diff --git a/Makefile b/Makefile
index 7d92bad21c..1eb4b8b55a 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,22 @@
-TOOLCHAIN := $(DEVKITARM)
-COMPARE ?= 0
+# GBA rom header
+TITLE       := POKEMON EMER
+GAME_CODE   := BPEE
+MAKER_CODE  := 01
+REVISION    := 0
+MODERN      ?= 0
 
+# `File name`.gba ('_modern' will be appended to the modern builds)
+FILE_NAME := pokeemerald
+BUILD_DIR := build
+
+# Builds the ROM using a modern compiler
+MODERN      ?= 0
+# Compares the ROM to a checksum of the original - only makes sense using when non-modern
+COMPARE     ?= 0
+
+ifeq (modern,$(MAKECMDGOALS))
+  MODERN := 1
+endif
 ifeq (compare,$(MAKECMDGOALS))
   COMPARE := 1
 endif
@@ -8,45 +24,29 @@ endif
 # Default make rule
 all: rom
 
+# Toolchain selection
+TOOLCHAIN := $(DEVKITARM)
 # don't use dkP's base_tools anymore
 # because the redefinition of $(CC) conflicts
 # with when we want to use $(CC) to preprocess files
 # thus, manually create the variables for the bin
 # files, or use arm-none-eabi binaries on the system
 # if dkP is not installed on this system
-
 ifneq (,$(TOOLCHAIN))
-ifneq ($(wildcard $(TOOLCHAIN)/bin),)
-export PATH := $(TOOLCHAIN)/bin:$(PATH)
-endif
+  ifneq ($(wildcard $(TOOLCHAIN)/bin),)
+    export PATH := $(TOOLCHAIN)/bin:$(PATH)
+  endif
 endif
 
 PREFIX := arm-none-eabi-
 OBJCOPY := $(PREFIX)objcopy
 OBJDUMP := $(PREFIX)objdump
 AS := $(PREFIX)as
-
 LD := $(PREFIX)ld
 
-# note: the makefile must be set up so MODERNCC is never called
-# if MODERN=0
-MODERNCC := $(PREFIX)gcc
-PATH_MODERNCC := PATH="$(PATH)" $(MODERNCC)
-
-ifeq ($(OS),Windows_NT)
-EXE := .exe
-else
 EXE :=
-endif
-
-TITLE       := POKEMON EMER
-GAME_CODE   := BPEE
-MAKER_CODE  := 01
-REVISION    := 0
-MODERN      ?= 0
-
-ifeq (modern,$(MAKECMDGOALS))
-  MODERN := 1
+ifeq ($(OS),Windows_NT)
+  EXE := .exe
 endif
 
 # use arm-none-eabi-cpp for macOS
@@ -66,22 +66,29 @@ else
   CPP := $(PREFIX)cpp
 endif
 
-ROM_NAME := pokeemerald.gba
+ROM_NAME := $(FILE_NAME).gba
+OBJ_DIR_NAME := $(BUILD_DIR)/emerald
+MODERN_ROM_NAME := $(FILE_NAME)_modern.gba
+MODERN_OBJ_DIR_NAME := $(BUILD_DIR)/modern
+
 ELF_NAME := $(ROM_NAME:.gba=.elf)
 MAP_NAME := $(ROM_NAME:.gba=.map)
-OBJ_DIR_NAME := build/emerald
-
-MODERN_ROM_NAME := pokeemerald_modern.gba
 MODERN_ELF_NAME := $(MODERN_ROM_NAME:.gba=.elf)
 MODERN_MAP_NAME := $(MODERN_ROM_NAME:.gba=.map)
-MODERN_OBJ_DIR_NAME := build/modern
 
-SHELL := /bin/bash -o pipefail
-
-ELF = $(ROM:.gba=.elf)
-MAP = $(ROM:.gba=.map)
-SYM = $(ROM:.gba=.sym)
+# Pick our active variables
+ifeq ($(MODERN),0)
+  ROM := $(ROM_NAME)
+  OBJ_DIR := $(OBJ_DIR_NAME)
+else
+  ROM := $(MODERN_ROM_NAME)
+  OBJ_DIR := $(MODERN_OBJ_DIR_NAME)
+endif
+ELF := $(ROM:.gba=.elf)
+MAP := $(ROM:.gba=.map)
+SYM := $(ROM:.gba=.sym)
 
