diff --git a/Makefile b/Makefile
index 6d4e088..16a8252 100644
--- a/Makefile
+++ b/Makefile
@@ -37,7 +37,7 @@ LIBC_OBJ := $(addprefix $(BUILD_DIR)/,$(LIBC_C_FILES:.c=.o))
 BUILD_ID := $(shell tools/generate_build_id.py --arch $(ARCH))
 
 CFLAGS := $(CFLAGS) -DBUILD_ID=\"$(BUILD_ID)\" -g -Wall -Werror -pedantic \
-	"-I$(ROOT_DIR)/include" "-I$(ROOT_DIR)/arch/$(ARCH)/include" "-I$(ROOT_DIR)/libc/include"
+	-Iinclude -Iarch/$(ARCH)/include -Ilibc/include
 
 ASMFLAGS := $(ASMFLAGS) -DBUILD_ID=\"$(BUILD_ID)\"
 LDFLAGS := $(LDFLAGS) -g
diff --git a/sandbox/Makefile b/sandbox/Makefile
index 21fe1a8..ee45611 100644
--- a/sandbox/Makefile
+++ b/sandbox/Makefile
@@ -7,7 +7,7 @@ BUILD_DIR := $(SANDBOX_BASE_DIR)/../build/sandbox
 include $(SANDBOX_BASE_DIR)/../tools/make/gcc-host.mk
 EXEC_NAME := sandbox
 DIR_LIST := memblock vm base
-INCLUDE_DIRS := $(foreach dir,$(DIR_LIST),"-I$(dir)/include")
+INCLUDE_DIRS := $(foreach dir,$(DIR_LIST),-I$(dir)/include)
 SRC := $(foreach dir,$(DIR_LIST),$(wildcard $(dir)/*.c))
 OBJ := $(addprefix $(BUILD_DIR)/,$(SRC:.c=.o))
 
@@ -25,7 +25,7 @@ $(BUILD_DIR)/$(EXEC_NAME): $(OBJ)
 	@$(CC) $^ -o $@ $(CFLAGS) $(LDFLAGS)
 
 $(BUILD_DIR)/%.o: %.c
-	@printf "    \033[1;32mHOSTCC\033[0m sandbox/$<\n"
+	@printf "    \033[1;32mHOSTCC\033[0m \033[35msandbox\033[0m/$<\n"
 	@mkdir -p $(@D)
 
 	@$(CC) $< -o $@ -c $(CFLAGS)
diff --git a/sandbox/sandbox-config.mk b/sandbox/sandbox-config.mk
deleted file mode 100644
index c81a9f4..0000000
--- a/sandbox/sandbox-config.mk
+++ /dev/null
@@ -1,11 +0,0 @@
-THIS_FILE_PATH := $(abspath $(lastword $(MAKEFILE_LIST)))
-SANDBOX_PROG_MAKEFILE_PATH := $(abspath $(firstword $(MAKEFILE_LIST)))
-SANDBOX_BASE_DIR := $(patsubst %/,%,$(dir $(THIS_FILE_PATH)))
-SANDBOX_PROG_DIR := $(patsubst %/,%,$(dir $(SANDBOX_PROG_MAKEFILE_PATH)))
-
-include $(SANDBOX_BASE_DIR)/../tools/make/gcc-host.mk
-
-SANDBOX_PROG_NAME := $(notdir $(SANDBOX_PROG_DIR))
-
-SANDBOX_BUILD_DIR := $(SANDBOX_BASE_DIR)/../build/sandbox
-BUILD_DIR := $(SANDBOX_BUILD_DIR)/$(SANDBOX_PROG_NAME)
diff --git a/sandbox/sandbox-template.mk b/sandbox/sandbox-template.mk
deleted file mode 100644
index 893cc88..0000000
--- a/sandbox/sandbox-template.mk
+++ /dev/null
@@ -1,24 +0,0 @@
-BUILD_DIR := $(SANDBOX_BUILD_DIR)/$(SANDBOX_PROG_NAME)
-
-SRC := $(wildcard *.c)
-OBJ := $(addprefix $(BUILD_DIR)/,$(SRC:.c=.o))
-
-CFLAGS := -g "-I$(SANDBOX_BASE_DIR)/include"
-
-$(BUILD_DIR)/$(SANDBOX_PROG_NAME): $(OBJ)
-	@mkdir -p $(@D)
-
-	@printf "    \033[1;36mHOSTLD\033[0m \033[1msandbox/\033[35m$(SANDBOX_PROG_NAME)\n"
-	@$(CC) $^ -o $@ $(CFLAGS) $(LDFLAGS)
-
-$(BUILD_DIR)/%.o: %.c
-	@printf "    \033[1;32mHOSTCC\033[0m sandbox/\033[35m$(SANDBOX_PROG_NAME)\033[0m/$<\n"
-	@mkdir -p $(@D)
-
-	@$(CC) $< -o $@ -c $(CFLAGS)
-
-all: $(SANDBOX_PROG_NAME)
-
-clean:
-	@printf "    \033[1;93mRM\033[0m     Deleting sandbox/$(SANDBOX_PROG_NAME)\n"
-	@rm -rf $(BUILD_DIR)
diff --git a/tools/make/generate_compile_commands.py b/tools/make/generate_compile_commands.py
index 9bd2e2d..e2ac0ad 100755
--- a/tools/make/generate_compile_commands.py
+++ b/tools/make/generate_compile_commands.py
@@ -7,11 +7,12 @@ import os
 def is_source_file(filepath):
     return filepath.endswith('.c') or filepath.endswith('.h') or filepath.endswith('.S')
 
+dir_stack = []
 rootdir = os.getcwd()
 
 compile_db = []
 
-make_output = subprocess.check_output(['make', '-n']).decode('utf-8')
+make_output = subprocess.check_output(['make', '-nw']).decode('utf-8')
 
 make_output_lines = make_output.split('\n')
 
@@ -19,6 +20,15 @@ for line in make_output_lines:
     line_parts = line.split(' ')
     new_line_parts = []
 
+    if len(line_parts) >= 2 and 'Entering directory' in line:
+        new_dir = line[line.find('`') + 1:-1]
+        dir_stack.append(new_dir)
+        continue
+
+    if len(line_parts) >= 2 and 'Leaving directory' in line:
+        dir_stack.pop()
+        continue;
+
     if 'gcc' not in line_parts[0]:
         continue
 
@@ -27,7 +37,7 @@ for line in make_output_lines:
         part = part.strip()
         if is_source_file(part):
             src_file = part
-            part = '../{}'.format(part)
+            part = os.path.join(dir_stack[-1], part)
 
         new_line_parts.append(part)
 
@@ -35,9 +45,9 @@ for line in make_output_lines:
         continue
 
     db_entry = {
-            'directory': '{}/build'.format(rootdir),
+            'directory': dir_stack[-1],
             'command': ' '.join(new_line_parts).strip(),
-            'file': '{}/{}'.format(rootdir, src_file)
+            'file': os.path.join(dir_stack[-1], src_file)
     }
 
     compile_db.append(db_entry)