -f "$CSV_FILE" ]; then
     echo "CSV file not found: $CSV_FILE"
diff --git a/tests/record_test.sh b/tests/record_test.sh
index 3d5a7c19..b5479461 100755
--- a/tests/record_test.sh
+++ b/tests/record_test.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 
-HELIOS="../HeliosCLI/helios"
+# Helios path relative to HeliosCLI CWD
+HELIOS="./output/helios_cli"
 
 FILE=$1
 VALIDATE=$2
@@ -24,12 +25,15 @@ fi
 INPUT="$(grep "Input=" $FILE | cut -d= -f2 | tr -d '\n' | tr -d '\r')"
 BRIEF="$(grep "Brief=" $FILE | cut -d= -f2 | tr -d '\n' | tr -d '\r')"
 ARGS="$(grep "Args=" $FILE | cut -d= -f2 | tr -d '\n' | tr -d '\r')"
-TESTNUM="$(echo $FILE | cut -d/ -f3 | cut -d_ -f1 | cut -d/ -f2)"
-TESTNUM=$((10#$TESTNUM))
+# Extract Test number correctly from basename
+TESTNUM_FILENAME_PART=$(basename "$FILE")
+TESTNUM_PREFIX=$(echo "$TESTNUM_FILENAME_PART" | cut -d_ -f1)
+TESTNUM=$((10#$TESTNUM_PREFIX))
 
 if [ "$QUIET" -eq 0 ]; then
   echo -e -n "\e[31mRecording test ($TESTCOUNT/$NUMFILES) \e[33m[\e[97m$BRIEF\e[33m] \e[33m[\e[97m$ARGS\e[33m]...\e[0m"
 fi
+# Temp file path relative to CWD (HeliosCLI)
 TEMP_FILE="tmp/${FILE}.out"
 # Append the output of the $HELIOS command to the temp file
 # NOTE: When recording the tests we don't use valgrind because
@@ -40,10 +44,11 @@ echo "Brief=${BRIEF}" >> "$TEMP_FILE"
 echo "Args=${ARGS}" >> "$TEMP_FILE"
 echo "--------------------------------------------------------------------------------" >> "$TEMP_FILE"
 
-# ensure there is no existing storage file
+# ensure there is no existing storage file (in CWD: HeliosCLI)
 rm -f Helios.storage
 
 # strip any \r in case this was run on windows
+# Run Helios from CWD (HeliosCLI)
 $HELIOS $ARGS --no-timestep --hex <<< $INPUT >> $TEMP_FILE
 
 sed -i 's/\r//g' $TEMP_FILE
@@ -55,6 +60,7 @@ else
   echo -n "."
 fi
 if [ "$VALIDATE" -eq 1 ]; then
+  # Run Helios from CWD (HeliosCLI) for validation
   $HELIOS $ARGS --no-timestep --color <<< $INPUT
   echo -e "\e[31mRecorded \e[33m[\e[97m$BRIEF\e[33m] \e[33m[\e[97m$ARGS\e[33m]\e[0m"
   echo -en "${YELLOW}Is this correct? (Y/n):${WHITE} "
diff --git a/tests/recordtests.sh b/tests/record_tests.sh
similarity index 82%
rename from tests/recordtests.sh
rename to tests/record_tests.sh
index d9fbf8ad..cf9f469f 100755
--- a/tests/recordtests.sh
+++ b/tests/record_tests.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 VALGRIND="valgrind --quiet --leak-check=full --show-leak-kinds=all"
-HELIOS="../HeliosCLI/helios"
+HELIOS="./output/helios_cli"
 
 VALIDATE=0
 QUIET=0
@@ -42,16 +42,17 @@ fi
 echo -e "\e[32mSuccess\e[0m"
 
 function record_tests() {
-  # Directory where this script is located
-  SCRIPT_DIR="$(dirname "$0")"
+  # Directory where this script is located relative to CWD (HeliosCLI)
+  SCRIPT_DIR="../tests"
 