+# Commonly used directories
 C_SUBDIR = src
 GFLIB_SUBDIR = gflib
 ASM_SUBDIR = asm
@@ -99,34 +106,43 @@ DATA_ASM_BUILDDIR = $(OBJ_DIR)/$(DATA_ASM_SUBDIR)
 SONG_BUILDDIR = $(OBJ_DIR)/$(SONG_SUBDIR)
 MID_BUILDDIR = $(OBJ_DIR)/$(MID_SUBDIR)
 
+SHELL := /bin/bash -o pipefail
+
+# Set flags for tools
 ASFLAGS := -mcpu=arm7tdmi --defsym MODERN=$(MODERN)
 
-ifeq ($(MODERN),0)
-CC1             := tools/agbcc/bin/agbcc$(EXE)
-override CFLAGS += -mthumb-interwork -Wimplicit -Wparentheses -Werror -O2 -fhex-asm -g
-ROM := $(ROM_NAME)
-OBJ_DIR := $(OBJ_DIR_NAME)
-LIBPATH := -L ../../tools/agbcc/lib
-LIB := $(LIBPATH) -lgcc -lc -L../../libagbsyscall -lagbsyscall
-else
-CC1              = $(shell $(PATH_MODERNCC) --print-prog-name=cc1) -quiet
-override CFLAGS += -mthumb -mthumb-interwork -O2 -mabi=apcs-gnu -mtune=arm7tdmi -march=armv4t -fno-toplevel-reorder -Wno-pointer-to-int-cast
-ROM := $(MODERN_ROM_NAME)
-OBJ_DIR := $(MODERN_OBJ_DIR_NAME)
-LIBPATH := -L "$(dir $(shell $(PATH_MODERNCC) -mthumb -print-file-name=libgcc.a))" -L "$(dir $(shell $(PATH_MODERNCC) -mthumb -print-file-name=libnosys.a))" -L "$(dir $(shell $(PATH_MODERNCC) -mthumb -print-file-name=libc.a))"
-LIB := $(LIBPATH) -lc -lnosys -lgcc -L../../libagbsyscall -lagbsyscall
-endif
+INCLUDE_DIRS := include
+INCLUDE_CPP_ARGS := $(INCLUDE_DIRS:%=-iquote %)
+INCLUDE_SCANINC_ARGS := $(INCLUDE_DIRS:%=-I %)
 
-CPPFLAGS := -iquote include -iquote $(GFLIB_SUBDIR) -Wno-trigraphs -DMODERN=$(MODERN)
-ifneq ($(MODERN),1)
-CPPFLAGS += -I tools/agbcc/include -I tools/agbcc -nostdinc -undef
+O_LEVEL ?= 2
+CPPFLAGS := $(INCLUDE_CPP_ARGS) -iquote $(GFLIB_SUBDIR) -Wno-trigraphs -DMODERN=$(MODERN)
+ifeq ($(MODERN),0)
+  CPPFLAGS += -I tools/agbcc/include -I tools/agbcc -nostdinc -undef
+  CC1 := tools/agbcc/bin/agbcc$(EXE)
+  override CFLAGS += -mthumb-interwork -Wimplicit -Wparentheses -Werror -O$(O_LEVEL) -fhex-asm -g
+  LIBPATH := -L ../../tools/agbcc/lib
+  LIB := $(LIBPATH) -lgcc -lc -L../../libagbsyscall -lagbsyscall
+else
+  # Note: The makefile must be set up to not call these if modern == 0
+  MODERNCC := $(PREFIX)gcc
+  PATH_MODERNCC := PATH="$(PATH)" $(MODERNCC)
+  CC1 := $(shell $(PATH_MODERNCC) --print-prog-name=cc1) -quiet
+  override CFLAGS += -mthumb -mthumb-interwork -O$(O_LEVEL) -mabi=apcs-gnu -mtune=arm7tdmi -march=armv4t -fno-toplevel-reorder -Wno-pointer-to-int-cast
+  LIBPATH := -L "$(dir $(shell $(PATH_MODERNCC) -mthumb -print-file-name=libgcc.a))" -L "$(dir $(shell $(PATH_MODERNCC) -mthumb -print-file-name=libnosys.a))" -L "$(dir $(shell $(PATH_MODERNCC) -mthumb -print-file-name=libc.a))"
+  LIB := $(LIBPATH) -lc -lnosys -lgcc -L../../libagbsyscall -lagbsyscall
+endif
+# Enable debug info if set
+ifeq ($(DINFO),1)
+  override CFLAGS += -g
 endif
 
