diff --git a/Makefile b/Makefile
index c8a52b7..e725133 100644
--- a/Makefile
+++ b/Makefile
@@ -10,15 +10,19 @@ PRNGS          :=
 # we use the gnu make standard library
 include gmsl
 include avr-makefile.inc
-include *.mk
+include mkfiles/*.mk
 
 ALGORITHMS = $(BLOCK_CIPHERS) $(STREAM_CIPHERS) $(HASHES) $(PRNGS) $(MACS)
 ALGORITHMS_OBJ = $(patsubst %,%_OBJ, $(ALGORITHMS))
-ALGORITHMS_OBJ_IMM = $(foreach a, $(ALGORITHMS_OBJ), $($(a)))
+define OBJinBINDIR_TEMPLATE
+$(1) = $(2)
+endef
+$(foreach a, $(ALGORITHMS_OBJ), $(eval $(call OBJinBINDIR_TEMPLATE, $(a), $(patsubst %.o,$(BIN_DIR)%.o,$($(a))))))
 ALGORITHMS_TEST_BIN = $(patsubst %,%_TEST_BIN, $(ALGORITHMS))
+$(foreach a, $(ALGORITHMS_TEST_BIN), $(eval $(call OBJinBINDIR_TEMPLATE, $(a), $(patsubst %.o,$(BIN_DIR)%.o,$($(a))))))
 ALGORITHMS_TEST_BIN_MAIN = $(foreach a, $(ALGORITHMS_TEST_BIN), $(firstword $($(a))))
-ALGORITHMS_TEST_BIN_MAIN_ELF = $(patsubst %.o, %.elf, $(ALGORITHMS_TEST_BIN_MAIN))
-ALGORITHMS_TEST_BIN_MAIN_HEX = $(patsubst %.o, %.hex, $(ALGORITHMS_TEST_BIN_MAIN))
+ALGORITHMS_TEST_BIN_MAIN_ELF = $(patsubst $(BIN_DIR)%.o, $(TESTBIN_DIR)%.elf, $(ALGORITHMS_TEST_BIN_MAIN))
+ALGORITHMS_TEST_BIN_MAIN_HEX = $(patsubst $(BIN_DIR)%.o, $(TESTBIN_DIR)%.hex, $(ALGORITHMS_TEST_BIN_MAIN))
 
 ALGORITHMS_TEST_BIN_IMM =  $(foreach a, $(ALGORITHMS_TEST_BIN), $($(a)))
 ALGORITHMS_NESSIE_TEST = $(patsubst %,%_NESSIE_TEST, $(ALGORITHMS))
@@ -26,7 +30,6 @@ ALGORITHMS_PERFORMANCE_TEST = $(patsubst %,%_PERORMANCE_TEST, $(ALGORITHMS))
 
 ALGORITHMS_LC = $(call lc,$(ALGORITHMS))
 
-PRG = remove_me
 
 #-------------------------------------------------------------------------------
 
@@ -44,7 +47,7 @@ $(2): $(3)
 	$(LIBS)
 endef
 
-$(foreach algo, $(ALGORITHMS), $(eval $(call BLA_TEMPLATE2, $(algo), $(patsubst %.o,%.elf,$(firstword $($(algo)_TEST_BIN))), $($(algo)_TEST_BIN) )))
+$(foreach algo, $(ALGORITHMS), $(eval $(call BLA_TEMPLATE2, $(algo), $(patsubst $(BIN_DIR)%.o,$(TESTBIN_DIR)%.elf,$(firstword $($(algo)_TEST_BIN))), $(patsubst %.o,%.o,$($(algo)_TEST_BIN)) )))
 
 #-------------------------------------------------------------------------------
 
@@ -61,22 +64,18 @@ info:
 	@echo "    $(MACS)"
 	@echo "  PRNG functions:"
 	@echo "    $(PRNGS)"
-#	@echo "  LC functions:"
-#	@echo "    $(ALGORITHMS_LC)"
-	
-#	echo $(ALGORITHMS_TEST_BIN_MAIN)
-#	echo $(ALGORITHMS)
-#	echo $(firstword $(XTEA_TEST_BIN))
-#	echo $(patsubst %.o,%.elf,$(firstword $(XTEA_TEST_BIN)))
-#	echo $(ALGORITHMS_OBJ)
-#	echo $(ALGORITHMS_OBJ_IMM)
-#	echo $(ALGORITHMS_TEST_BIN)
-#	echo $(ALGORITHMS_NESSIE_TEST)
-#	echo $(ALGORITHMS_PERFORMANCE_TEST)
+
+$(BIN_DIR)%.o: %.c
+	@echo "[gcc]:  $@"
+	@$(CC) $(CFLAGS)  -c -o $@ $<
+
+$(BIN_DIR)%.o: %.S
+	@echo "[as] :  $@"
+	@$(CC) $(ASFLAGS) -c -o $@ $<
 
