- Make build system verbose by default, as required by Gentoo policy
  See also: https://bugs.gentoo.org/show_bug.cgi?id=429308
- Remove CFLAGS and CXXFLAGS defaults
- Fix order of flags and honour CPPFLAGS for LFS support
  and LDFLAGS for --as-needed, respectively

--- a/CommonSource/DataStructures/Makefile
+++ b/CommonSource/DataStructures/Makefile
@@ -22,7 +22,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/CommonSource/ExternalReadFormats/Makefile
+++ b/CommonSource/ExternalReadFormats/Makefile
@@ -22,7 +22,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/CommonSource/MosaikReadFormat/Makefile
+++ b/CommonSource/MosaikReadFormat/Makefile
@@ -22,7 +22,7 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 clean:
 	@echo "Cleaning up."
--- a/CommonSource/PairwiseAlignment/Makefile
+++ b/CommonSource/PairwiseAlignment/Makefile
@@ -26,11 +26,11 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(CBUILT_OBJECTS): $(CSOURCES)
 	@echo "  * compiling" $(*F).c
-	@$(CC) -c -o $@ $(*F).c -O3 $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).c
 
 clean:
 	@echo "Cleaning up."
--- a/CommonSource/Utilities/Makefile
+++ b/CommonSource/Utilities/Makefile
@@ -48,11 +48,11 @@
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(CBUILT_OBJECTS): $(CSOURCES)
 	@echo "  * compiling" $(*F).c
-	@$(CC) -c -o $@ $(*F).c -O3 -w -DSQLITE_OMIT_LOAD_EXTENSION $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CC) $(CFLAGS) $(CPPFLAGS) -DSQLITE_OMIT_LOAD_EXTENSION $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).c
 
 clean:
 	@echo "Cleaning up."
--- a/fann-2.1.0/Makefile
+++ b/fann-2.1.0/Makefile
@@ -12,7 +12,7 @@
 
 $(CBUILT_OBJECTS): $(CSOURCES)
 	@echo "  * compiling" $(*F).c
-	@$(CC) -c -o $@ $(*F).c -O3 $(PLATFORM_FLAGS) -I$(INCLUDES) 
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) -I$(INCLUDES) -c -o $@ $(*F).c
 
 clean:
 	@echo "Cleaning up."
--- a/Makefile
+++ b/Makefile
@@ -4,8 +4,8 @@
 # ==========================
 
 # define our object and binary directories
-export OBJ_DIR = ../obj
-export BIN_DIR = ../bin
+export OBJ_DIR = ./obj
+export BIN_DIR = ./bin
 
 # define our common source directories
 export ASSEMBLY_DIR = CommonSource/AssemblyFormats
@@ -16,20 +16,6 @@
 export PAIRWISE_DIR = CommonSource/PairwiseAlignment
 export UTILITIES_DIR = CommonSource/Utilities
 
-# define some default flags
-FLAGS = -Wall -Wno-char-subscripts -ansi -O3
-#FLAGS = -Wall -Wno-char-subscripts -ansi -g -D VERBOSE_DEBUG #gdb debugging
-#FLAGS = -Wall -Wno-char-subscripts -ansi -O3 -D VERBOSE_DEBUG #enables verbose debugging
-CFLAGS =
-CXXFLAGS =
-#CXXFLAGS = -ansi -pedantic -Wextra -Weffc++
-CFLAGS += $(FLAGS)
-CXXFLAGS += $(FLAGS)
-export CFLAGS
-export CXXFLAGS
-#export LDFLAGS = -Wl
-export CXX ?= g++
-
 # define our platform
 export BLD_PLATFORM ?= linux
 include includes/$(BLD_PLATFORM).inc
--- a/MosaikAligner/Makefile
+++ b/MosaikAligner/Makefile
@@ -68,11 +68,11 @@
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(TD)$(DATA_STRUCT_DIR)
--- a/MosaikBuild/Makefile
+++ b/MosaikBuild/Makefile
@@ -26,11 +26,11 @@
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(TD)$(DATA_STRUCT_DIR)
--- a/MosaikJump/Makefile
+++ b/MosaikJump/Makefile
@@ -26,11 +26,11 @@
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(TD)$(MOSAIKREAD_DIR)
--- a/MosaikText/Makefile
+++ b/MosaikText/Makefile
@@ -26,11 +26,11 @@
 
 $(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
 	@echo "  * linking $(PROGRAM)"
-	@$(CXX) $(LDFLAGS) $(CXXFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) $(PLATFORM_FLAGS) -o $(TD)$(BIN_DIR)/$@ $^ $(LIBS)
 
 $(BUILT_OBJECTS): $(SOURCES)
 	@echo "  * compiling" $(*F).cpp
-	@$(CXX) -c -o $@ $(*F).cpp $(CXXFLAGS) $(PLATFORM_FLAGS) $(INCLUDES)
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(PLATFORM_FLAGS) $(INCLUDES) -c -o $@ $(*F).cpp
 
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(TD)$(MOSAIKREAD_DIR)
--- a/networkFile/retrainCode/attachXC/Makefile
+++ b/networkFile/retrainCode/attachXC/Makefile
@@ -3,12 +3,11 @@
 # (c) 2012 Wan-Ping Lee
 # ==========================
 
-FLAGS = -Wall -O3
 
 
 all: xc_pe.cpp xc_se.cpp
-	@$(CXX) $(FLAGS) xc_pe.cpp -o xc_pe
-	@$(CXX) $(FLAGS) xc_se.cpp -o xc_se
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) xc_pe.cpp -o xc_pe
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS) xc_se.cpp -o xc_se
 
 .PHONY: all
 
--- a/networkFile/retrainCode/trainNetwork/Makefile
+++ b/networkFile/retrainCode/trainNetwork/Makefile
@@ -5,8 +5,6 @@
 
 OBJ_DIR = ./obj
 
-FLAGS =  -Wall -O3
-CFLAGS = -O3
 FANN=../../../fann-2.1.0
 
 SOURCES = sam_parser_float.cpp parameter_parser_float.cpp mq_train_float.cpp
@@ -15,12 +13,12 @@
 all: $(FANN)/floatfann.c $(SOURCES)
 	@test -d $(OBJ_DIR) || mkdir $(OBJ_DIR)
 	@echo "  * compiling ......"
-	@$(CC) $(CFLAGS) -c -o $(OBJ_DIR)/floatfann.o $(FANN)/floatfann.c -I$(FANN)/include
-	@$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/sam_parser_float.o sam_parser_float.cpp
-	@$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/parameter_parser_float.o parameter_parser_float.cpp
-	@$(CXX) -c $(FLAGS) -o $(OBJ_DIR)/mq_train_float.o mq_train_float.cpp -I$(FANN)/include
+	$(CC)  $(CFLAGS)   $(CPPFLAGS) -c -o $(OBJ_DIR)/floatfann.o $(FANN)/floatfann.c -I$(FANN)/include
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/sam_parser_float.o sam_parser_float.cpp
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/parameter_parser_float.o parameter_parser_float.cpp
+	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c -o $(OBJ_DIR)/mq_train_float.o mq_train_float.cpp -I$(FANN)/include
 	@echo "  * linking ......"
-	@$(CXX) $(FLAGS) $(OBJ_DIR)/*.o -o $(PROGRAM)
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) $(OBJ_DIR)/*.o -o $(PROGRAM)
 
 .PHONY: all