 LDFLAGS = -Map ../../$(MAP)
 
+# Variable filled out in other make files
 AUTO_GEN_TARGETS :=
 include make_tools.mk
-SHA1 := $(shell { command -v sha1sum || command -v shasum; } 2>/dev/null) -c
+# Tool executables
 GFX       := $(TOOLS_DIR)/gbagfx/gbagfx$(EXE)
 AIF       := $(TOOLS_DIR)/aif2pcm/aif2pcm$(EXE)
 MID       := $(TOOLS_DIR)/mid2agb/mid2agb$(EXE)
@@ -138,6 +154,7 @@ MAPJSON   := $(TOOLS_DIR)/mapjson/mapjson$(EXE)
 JSONPROC  := $(TOOLS_DIR)/jsonproc/jsonproc$(EXE)
 
 PERL := perl
+SHA1 := $(shell { command -v sha1sum || command -v shasum; } 2>/dev/null) -c
 
 MAKEFLAGS += --no-print-directory
 
@@ -147,39 +164,36 @@ MAKEFLAGS += --no-print-directory
 .SECONDARY:
 # Delete files that weren't built properly
 .DELETE_ON_ERROR:
-
 # Secondary expansion is required for dependency variables in object rules.
 .SECONDEXPANSION:
 
-.PHONY: all rom clean compare tidy mostlyclean libagbsyscall modern tidymodern tidynonmodern
+RULES_NO_SCAN += libagbsyscall clean clean-assets tidy tidymodern tidynonmodern generated clean-generated
+.PHONY: all rom modern compare
+.PHONY: $(RULES_NO_SCAN)
 
 infoshell = $(foreach line, $(shell $1 | sed "s/ /__SPACE__/g"), $(info $(subst __SPACE__, ,$(line))))
 
-# Build tools when building the rom
-# Disable dependency scanning for clean/tidy/tools
-# Use a separate minimal makefile for speed
-# Since we don't need to reload most of this makefile
-ifeq (,$(filter-out all rom compare modern libagbsyscall syms,$(MAKECMDGOALS)))
-$(call infoshell, $(MAKE) -f make_tools.mk)
-$(call infoshell, $(MAKE) generated)
-else
-NODEP ?= 1
-endif
-
-# check if we need to scan dependencies based on the rule
-ifeq (,$(MAKECMDGOALS))
-  SCAN_DEPS ?= 1
-else
-  # clean, tidy, tools, mostlyclean, clean-tools, $(TOOLDIRS), tidymodern, tidynonmodern don't even build the ROM
-  # libagbsyscall does its own thing
-  ifeq (,$(filter-out clean tidy tools mostlyclean clean-tools $(TOOLDIRS) tidymodern tidynonmodern libagbsyscall,$(MAKECMDGOALS)))
-    SCAN_DEPS ?= 0
-  else
-    SCAN_DEPS ?= 1
+# Check if we need to scan dependencies based on the chosen rule OR user preference
+NODEP ?= 0
+# Check if we need to pre-build tools and generate assets based on the chosen rule.
+SETUP_PREREQS ?= 1
+# Disable dependency scanning for rules that don't need it.
+ifneq (,$(MAKECMDGOALS))
+  ifeq (,$(filter-out $(RULES_NO_SCAN),$(MAKECMDGOALS)))
+    NODEP := 1
+    SETUP_PREREQS := 0
   endif
 endif
 
-ifeq ($(SCAN_DEPS),1)
+ifeq ($(SETUP_PREREQS),1)
+  # If set on: Default target or a rule requiring a scan
+  # Forcibly execute `make tools` since we need them for what we are doing.
+  $(call infoshell, $(MAKE) -f make_tools.mk)
+  # Oh and also generate mapjson sources before we use `SCANINC`.
+  $(call infoshell, $(MAKE) generated)
+endif
+
+# Collect sources
 C_SRCS_IN := $(wildcard $(C_SUBDIR)/*.c $(C_SUBDIR)/*/*.c $(C_SUBDIR)/*/*/*.c)
 C_SRCS := $(foreach src,$(C_SRCS_IN),$(if $(findstring .inc.c,$(src)),,$(src)))
 C_OBJS := $(patsubst $(C_SUBDIR)/%.c,$(C_BUILDDIR)/%.o,$(C_SRCS))
@@ -187,7 +201,7 @@ C_OBJS := $(patsubst $(C_SUBDIR)/%.c,$(C_BUILDDIR)/%.o,$(C_SRCS))
 GFLIB_SRCS := $(wildcard $(GFLIB_SUBDIR)/*.c)
 GFLIB_OBJS := $(patsubst $(GFLIB_SUBDIR)/%.c,$(GFLIB_BUILDDIR)/%.o,$(GFLIB_SRCS))
 
