diff --git a/Makefile b/Makefile
index 3d5059f7..9699a0ad 100644
--- a/Makefile
+++ b/Makefile
@@ -17,7 +17,7 @@
 #TEST_MMAP=1
 
 PROGNAME    = afl
-VERSION     = $(shell grep '^\#define VERSION ' config.h | cut -d '"' -f2)
+VERSION     = $(shell grep '^\#define VERSION ' include/config.h | cut -d '"' -f2)
 
 PREFIX     ?= /usr/local
 BIN_PATH    = $(PREFIX)/bin
@@ -31,7 +31,7 @@ PROGS       = afl-gcc afl-fuzz afl-showmap afl-tmin afl-gotcpu afl-analyze
 SH_PROGS    = afl-plot afl-cmin afl-whatsup afl-system-config
 
 CFLAGS     ?= -O3 -funroll-loops
-CFLAGS     += -Wall -D_FORTIFY_SOURCE=2 -g -Wno-pointer-sign \
+CFLAGS     += -Wall -D_FORTIFY_SOURCE=2 -g -Wno-pointer-sign -I include/ \
 	      -DAFL_PATH=\"$(HELPER_PATH)\" -DDOC_PATH=\"$(DOC_PATH)\" \
 	      -DBIN_PATH=\"$(BIN_PATH)\"
 
@@ -47,7 +47,7 @@ else
   TEST_CC   = afl-clang
 endif
 
-COMM_HDR    = alloc-inl.h config.h debug.h types.h
+COMM_HDR    = include/alloc-inl.h include/config.h include/debug.h include/types.h
 
 
 ifeq "$(shell echo '\#include <Python.h>@int main() {return 0; }' | tr @ '\n' | $(CC) -x c - -o .test -I$(PYTHON_INCLUDE) -lpython2.7 2>/dev/null && echo 1 || echo 0 )" "1"
@@ -123,37 +123,37 @@ endif
 ready:
 	@echo "[+] Everything seems to be working, ready to compile."
 
-afl-gcc: afl-gcc.c $(COMM_HDR) | test_x86
-	$(CC) $(CFLAGS) $@.c -o $@ $(LDFLAGS)
+afl-gcc: src/afl-gcc.c $(COMM_HDR) | test_x86
+	$(CC) $(CFLAGS) src/$@.c -o $@ $(LDFLAGS)
 	set -e; for i in afl-g++ afl-clang afl-clang++; do ln -sf afl-gcc $$i; done
 
-afl-as: afl-as.c afl-as.h $(COMM_HDR) | test_x86
-	$(CC) $(CFLAGS) $@.c -o $@ $(LDFLAGS)
+afl-as: src/afl-as.c include/afl-as.h $(COMM_HDR) | test_x86
+	$(CC) $(CFLAGS) src/$@.c -o $@ $(LDFLAGS)
 	ln -sf afl-as as
 
-afl-common.o : afl-common.c
-	$(CC) $(CFLAGS) -c afl-common.c
+afl-common.o : src/afl-common.c include/common.h
+	$(CC) $(CFLAGS) -c src/afl-common.c
 
-afl-forkserver.o : afl-forkserver.c
-	$(CC) $(CFLAGS) -c afl-forkserver.c
+afl-forkserver.o : src/afl-forkserver.c include/forkserver.h
+	$(CC) $(CFLAGS) -c src/afl-forkserver.c
 
-afl-sharedmem.o : afl-sharedmem.c
-	$(CC) $(CFLAGS) -c afl-sharedmem.c
+afl-sharedmem.o : src/afl-sharedmem.c include/sharedmem.h
+	$(CC) $(CFLAGS) -c src/afl-sharedmem.c
 
-afl-fuzz: afl-fuzz.c afl-common.o afl-sharedmem.o afl-forkserver.o $(COMM_HDR) | test_x86
-	$(CC) $(CFLAGS) $@.c afl-common.o afl-sharedmem.o afl-forkserver.o -o $@ $(LDFLAGS) $(PYFLAGS)
+afl-fuzz: src/afl-fuzz.c afl-common.o afl-sharedmem.o afl-forkserver.o $(COMM_HDR) | test_x86
+	$(CC) $(CFLAGS) src/$@.c afl-common.o afl-sharedmem.o afl-forkserver.o -o $@ $(LDFLAGS) $(PYFLAGS)
 
