Fix building and don't use bundled uchime.
--- a/Makefile
+++ b/Makefile
@@ -104,12 +104,19 @@ endif
 # INCLUDE directories for mothur
 #
 #
-	VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
+	VPATH=source:source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/
+    source := source
     skipUchime := source/uchime_src/
+    skipTestMothur := source/TestMothur/
+    skipSeqnoise := seqnoise.cpp
     subdirs :=  $(sort $(dir $(filter-out  $(skipUchime), $(wildcard source/*/))))
+    subdirs :=  $(filter-out  $(skipTestMothur), $(subdirs))
     subDirIncludes = $(patsubst %, -I %, $(subdirs))
+    subDirIncludes += $(patsubst %, -I %, $(source))
     subDirLinking =  $(patsubst %, -L%, $(subdirs))
-    CXXFLAGS += -I. $(subDirIncludes)
+    subDirLinking +=  $(patsubst %, -L%, $(source))
+    subdirs :=  $(dir source) $(sort $(dir $(filter-out  $(skipUchime), $(wildcard source/*/))))
+    CXXFLAGS += -Isource -I. $(subDirIncludes)
     LDFLAGS += $(subDirLinking)
 
 
@@ -118,15 +125,14 @@ endif
 #
     OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
     OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
+    OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard source/*.cpp)))
+    OBJECTS+=$(patsubst %.cpp,%.o,$(filter-out $(skipSeqnoise), $(wildcard source/*.c)))
     OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
     OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
 
-mothur : $(OBJECTS) uchime
+mothur : $(OBJECTS)
 	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
 
-uchime :
-	cd source/uchime_src && export CXX=$(CXX) && make clean && make && mv uchime ../../ && cd ..
-
 install : mothur
 
 ifeq  ($(strip $(INSTALL_DIR)),"\"Enter_your_mothur_install_path_here\"")
--- a/makefile-internal
+++ b/makefile-internal
@@ -115,7 +115,6 @@ endif
 
 mothur : $(OBJECTS)
     $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
-    strip mothur
 
 %.o : %.c %.h
     $(COMPILE.c) $(OUTPUT_OPTION) $<
--- a/source/uchime_src/makefile
+++ b/source/uchime_src/makefile
@@ -1,4 +1,4 @@
-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
+CXXFLAGS = -std=c++11 -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1
 LDFLAGS = -g
 
 #
@@ -26,4 +26,4 @@ install : uchime
 
 clean :
 	@rm -f $(OBJECTS)
-	
\ No newline at end of file
+	
--- a/source/writer.h
+++ b/source/writer.h
@@ -9,6 +9,7 @@
 #ifndef writer_h
 #define writer_h
 
+#include <memory>
 #include "sharedwriter.hpp"
 
 /***********************************************************************/