-C_ASM_SRCS += $(wildcard $(C_SUBDIR)/*.s $(C_SUBDIR)/*/*.s $(C_SUBDIR)/*/*/*.s)
+C_ASM_SRCS := $(wildcard $(C_SUBDIR)/*.s $(C_SUBDIR)/*/*.s $(C_SUBDIR)/*/*/*.s)
 C_ASM_OBJS := $(patsubst $(C_SUBDIR)/%.s,$(C_BUILDDIR)/%.o,$(C_ASM_SRCS))
 
 ASM_SRCS := $(wildcard $(ASM_SUBDIR)/*.s)
@@ -210,29 +224,29 @@ OBJS_REL := $(patsubst $(OBJ_DIR)/%,%,$(OBJS))
 
 SUBDIRS  := $(sort $(dir $(OBJS)))
 $(shell mkdir -p $(SUBDIRS))
-endif
 
-syms: $(SYM)
+# Pretend rules that are actually flags defer to `make all`
+modern: all
+compare: all
 
+# Other rules
 rom: $(ROM)
 ifeq ($(COMPARE),1)
 	@$(SHA1) rom.sha1
 endif
 
-# For contributors to make sure a change didn't affect the contents of the ROM.
-compare: all
+syms: $(SYM)
 
-clean: mostlyclean clean-tools
+clean: tidy clean-tools clean-generated clean-assets
+	@$(MAKE) clean -C libagbsyscall
 
-mostlyclean: tidynonmodern tidymodern
-	find sound -iname '*.bin' -exec rm {} +
+clean-assets:
 	rm -f $(MID_SUBDIR)/*.s
-	find . \( -iname '*.1bpp' -o -iname '*.4bpp' -o -iname '*.8bpp' -o -iname '*.gbapal' -o -iname '*.lz' -o -iname '*.rl' -o -iname '*.latfont' -o -iname '*.hwjpnfont' -o -iname '*.fwjpnfont' \) -exec rm {} +
 	rm -f $(DATA_ASM_SUBDIR)/layouts/layouts.inc $(DATA_ASM_SUBDIR)/layouts/layouts_table.inc
 	rm -f $(DATA_ASM_SUBDIR)/maps/connections.inc $(DATA_ASM_SUBDIR)/maps/events.inc $(DATA_ASM_SUBDIR)/maps/groups.inc $(DATA_ASM_SUBDIR)/maps/headers.inc
+	find sound -iname '*.bin' -exec rm {} +
+	find . \( -iname '*.1bpp' -o -iname '*.4bpp' -o -iname '*.8bpp' -o -iname '*.gbapal' -o -iname '*.lz' -o -iname '*.rl' -o -iname '*.latfont' -o -iname '*.hwjpnfont' -o -iname '*.fwjpnfont' \) -exec rm {} +
 	find $(DATA_ASM_SUBDIR)/maps \( -iname 'connections.inc' -o -iname 'events.inc' -o -iname 'header.inc' \) -exec rm {} +
-	rm -f $(AUTO_GEN_TARGETS)
-	@$(MAKE) clean -C libagbsyscall
 
 tidy: tidynonmodern tidymodern
 
@@ -244,18 +258,13 @@ tidymodern:
 	rm -f $(MODERN_ROM_NAME) $(MODERN_ELF_NAME) $(MODERN_MAP_NAME)
 	rm -rf $(MODERN_OBJ_DIR_NAME)
 
-ifneq ($(MODERN),0)
-$(C_BUILDDIR)/berry_crush.o: override CFLAGS += -Wno-address-of-packed-member
-endif
-
+# Other rules
 include graphics_file_rules.mk
 include map_data_rules.mk
 include spritesheet_rules.mk
 include json_data_rules.mk
 include songs.mk
 
