diff --git a/makefile b/makefile
index 52cf68c..6fe985f 100644
--- a/makefile
+++ b/makefile
@@ -1,101 +1,79 @@
 # Compiler and Flags
 CC = gcc
-CFLAGS = -Wall -Wextra -pedantic -std=c99
+CFLAGS = -Wall -Wextra -pedantic -std=c99 -Iinclude
 LDFLAGS = -lssl -lcrypto -lcurl
-INCLUDES = -Iinclude
 DEBUG_CFLAGS = -g -DDEBUG
 
-# Build Directories
-BUILD_DIR = build
+# Dynamic Directories
+SRC_DIR = ./src
+BUILD_DIR = ./build
+INCLUDE_DIR = ./include
+BINARIES_DIR = ./binaries
+LOG_DIR = ./logs
 INSTALL_DIR = /opt/pmll
-TEST_DIR = test_build
-LOG_DIR = logs
-
-# Source files
-SOURCES = \
-    unified_voice.c \
-    pml_logic_loop.c \
-    memory_silo.c \
-    io_socket.c \
-    persistence.c \
-    cross_talk.c \
-    custodian.c \
-    main.c \
-    vector_matrix.c \
-    arc_agi_benchmark.c \
-    pmll_np_solver.c \
-    SAT_Compare.c \
-    Pmll_NP_Solver.c \
-    MiniSAT.c \
-    generate_3sat_instance.c \
-    SAT_Solver.c \
-    API_Llama.c \
-    API.c \
-    silo_manager.c \
-    logic_loop.c \
-    free.c \
-    json.c
-
-# Object and Dependency files
-OBJECTS = $(patsubst %.c, $(BUILD_DIR)/%.o, $(SOURCES))
-DEPFILES = $(patsubst %.c, $(BUILD_DIR)/%.d, $(SOURCES))
-
-# Targets
+
+# Source files (search dynamically in the source directory)
+SOURCES = $(wildcard $(SRC_DIR)/*.c)
+
+# Object files generated from source files
+OBJECTS = $(patsubst $(SRC_DIR)/%.c, $(BUILD_DIR)/%.o, $(SOURCES))
+
+# Target binaries
 TARGETS = pmll arc_agi_benchmark pmll_np_solver sat_test api_llama api vector_matrix silo_manager logic_loop custodian free
 
-# Default target: Build all
+# Default target: Build all binaries
 .PHONY: all
 all: $(TARGETS)
 
-# Define each binary and its dependencies
+# Define rules for each binary and its dependencies
 pmll: $(BUILD_DIR)/unified_voice.o $(BUILD_DIR)/pml_logic_loop.o $(BUILD_DIR)/memory_silo.o \
       $(BUILD_DIR)/io_socket.o $(BUILD_DIR)/persistence.o $(BUILD_DIR)/cross_talk.o \
       $(BUILD_DIR)/custodian.o $(BUILD_DIR)/main.o $(BUILD_DIR)/vector_matrix.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
 arc_agi_benchmark: $(BUILD_DIR)/arc_agi_benchmark.o $(BUILD_DIR)/vector_matrix.o $(BUILD_DIR)/io_socket.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
 pmll_np_solver: $(BUILD_DIR)/pmll_np_solver.o $(BUILD_DIR)/vector_matrix.o $(BUILD_DIR)/io_socket.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
 sat_test: $(BUILD_DIR)/SAT_Compare.o $(BUILD_DIR)/Pmll_NP_Solver.o $(BUILD_DIR)/MiniSAT.o \
           $(BUILD_DIR)/generate_3sat_instance.o $(BUILD_DIR)/SAT_Solver.o $(BUILD_DIR)/vector_matrix.o \
           $(BUILD_DIR)/io_socket.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
 api_llama: $(BUILD_DIR)/API_Llama.o $(BUILD_DIR)/vector_matrix.o $(BUILD_DIR)/io_socket.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
 api: $(BUILD_DIR)/API.o $(BUILD_DIR)/vector_matrix.o $(BUILD_DIR)/io_socket.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
 vector_matrix: $(BUILD_DIR)/vector_matrix.o $(BUILD_DIR)/io_socket.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
 silo_manager: $(BUILD_DIR)/silo_manager.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
 logic_loop: $(BUILD_DIR)/logic_loop.o $(BUILD_DIR)/pml_logic_loop.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
 custodian: $(BUILD_DIR)/custodian.o $(BUILD_DIR)/io_socket.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
 free: $(BUILD_DIR)/free.o $(BUILD_DIR)/json.o
-	$(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -o $@ $^
-
-# Compile Rules
-$(BUILD_DIR)/%.o: %.c
-	@mkdir -p $(BUILD_DIR)
-	$(CC) $(CFLAGS) $(INCLUDES) -c $< -o $@
+	$(CC) $(CFLAGS) $(LDFLAGS) -o $(BINARIES_DIR)/$@ $^
 
