You can use Target-specific Variable Values. Example:
CXXFLAGS = -g3 -gdwarf2
CCFLAGS = -g3 -gdwarf2
all: executable
debug: CXXFLAGS += -DDEBUG -g
debug: CCFLAGS += -DDEBUG -g
debug: executable
executable: CommandParser.tab.o CommandParser.yy.o Command.o
$(CXX) -o output CommandParser.yy.o CommandParser.tab.o Command.o -lfl
CommandParser.yy.o: CommandParser.l
flex -o CommandParser.yy.c CommandParser.l
$(CC) -c CommandParser.yy.c
Remember to use $(CXX) or $(CC) in all your compile commands.
Then, ‘make debug’ will have extra flags like -DDEBUG and -g where as ‘make’ will not.
On a side note, you can make your Makefile a lot more concise like other posts had suggested.