-generated: $(AUTO_GEN_TARGETS)
-
 %.s: ;
 %.png: ;
 %.pal: ;
@@ -271,119 +280,101 @@ generated: $(AUTO_GEN_TARGETS)
 $(CRY_SUBDIR)/%.bin: $(CRY_SUBDIR)/%.aif ; $(AIF) $< $@ --compress
 sound/%.bin: sound/%.aif ; $(AIF) $< $@
 
+# NOTE: Tools must have been built prior (FIXME)
+generated: tools $(AUTO_GEN_TARGETS)
+clean-generated:
+	-rm -f $(AUTO_GEN_TARGETS)
 
 ifeq ($(MODERN),0)
-$(C_BUILDDIR)/libc.o: CC1 := $(TOOLS_DIR)/agbcc/bin/old_agbcc$(EXE)
+$(C_BUILDDIR)/libc.o: CC1 := tools/agbcc/bin/old_agbcc$(EXE)
 $(C_BUILDDIR)/libc.o: CFLAGS := -O2
-
 $(C_BUILDDIR)/siirtc.o: CFLAGS := -mthumb-interwork
-
 $(C_BUILDDIR)/agb_flash.o: CFLAGS := -O -mthumb-interwork
 $(C_BUILDDIR)/agb_flash_1m.o: CFLAGS := -O -mthumb-interwork
 $(C_BUILDDIR)/agb_flash_mx.o: CFLAGS := -O -mthumb-interwork
-
-$(C_BUILDDIR)/m4a.o: CC1 := $(TOOLS_DIR)/agbcc/bin/old_agbcc$(EXE)
-
+$(C_BUILDDIR)/m4a.o: CC1 := tools/agbcc/bin/old_agbcc$(EXE)
 $(C_BUILDDIR)/record_mixing.o: CFLAGS += -ffreestanding
-$(C_BUILDDIR)/librfu_intr.o: CC1 := $(TOOLS_DIR)/agbcc/bin/agbcc_arm$(EXE)
+$(C_BUILDDIR)/librfu_intr.o: CC1 := tools/agbcc/bin/agbcc_arm$(EXE)
 $(C_BUILDDIR)/librfu_intr.o: CFLAGS := -O2 -mthumb-interwork -quiet
 else
 $(C_BUILDDIR)/librfu_intr.o: CFLAGS := -mthumb-interwork -O2 -mabi=apcs-gnu -mtune=arm7tdmi -march=armv4t -fno-toplevel-reorder -Wno-pointer-to-int-cast
+$(C_BUILDDIR)/berry_crush.o: override CFLAGS += -Wno-address-of-packed-member
 endif
 
-ifeq ($(DINFO),1)
-override CFLAGS += -g
-endif
+# Dependency rules (for the *.c & *.s sources to .o files)
+# Have to be explicit or else missing files won't be reported.
 
-# The dep rules have to be explicit or else missing files won't be reported.
 # As a side effect, they're evaluated immediately instead of when the rule is invoked.
-# It doesn't look like $(shell) can be deferred so there might not be a better way.
+# It doesn't look like $(shell) can be deferred so there might not be a better way (Icedude_907: there is soon).
 