-# Dependency Generation
-$(BUILD_DIR)/%.d: %.c
+# Compile source files into object files
+$(BUILD_DIR)/%.o: $(SRC_DIR)/%.c
 	@mkdir -p $(BUILD_DIR)
-	$(CC) -M $(CFLAGS) $(INCLUDES) $< > $@
+	$(CC) $(CFLAGS) -I$(INCLUDE_DIR) -c $< -o $@
 
-include $(wildcard $(DEPFILES))
+# Clean build artifacts
+.PHONY: clean
+clean:
+	@echo "Cleaning build artifacts..."
+	@rm -rf $(BUILD_DIR) $(BINARIES_DIR) $(LOG_DIR)
+	@echo "Clean complete."
 
 # Orchestrate Health Check, Payload, and Binary Deployment
 .PHONY: orchestrate
@@ -104,40 +82,26 @@ orchestrate: all
 	bash Orchestrate.sh
 	@echo "Orchestration completed."
 
-# Test Build
-.PHONY: test
-test: clean
-	@echo "Building test executables in $(TEST_DIR)..."
-	@mkdir -p $(TEST_DIR)
-	@$(MAKE) all CFLAGS="$(CFLAGS) -g -O0 -DTEST" LDFLAGS="$(LDFLAGS)" BUILD_DIR=$(TEST_DIR)
-
-# Deployment
+# Deployment to system directory
 .PHONY: deploy
-deploy: $(TARGETS)
+deploy: all
+	@echo "Deploying binaries to $(INSTALL_DIR)..."
 	@sudo mkdir -p $(INSTALL_DIR)
-	@sudo install -m 755 $(TARGETS) $(INSTALL_DIR)/
-	@echo "Deployment complete to $(INSTALL_DIR)."
+	@sudo install -m 755 $(BINARIES_DIR)/* $(INSTALL_DIR)/
+	@echo "Deployment complete."
 
-# Debug Build
+# Debug build
 .PHONY: debug
 debug: CFLAGS += $(DEBUG_CFLAGS)
 debug: all
 
-# Clean Build Artifacts
-.PHONY: clean
-clean:
-	@echo "Cleaning up..."
-	-rm -f $(BUILD_DIR)/*.o $(TARGETS) $(DEPFILES) *.pid
-	@echo "Clean complete."
-
-# Help Target
+# Help
 .PHONY: help
 help:
 	@echo "Makefile commands:"
-	@echo "  all                  Build all executables."
-	@echo "  test                 Build test executables with debug flags."
+	@echo "  all                  Build all binaries."
+	@echo "  clean                Remove all build artifacts."
 	@echo "  orchestrate          Run orchestration script (Orchestrate.sh)."
 	@echo "  deploy               Deploy binaries to $(INSTALL_DIR)."
 	@echo "  debug                Build with debug flags."
-	@echo "  clean                Remove all build artifacts."
 	@echo "  help                 Show this help message."