--- Makefile.orig	2019-09-30 19:02:13 UTC
+++ Makefile
@@ -100,7 +100,7 @@ endif
     subdirs :=  $(sort $(dir $(filter-out  $(skipUchime), $(wildcard source/*/))))
     subDirIncludes = $(patsubst %, -I %, $(subdirs))
     subDirLinking =  $(patsubst %, -L%, $(subdirs))
-    CXXFLAGS += -I. $(subDirIncludes)
+    CXXFLAGS += -Isource $(subDirIncludes)
     LDFLAGS += $(subDirLinking)
 
 
@@ -109,8 +109,8 @@ endif
 #
     OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
     OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
-    OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
-    OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+    OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard source/*.cpp))
+    OBJECTS+=$(patsubst %.c,%.o,$(wildcard source/*.c))
 
 mothur : $(OBJECTS) uchime
 	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)