-ifeq ($(SCAN_DEPS),1)
-ifeq ($(NODEP),1)
-$(C_BUILDDIR)/%.o: $(C_SUBDIR)/%.c
-ifeq (,$(KEEP_TEMPS))
-	@echo "$(CC1) <flags> -o $@ $<"
-	@$(CPP) $(CPPFLAGS) $< | $(PREPROC) $< charmap.txt -i | $(CC1) $(CFLAGS) -o - - | cat - <(echo -e ".text\n\t.align\t2, 0") | $(AS) $(ASFLAGS) -o $@ -
-else
-	@$(CPP) $(CPPFLAGS) $< -o $(C_BUILDDIR)/$*.i
-	@$(PREPROC) $(C_BUILDDIR)/$*.i charmap.txt | $(CC1) $(CFLAGS) -o $(C_BUILDDIR)/$*.s
-	@echo -e ".text\n\t.align\t2, 0\n" >> $(C_BUILDDIR)/$*.s
-	$(AS) $(ASFLAGS) -o $@ $(C_BUILDDIR)/$*.s
-endif
-else
+# For C dependencies.
+# Args: $1 = Output file without extension (build/assets/src/data), $2 = Input file (src/data.c)
 define C_DEP
-$1: $2 $$(shell $(SCANINC) -I include -I $(TOOLS_DIR)/agbcc/include -I gflib $2)
-ifeq (,$$(KEEP_TEMPS))
-	@echo "$$(CC1) <flags> -o $$@ $$<"
-	@$$(CPP) $$(CPPFLAGS) $$< | $$(PREPROC) $$< charmap.txt -i | $$(CC1) $$(CFLAGS) -o - - | cat - <(echo -e ".text\n\t.align\t2, 0") | $$(AS) $$(ASFLAGS) -o $$@ -
-else
-	@$$(CPP) $$(CPPFLAGS) $$< -o $$(C_BUILDDIR)/$3.i
-	@$$(PREPROC) $$(C_BUILDDIR)/$3.i charmap.txt | $$(CC1) $$(CFLAGS) -o $$(C_BUILDDIR)/$3.s
-	@echo -e ".text\n\t.align\t2, 0\n" >> $$(C_BUILDDIR)/$3.s
-	$$(AS) $$(ASFLAGS) -o $$@ $$(C_BUILDDIR)/$3.s
-endif
+$(call C_DEP_IMPL,$1,$2,$1)
 endef
-$(foreach src, $(C_SRCS), $(eval $(call C_DEP,$(patsubst $(C_SUBDIR)/%.c,$(C_BUILDDIR)/%.o,$(src)),$(src),$(patsubst $(C_SUBDIR)/%.c,%,$(src)))))
-endif
-
-ifeq ($(NODEP),1)
-$(GFLIB_BUILDDIR)/%.o: $(GFLIB_SUBDIR)/%.c $$(c_dep)
+# Internal implementation details.
+# $1: Output file without extension, $2 input file, $3 temp path (if keeping)
+define C_DEP_IMPL
+$1.o: $2
 ifeq (,$(KEEP_TEMPS))
-	@echo "$(CC1) <flags> -o $@ $<"
-	@$(CPP) $(CPPFLAGS) $< | $(PREPROC) $< charmap.txt -i | $(CC1) $(CFLAGS) -o - - | cat - <(echo -e ".text\n\t.align\t2, 0") | $(AS) $(ASFLAGS) -o $@ -
-else
-	@$(CPP) $(CPPFLAGS) $< -o $(GFLIB_BUILDDIR)/$*.i
-	@$(PREPROC) $(GFLIB_BUILDDIR)/$*.i charmap.txt | $(CC1) $(CFLAGS) -o $(GFLIB_BUILDDIR)/$*.s
-	@echo -e ".text\n\t.align\t2, 0\n" >> $(GFLIB_BUILDDIR)/$*.s
-	$(AS) $(ASFLAGS) -o $@ $(GFLIB_BUILDDIR)/$*.s
-endif
-else
-define GFLIB_DEP
-$1: $2 $$(shell $(SCANINC) -I include -I $(TOOLS_DIR)/agbcc/include -I gflib $2)
-ifeq (,$$(KEEP_TEMPS))
 	@echo "$$(CC1) <flags> -o $$@ $$<"
 	@$$(CPP) $$(CPPFLAGS) $$< | $$(PREPROC) $$< charmap.txt -i | $$(CC1) $$(CFLAGS) -o - - | cat - <(echo -e ".text\n\t.align\t2, 0") | $$(AS) $$(ASFLAGS) -o $$@ -
 else
-	@$$(CPP) $$(CPPFLAGS) $$< -o $$(GFLIB_BUILDDIR)/$3.i
-	@$$(PREPROC) $$(GFLIB_BUILDDIR)/$3.i charmap.txt | $$(CC1) $$(CFLAGS) -o $$(GFLIB_BUILDDIR)/$3.s
-	@echo -e ".text\n\t.align\t2, 0\n" >> $$(GFLIB_BUILDDIR)/$3.s
-	$$(AS) $$(ASFLAGS) -o $$@ $$(GFLIB_BUILDDIR)/$3.s
+	@$$(CPP) $$(CPPFLAGS) $$< -o $3.i
+	@$$(PREPROC) $3.i charmap.txt | $$(CC1) $$(CFLAGS) -o $3.s
+	@echo -e ".text\n\t.align\t2, 0\n" >> $3.s
+	$$(AS) $$(ASFLAGS) -o $$@ $3.s
+endif
+$(call C_SCANINC,$1,$2)
+endef
+# Calls SCANINC to find dependencies
+define C_SCANINC
+ifneq ($(NODEP),1)
+$1.o: $2 $$(shell $(SCANINC) $(INCLUDE_SCANINC_ARGS) -I tools/agbcc/include -I gflib $2)
 endif
 endef
-$(foreach src, $(GFLIB_SRCS), $(eval $(call GFLIB_DEP,$(patsubst $(GFLIB_SUBDIR)/%.c,$(GFLIB_BUILDDIR)/%.o, $(src)),$(src),$(patsubst $(GFLIB_SUBDIR)/%.c,%, $(src)))))
+
+# Create generic rules if no dependency scanning, else create the real rules
+ifeq ($(NODEP),1)
+$(eval $(call C_DEP,$(C_BUILDDIR)/%,$(C_SUBDIR)/%.c))
+$(eval $(call C_DEP,$(GFLIB_BUILDDIR)/%,$(GFLIB_SUBDIR)/%.c))
+else
+$(foreach src,$(C_SRCS),$(eval $(call C_DEP,$(OBJ_DIR)/$(basename $(src)),$(src))))
+$(foreach src,$(GFLIB_SRCS),$(eval $(call C_DEP,$(OBJ_DIR)/$(basename $(src)),$(src))))
 endif
 