-  # Full path to the tests directory
+  # Full path to the tests directory relative to CWD (HeliosCLI)
   PROJECT="$SCRIPT_DIR/tests"
 
   FILES=()
 
-  rm -rf "$SCRIPT_DIR"/tmp/$PROJECT
-  mkdir -p "$SCRIPT_DIR"/tmp/$PROJECT
+  # Temp dir relative to CWD (HeliosCLI)
+  rm -rf tmp/$PROJECT
+  mkdir -p tmp/$PROJECT
 
 
   if [ "$TODO" != "" ]; then
@@ -74,7 +75,7 @@ function record_tests() {
   TESTCOUNT=0
 
   for FILE in "${FILES[@]}"; do
-    # Call the record_test.sh using its relative path
+    # Call the record_test.sh using its relative path from CWD (HeliosCLI)
     "$SCRIPT_DIR"/record_test.sh "$FILE" $VALIDATE $TESTCOUNT "$NUMFILES" $QUIET
     TESTCOUNT=$((TESTCOUNT + 1))
   done
diff --git a/tests/runtests.sh b/tests/run_tests.sh
similarity index 88%
rename from tests/runtests.sh
rename to tests/run_tests.sh
index 62443312..457a450b 100755
--- a/tests/runtests.sh
+++ b/tests/run_tests.sh
@@ -1,7 +1,8 @@
 #!/bin/bash
 
 VALGRIND=
-HELIOS="../HeliosCLI/helios"
+# Path relative to HeliosCLI CWD
+HELIOS="./output/helios_cli"
 DIFF="diff --strip-trailing-cr"
 
 # select the target repo to create a test for
@@ -34,7 +35,8 @@ do
 done
 
 function run_tests() {
-  PROJECT="tests"
+  # Path relative to HeliosCLI CWD
+  PROJECT="../tests/tests"
 
   ALLSUCCES=1
 
@@ -66,7 +68,7 @@ function run_tests() {
 
   echo -e "\e[33m== [\e[97mRunning $NUMFILES Helios Integration Tests\e[33m] ==\e[0m"
 
-  # clear tmp folder
+  # clear tmp folder relative to HeliosCLI CWD
   rm -rf tmp/$PROJECT
   mkdir -p tmp/$PROJECT
 
@@ -76,8 +78,10 @@ function run_tests() {
     INPUT="$(grep "Input=" $FILE | cut -d= -f2 | tr -d '\n' | tr -d '\r')"
     BRIEF="$(grep "Brief=" $FILE | cut -d= -f2 | tr -d '\n' | tr -d '\r')"
     ARGS="$(grep "Args=" $FILE | cut -d= -f2 | tr -d '\n' | tr -d '\r')"
-    TESTNUM="$(echo $FILE | cut -d/ -f2 | cut -d_ -f1 | cut -d/ -f2)"
-    TESTNUM=$((10#$TESTNUM))
+    # Extract Test number correctly from basename
+    TESTNUM_FILENAME_PART=$(basename "$FILE")
+    TESTNUM_PREFIX=$(echo "$TESTNUM_FILENAME_PART" | cut -d_ -f1)
+    TESTNUM=$((10#$TESTNUM_PREFIX)) # Use the extracted prefix
     TESTCOUNT=$((TESTCOUNT + 1))
     echo -e -n "\e[33mRunning test ($TESTCOUNT/$NUMFILES) [\e[97m$BRIEF\e[33m] "
     if [ "$ARGS" != "" ]; then
@@ -104,9 +108,9 @@ function run_tests() {
       echo "Test: $TESTNUM"
       echo "-----------------------------"
     fi
-    # ensure there is no leftover storage file
+    # ensure there is no leftover storage file (in HeliosCLI CWD)
     rm -f Helios.storage
-    # now run the test
+    # now run the test (from HeliosCLI CWD)
     $VALGRIND $HELIOS $ARGS --no-timestep --hex <<< $INPUT &> $OUTPUT
     # and diff the result
     $DIFF --brief $EXPECTED $OUTPUT &> $DIFFOUT