 %.o: %.c
 	@echo "[gcc]:  $@"
-	@$(CC) $(CFLAGS) -c	-o $@ $<
+	@$(CC) $(CFLAGS)  -c -o $@ $<
 
 %.o: %.S
 	@echo "[as] :  $@"
@@ -107,7 +106,6 @@ tests: $(ALGORITHMS_TEST_BIN) \
 
 .PHONY:  stats
 stats: $(SIZESTAT_FILE)
-#$(patsubst %, %_size.txt, $(ALGORITHMS_LC))
 	
 	
 $(SIZESTAT_FILE): $(patsubst %, %_size.txt, $(ALGORITHMS_LC))
@@ -158,28 +156,20 @@ $(foreach algo, $(ALGORITHMS),$(eval $(call FLASH_TEMPLATE, $(algo), \
 
 .PHONY: clean
 clean:
-	rm -rf *.o *.elf *.eps *.png *.pdf *.bak *_size.txt
+	rm -rf $(BIN_DIR)*.o *.o $(TESTBIN_DIR)*.elf $(TESTBIN_DIR)* *.elf *.eps *.png *.pdf *.bak *_size.txt
 	rm -rf *.lst *.map $(EXTRA_CLEAN_FILES) $(SIZESTAT_FILE)
 xclean: clean
-	rm -rf *.d
+	rm -rf $(DEP_DIR)*.d
 
 flash:
 	$(ERASECMD)
 	$(FLASHCMD)
-	
-lst:  $(PRG).lst
 
 %.lst: %.elf
 	$(OBJDUMP) -h -S $< > $@
 
 # Rules for building the .text rom images
 
-text: hex bin srec
-
-hex:  $(PRG).hex
-bin:  $(PRG).bin
-srec: $(PRG).srec
-
 %.hex: %.elf
 	$(OBJCOPY) -j .text -j .data -O ihex $< $@
 
@@ -191,11 +181,6 @@ srec: $(PRG).srec
 
 # Rules for building the .eeprom rom images
 
-eeprom: ehex ebin esrec
-
-ehex:  $(PRG)_eeprom.hex
-ebin:  $(PRG)_eeprom.bin
-esrec: $(PRG)_eeprom.srec
 
 %_eeprom.hex: %.elf
 	$(OBJCOPY) -j .eeprom --change-section-lma .eeprom=0 -O ihex $< $@
@@ -213,12 +198,6 @@ esrec: $(PRG)_eeprom.srec
 FIG2DEV		 = fig2dev
 EXTRA_CLEAN_FILES       = *.hex *.bin *.srec
 
-dox: eps png pdf
-
-eps: $(PRG).eps
-png: $(PRG).png
-pdf: $(PRG).pdf
-
 
 %.eps: %.fig
 	$(FIG2DEV) -L eps $< $@
@@ -230,7 +209,8 @@ pdf: $(PRG).pdf
 	$(FIG2DEV) -L png $< $@
 
 
-DEPS := $(wildcard *.d)
+DEPS := $(wildcard $(DEP_DIR)*.d)
+
 ifneq ($(DEPS),)
 include $(DEPS)
 endif
diff --git a/avr-makefile.inc b/avr-makefile.inc
index 0fe9e4f..f0ea6c8 100644
--- a/avr-makefile.inc
+++ b/avr-makefile.inc
@@ -4,13 +4,15 @@ MCU_TARGET     = atmega644
 OPTIMIZE       = -Os
 DEFS           = -D$(call uc, $(MCU_TARGET))
 FLASHCMD       = avrdude -p $(MCU_TARGET) -P /dev/ttyUSB0 -c avr911 -U flash:w:# no space at the end
-
+DEP_DIR        = deps/
+BIN_DIR        = bin/
+TESTBIN_DIR    = test_bin/
 #uisp -dprog=bsd -dlpt=/dev/parport1 --upload if=$(PRG).hex
 ERASECMD       = 
 