-ifeq ($(NODEP),1)
-$(C_BUILDDIR)/%.o: $(C_SUBDIR)/%.s
-	$(PREPROC) $< charmap.txt | $(CPP) -I include - | $(AS) $(ASFLAGS) -o $@
-else
-define SRC_ASM_DATA_DEP
-$1: $2 $$(shell $(SCANINC) -I include -I "" $2)
-	$$(PREPROC) $$< charmap.txt | $$(CPP) -I include - | $$(AS) $$(ASFLAGS) -o $$@
-endef
-$(foreach src, $(C_ASM_SRCS), $(eval $(call SRC_ASM_DATA_DEP,$(patsubst $(C_SUBDIR)/%.s,$(C_BUILDDIR)/%.o, $(src)),$(src))))
-endif
-
-ifeq ($(NODEP),1)
-$(ASM_BUILDDIR)/%.o: $(ASM_SUBDIR)/%.s
-	$(AS) $(ASFLAGS) -o $@ $<
-else
+# Similar methodology for Assembly files
+# $1: Output path without extension, $2: Input file (`*.s`)
 define ASM_DEP
-$1: $2 $$(shell $(SCANINC) -I include -I "" $2)
+$1.o: $2
 	$$(AS) $$(ASFLAGS) -o $$@ $$<
+$(call ASM_SCANINC,$1,$2)
+endef
+# As above but first doing a preprocessor pass
+define ASM_DEP_PREPROC
+$1.o: $2
+	$$(PREPROC) $$< charmap.txt | $$(CPP) $(INCLUDE_SCANINC_ARGS) - | $$(AS) $$(ASFLAGS) -o $$@
+$(call ASM_SCANINC,$1,$2)
 endef
-$(foreach src, $(ASM_SRCS), $(eval $(call ASM_DEP,$(patsubst $(ASM_SUBDIR)/%.s,$(ASM_BUILDDIR)/%.o, $(src)),$(src))))
-endif
 
+define ASM_SCANINC
+ifneq ($(NODEP),1)
+$1.o: $2 $$(shell $(SCANINC) $(INCLUDE_SCANINC_ARGS) -I "" $2)
+endif
+endef
+
+# Dummy rules or real rules
 ifeq ($(NODEP),1)
-$(DATA_ASM_BUILDDIR)/%.o: $(DATA_ASM_SUBDIR)/%.s
-	$(PREPROC) $< charmap.txt | $(CPP) -I include - | $(AS) $(ASFLAGS) -o $@
+$(eval $(call ASM_DEP,$(ASM_BUILDDIR)/%,$(ASM_SUBDIR)/%.s))
+$(eval $(call ASM_DEP_PREPROC,$(C_BUILDDIR)/%,$(C_SUBDIR)/%.s))
+$(eval $(call ASM_DEP_PREPROC,$(DATA_ASM_BUILDDIR)/%,$(DATA_ASM_SUBDIR)/%.s))
 else
-$(foreach src, $(REGULAR_DATA_ASM_SRCS), $(eval $(call SRC_ASM_DATA_DEP,$(patsubst $(DATA_ASM_SUBDIR)/%.s,$(DATA_ASM_BUILDDIR)/%.o, $(src)),$(src))))
-endif
+$(foreach src, $(ASM_SRCS), $(eval $(call ASM_DEP,$(src:%.s=$(OBJ_DIR)/%),$(src))))
+$(foreach src, $(C_ASM_SRCS), $(eval $(call ASM_DEP_PREPROC,$(src:%.s=$(OBJ_DIR)/%),$(src))))
+$(foreach src, $(REGULAR_DATA_ASM_SRCS), $(eval $(call ASM_DEP_PREPROC,$(src:%.s=$(OBJ_DIR)/%),$(src))))
 endif
 
