Update Makefile: Correctly compiles and cleans all subdirectories

src/Makefile

@@ -1,16 +1,40 @@
-CC      ?= gcc
-CFLAGS  ?= -std=c17 -g\
-	-D_POSIX_SOURCE -D_DEFAULT_SOURCE\
-	-Wall -Werror -pedantic
+# Compiler and flags
+CC      := gcc
+CFLAGS  := -std=c17 -g -D_POSIX_SOURCE -D_DEFAULT_SOURCE -Wall -Werror -pedantic
 
-.SUFFIXES: .c .o
+# Directories
+SRC_DIR := .
+UTIL_DIR := util
+ASM_DIR := assembler
+EMU_DIR := emulator
 
-.PHONY: all clean
+# Source files
+ASSEMBLE_SRC := $(UTIL_DIR)/fileio.c $(UTIL_DIR)/binary_util.c $(ASM_DIR)/encode.c $(ASM_DIR)/parse.c $(ASM_DIR)/tokenise.c $(ASM_DIR)/string_util.c $(ASM_DIR)/symboltable.c
+EMULATE_SRC  := $(UTIL_DIR)/fileio.c $(UTIL_DIR)/binary_util.c $(EMU_DIR)/execute.c $(EMU_DIR)/decode.c $(EMU_DIR)/print.c $(EMU_DIR)/machine_util.c
 
-all: emulate assemble
+# Object files
+ASSEMBLE_OBJ := $(ASSEMBLE_SRC:.c=.o) assemble.o
+EMULATE_OBJ  := $(EMULATE_SRC:.c=.o) emulate.o
 
-assemble: assemble.o util/fileio.o util/binary_util.o assembler/encode.o assembler/parse.o assembler/tokenise.o assembler/string_util.o assembler/symboltable.o
-emulate: emulate.o util/fileio.o emulator/execute.o emulator/decode.o emulator/print.o emulator/machine_util.o util/binary_util.o
+# Targets
+TARGETS := assemble emulate
 
+# Default target
+.PHONY: all
+all: $(TARGETS)
+
+# Rules to build each target
+assemble: $(ASSEMBLE_OBJ)
+	$(CC) $(CFLAGS) -o $@ $^
+
+emulate: $(EMULATE_OBJ)
+	$(CC) $(CFLAGS) -o $@ $^
+
+# Pattern rule to compile C files
+%.o: %.c
+	$(CC) $(CFLAGS) -c -o $@ $<
+
+# Clean up
+.PHONY: clean
 clean:
-	$(RM) *.o assemble emulate emulator/execute.o emulator/decode.o 
+	$(RM) $(ASSEMBLE_OBJ) $(EMULATE_OBJ) $(TARGETS)