 CC	     = avr-gcc
 
-override CFLAGS	= -MMD -pedantic -std=c99 -Wall -Wstrict-prototypes  $(OPTIMIZE) -mmcu=$(MCU_TARGET) $(DEFS)
+override CFLAGS	= -MMD -MF$(DEP_DIR)$(patsubst %.c,%.d,$^) -pedantic -std=c99 -Wall -Wstrict-prototypes  $(OPTIMIZE) -mmcu=$(MCU_TARGET) $(DEFS)
 
 override LDFLAGS       = -Wl,-Map,
 override ASFLAGS	   = -mmcu=$(MCU_TARGET)
diff --git a/arcfour.mk b/mkfiles/arcfour.mk
similarity index 100%
rename from arcfour.mk
rename to mkfiles/arcfour.mk
diff --git a/camellia.mk b/mkfiles/camellia.mk
similarity index 100%
rename from camellia.mk
rename to mkfiles/camellia.mk
diff --git a/cast5.mk b/mkfiles/cast5.mk
similarity index 100%
rename from cast5.mk
rename to mkfiles/cast5.mk
diff --git a/des.mk b/mkfiles/des.mk
similarity index 100%
rename from des.mk
rename to mkfiles/des.mk
diff --git a/entropium.mk b/mkfiles/entropium.mk
similarity index 100%
rename from entropium.mk
rename to mkfiles/entropium.mk
diff --git a/grain.mk b/mkfiles/grain.mk
similarity index 100%
rename from grain.mk
rename to mkfiles/grain.mk
diff --git a/hmac-sha256.mk b/mkfiles/hmac-sha256.mk
similarity index 100%
rename from hmac-sha256.mk
rename to mkfiles/hmac-sha256.mk
diff --git a/md5.mk b/mkfiles/md5.mk
similarity index 100%
rename from md5.mk
rename to mkfiles/md5.mk
diff --git a/mkfiles/mickey128.mk b/mkfiles/mickey128.mk
new file mode 100644
index 0000000..3cb7a42
--- /dev/null
+++ b/mkfiles/mickey128.mk
@@ -0,0 +1,12 @@
+# Makefile for Mickey128
+ALGO_NAME := MICKEY128
+
+# comment out the following line for removement of Mickey128 from the build process
+STREAM_CIPHERS += $(ALGO_NAME)
+
+$(ALGO_NAME)_OBJ      := mickey128.o
+$(ALGO_NAME)_TEST_BIN := main-mickey128-test.o debug.o uart.o serial-tools.o \
+                         nessie_stream_test.o nessie_common.o mickey128.o cli.o
+$(ALGO_NAME)_NESSIE_TEST      := "nessie"
+$(ALGO_NAME)_PEROFRMANCE_TEST := "performance"
+
diff --git a/noekeon.mk b/mkfiles/noekeon.mk
similarity index 100%
rename from noekeon.mk
rename to mkfiles/noekeon.mk
diff --git a/present.mk b/mkfiles/present.mk
similarity index 100%
rename from present.mk
rename to mkfiles/present.mk
diff --git a/rc5.mk b/mkfiles/rc5.mk
similarity index 100%
rename from rc5.mk
rename to mkfiles/rc5.mk
diff --git a/rc6.mk b/mkfiles/rc6.mk
similarity index 100%
rename from rc6.mk
rename to mkfiles/rc6.mk
diff --git a/seed.mk b/mkfiles/seed.mk
similarity index 100%
rename from seed.mk
rename to mkfiles/seed.mk
diff --git a/serpent.mk b/mkfiles/serpent.mk
similarity index 100%
rename from serpent.mk
rename to mkfiles/serpent.mk
diff --git a/sha1.mk b/mkfiles/sha1.mk
similarity index 100%
rename from sha1.mk
rename to mkfiles/sha1.mk
diff --git a/sha256.mk b/mkfiles/sha256.mk
similarity index 100%
rename from sha256.mk
rename to mkfiles/sha256.mk
diff --git a/shabea.mk b/mkfiles/shabea.mk
similarity index 100%
rename from shabea.mk
rename to mkfiles/shabea.mk
diff --git a/shacal1enc.mk b/mkfiles/shacal1enc.mk
similarity index 100%
rename from shacal1enc.mk
rename to mkfiles/shacal1enc.mk
diff --git a/shacal2enc.mk b/mkfiles/shacal2enc.mk
similarity index 100%
rename from shacal2enc.mk
rename to mkfiles/shacal2enc.mk
diff --git a/skipjack.mk b/mkfiles/skipjack.mk
similarity index 100%
rename from skipjack.mk
rename to mkfiles/skipjack.mk
diff --git a/tdes.mk b/mkfiles/tdes.mk
similarity index 100%
rename from tdes.mk
rename to mkfiles/tdes.mk
diff --git a/trivium.mk b/mkfiles/trivium.mk
similarity index 100%
rename from trivium.mk
rename to mkfiles/trivium.mk
diff --git a/xtea.mk b/mkfiles/xtea.mk
similarity index 100%
rename from xtea.mk
rename to mkfiles/xtea.mk