+# Additional rules
 $(SONG_BUILDDIR)/%.o: $(SONG_SUBDIR)/%.s
 	$(AS) $(ASFLAGS) -I sound -o $@ $<
 
@@ -396,6 +387,7 @@ $(OBJ_DIR)/sym_common.ld: sym_common.txt $(C_OBJS) $(wildcard common_syms/*.txt)
 $(OBJ_DIR)/sym_ewram.ld: sym_ewram.txt
 	$(RAMSCRGEN) ewram_data $< ENGLISH > $@
 
+# Linker script
 ifeq ($(MODERN),0)
 LD_SCRIPT := ld_script.txt
 LD_SCRIPT_DEPS := $(OBJ_DIR)/sym_bss.ld $(OBJ_DIR)/sym_common.ld $(OBJ_DIR)/sym_ewram.ld
@@ -405,25 +397,24 @@ LD_SCRIPT_DEPS :=
 endif
 
 $(OBJ_DIR)/ld_script.ld: $(LD_SCRIPT) $(LD_SCRIPT_DEPS)
-	cd $(OBJ_DIR) && sed "s#tools/#../../tools/#g" ../../$(LD_SCRIPT) > ld_script.ld
+	sed "s#tools/#tools/#g" $(LD_SCRIPT) > $(OBJ_DIR)/ld_script.ld
 
+# Final rules
+
+libagbsyscall:
+	@$(MAKE) -C libagbsyscall TOOLCHAIN=$(TOOLCHAIN) MODERN=$(MODERN)
+
+# Elf from object files
 $(ELF): $(OBJ_DIR)/ld_script.ld $(OBJS) libagbsyscall
 	@echo "cd $(OBJ_DIR) && $(LD) $(LDFLAGS) -T ld_script.ld -o ../../$@ <objects> <lib>"
 	@cd $(OBJ_DIR) && $(LD) $(LDFLAGS) -T ld_script.ld -o ../../$@ $(OBJS_REL) $(LIB)
 	$(FIX) $@ -t"$(TITLE)" -c$(GAME_CODE) -m$(MAKER_CODE) -r$(REVISION) --silent
 
+# Builds the rom from the elf file
 $(ROM): $(ELF)
 	$(OBJCOPY) -O binary $< $@
 	$(FIX) $@ -p --silent
 
-modern: all
-
-libagbsyscall:
-	@$(MAKE) -C libagbsyscall TOOLCHAIN=$(TOOLCHAIN) MODERN=$(MODERN)
-
-###################
-### Symbol file ###
-###################
-
+# Symbol file (`make syms`)
 $(SYM): $(ELF)
 	$(OBJDUMP) -t $< | sort -u | grep -E "^0[2389]" | $(PERL) -p -e 's/^(\w{8}) (\w).{6} \S+\t(\w{8}) (\S+)$$/\1 \2 \3 \4/g' > $@
diff --git a/make_tools.mk b/make_tools.mk
index 00824adda6..78ff1beeb0 100644
--- a/make_tools.mk
+++ b/make_tools.mk
@@ -9,7 +9,9 @@ TOOL_NAMES := aif2pcm bin2c gbafix gbagfx jsonproc mapjson mid2agb preproc ramsc
 
 TOOLDIRS := $(TOOL_NAMES:%=$(TOOLS_DIR)/%)
 
-.PHONY: tools check-tools clean-tools $(TOOLDIRS) $(CHECKTOOLDIRS)
+# Tool making doesnt require a pokeemerald dependency scan.
+RULES_NO_SCAN += tools check-tools clean-tools $(TOOLDIRS) $(CHECKTOOLDIRS)
+.PHONY: $(RULES_NO_SCAN)
 
 tools: $(TOOLDIRS)
 check-tools: $(CHECKTOOLDIRS)