diff --git a/.gitignore b/.gitignore
index fd61fff58..2e95681e1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,34 +1,19 @@
 # Produced files
 
-out/
-build/
+build/bin
+build/obj
+build/tests
 
 # IDE related files
 nbproject
 **.sublime-project
 **.sublime-workspace
-
-# Compiled Object files
-*.slo
-*.lo
-*.o
-
-# Compiled Dynamic libraries
-*.so
-*.dylib
-
-# Compiled Static libraries
-*.lai
-*.la
-*.a
+.idea
 
 # Random Trash
 *.swp
+*.swo
 *~
-js.files
-js.fail.files
-jerry.error
-jerry.passed
 core
 vgcore.*
 **.orig
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ae9f4a6b1..64bf6a9f9 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -536,11 +536,12 @@ project (Jerry CXX C ASM)
      target_link_libraries(${TARGET_NAME} ${TARGET_NAME}.jerry.lib ${TARGET_NAME}.third_party.lib imported_libgcc)
      add_dependencies(${TARGET_NAME} mcu_header_with_script_to_run.${TARGET_NAME})
 
-     add_custom_target(${TARGET_NAME}.flash
+     add_custom_target(${TARGET_NAME}.bin
                        COMMAND ${CMAKE_OBJCOPY} -Obinary $<TARGET_FILE:${TARGET_NAME}> $<TARGET_FILE:${TARGET_NAME}>.bin
-                       # Flash, ignoring failures to remove temporary flashable binary any way
-                       COMMAND st-flash write $<TARGET_FILE:${TARGET_NAME}>.bin 0x08000000 || /bin/true
-                       COMMAND rm $<TARGET_FILE:${TARGET_NAME}>.bin)
+                       DEPENDS ${TARGET_NAME})
+     add_custom_target(${TARGET_NAME}.flash
+                       COMMAND st-flash write $<TARGET_FILE:${TARGET_NAME}>.bin 0x08000000
+                       DEPENDS ${TARGET_NAME}.bin)
     endfunction()
 
     declare_target_with_modifiers(COMPACT_PROFILE)
diff --git a/Makefile b/Makefile
index f6fd64f2c..f527af709 100644
--- a/Makefile
+++ b/Makefile
@@ -58,8 +58,8 @@ export JERRY_TARGETS = $(JERRY_LINUX_TARGETS) $(JERRY_MCU_TARGETS)
 export CHECK_TARGETS = $(foreach __TARGET,$(JERRY_TARGETS),$(__TARGET).check)
 export FLASH_TARGETS = $(foreach __TARGET,$(foreach __MODE,$(TARGET_RELEASE_MODES),$(foreach __SYSTEM,$(TARGET_MCU_SYSTEMS_MODS),$(__MODE).$(__SYSTEM))),$(__TARGET).flash)
 
-export OUT_DIR = ./out
-export BUILD_DIR = ./build
+export OUT_DIR = ./build/bin
+export BUILD_DIR = ./build/obj
 
 export SHELL=/bin/bash
 
@@ -67,11 +67,11 @@ all: precommit
 
 $(BUILD_DIR)/native:
 	@ mkdir -p $(BUILD_DIR)/native
-	@ cd $(BUILD_DIR)/native; cmake ../.. &>cmake.log
+	@ cd $(BUILD_DIR)/native; cmake ../../.. &>cmake.log
 
 $(BUILD_DIR)/mcu:
 	@ mkdir -p $(BUILD_DIR)/mcu
-	@ cd $(BUILD_DIR)/mcu; cmake -DCMAKE_TOOLCHAIN_FILE=cmake/toolchain_mcu_armv7l.cmake ../.. &>cmake.log
+	@ cd $(BUILD_DIR)/mcu; cmake -DCMAKE_TOOLCHAIN_FILE=build/configs/toolchain_mcu_armv7l.cmake ../../.. &>cmake.log
 
 $(JERRY_LINUX_TARGETS): $(BUILD_DIR)/native
 	@ mkdir -p $(OUT_DIR)/$@
@@ -85,8 +85,9 @@ unittests: $(BUILD_DIR)/native
 
 $(JERRY_MCU_TARGETS): $(BUILD_DIR)/mcu
 	@ mkdir -p $(OUT_DIR)/$@
-	@ $(MAKE) -C $(BUILD_DIR)/mcu VERBOSE=1 $@ &>$(OUT_DIR)/$@/make.log
+	@ $(MAKE) -C $(BUILD_DIR)/mcu VERBOSE=1 $@.bin &>$(OUT_DIR)/$@/make.log
 	@ cp $(BUILD_DIR)/mcu/$@ $(OUT_DIR)/$@/jerry
+	@ cp $(BUILD_DIR)/mcu/$@.bin $(OUT_DIR)/$@/jerry.bin
 
 build: $(JERRY_TARGETS) unittests
 
diff --git a/cmake/toolchain_linux_armv7l-hf.cmake b/build/configs/toolchain_linux_armv7l-hf.cmake
similarity index 100%
rename from cmake/toolchain_linux_armv7l-hf.cmake
rename to build/configs/toolchain_linux_armv7l-hf.cmake
diff --git a/cmake/toolchain_linux_x86_64.cmake b/build/configs/toolchain_linux_x86_64.cmake
similarity index 100%
rename from cmake/toolchain_linux_x86_64.cmake
rename to build/configs/toolchain_linux_x86_64.cmake
diff --git a/cmake/toolchain_mcu_armv7l.cmake b/build/configs/toolchain_mcu_armv7l.cmake
similarity index 100%
rename from cmake/toolchain_mcu_armv7l.cmake
rename to build/configs/toolchain_mcu_armv7l.cmake