-afl-showmap: afl-showmap.c afl-common.o afl-sharedmem.o $(COMM_HDR) | test_x86
-	$(CC) $(CFLAGS) $@.c afl-common.o afl-sharedmem.o -o $@ $(LDFLAGS)
+afl-showmap: src/afl-showmap.c afl-common.o afl-sharedmem.o $(COMM_HDR) | test_x86
+	$(CC) $(CFLAGS) src/$@.c afl-common.o afl-sharedmem.o -o $@ $(LDFLAGS)
 
-afl-tmin: afl-tmin.c afl-common.o afl-sharedmem.o afl-forkserver.o $(COMM_HDR) | test_x86
-	$(CC) $(CFLAGS) $@.c afl-common.o afl-sharedmem.o afl-forkserver.o -o $@ $(LDFLAGS)
+afl-tmin: src/afl-tmin.c afl-common.o afl-sharedmem.o afl-forkserver.o $(COMM_HDR) | test_x86
+	$(CC) $(CFLAGS) src/$@.c afl-common.o afl-sharedmem.o afl-forkserver.o -o $@ $(LDFLAGS)
 
-afl-analyze: afl-analyze.c afl-common.o afl-sharedmem.o $(COMM_HDR) | test_x86
-	$(CC) $(CFLAGS) $@.c afl-common.o afl-sharedmem.o -o $@ $(LDFLAGS)
+afl-analyze: src/afl-analyze.c afl-common.o afl-sharedmem.o $(COMM_HDR) | test_x86
+	$(CC) $(CFLAGS) src/$@.c afl-common.o afl-sharedmem.o -o $@ $(LDFLAGS)
 
-afl-gotcpu: afl-gotcpu.c $(COMM_HDR) | test_x86
-	$(CC) $(CFLAGS) $@.c -o $@ $(LDFLAGS)
+afl-gotcpu: src/afl-gotcpu.c $(COMM_HDR) | test_x86
+	$(CC) $(CFLAGS) src/$@.c -o $@ $(LDFLAGS)
 
 
 ifndef AFL_NO_X86
diff --git a/TODO b/TODO
index cc075abd..08dc1bb8 100644
--- a/TODO
+++ b/TODO
@@ -68,5 +68,5 @@ Problem: Average targets (tiff, jpeg, unrar) go through 1500 edges.
     
 qemu_mode:
  - persistent mode patching the return address (WinAFL style)
- - instrument only comparison with immediate values by default when using compcov
+ - instrument only comparison with immediate values by default when using compcov (done)
 
diff --git a/alloc-inl.h b/include/alloc-inl.h
similarity index 100%
rename from alloc-inl.h
rename to include/alloc-inl.h
diff --git a/afl-as.h b/include/as.h
similarity index 100%
rename from afl-as.h
rename to include/as.h
diff --git a/afl-common.h b/include/common.h
similarity index 100%
rename from afl-common.h
rename to include/common.h
diff --git a/config.h b/include/config.h
similarity index 100%
rename from config.h
rename to include/config.h
diff --git a/debug.h b/include/debug.h
similarity index 100%
rename from debug.h
rename to include/debug.h
diff --git a/afl-forkserver.h b/include/forkserver.h
similarity index 100%
rename from afl-forkserver.h
rename to include/forkserver.h
diff --git a/hash.h b/include/hash.h
similarity index 100%
rename from hash.h
rename to include/hash.h
diff --git a/afl-sharedmem.h b/include/sharedmem.h
similarity index 100%
rename from afl-sharedmem.h
rename to include/sharedmem.h
diff --git a/types.h b/include/types.h
similarity index 100%
rename from types.h
rename to include/types.h
diff --git a/afl-analyze.c b/src/afl-analyze.c
similarity index 99%
rename from afl-analyze.c
rename to src/afl-analyze.c
index 18b7456d..e12f9194 100644
--- a/afl-analyze.c
+++ b/src/afl-analyze.c
@@ -26,8 +26,8 @@
 #include "debug.h"
 #include "alloc-inl.h"
 #include "hash.h"
-#include "afl-sharedmem.h"
-#include "afl-common.h"
+#include "sharedmem.h"
+#include "common.h"
 
 #include <stdio.h>
 #include <unistd.h>
diff --git a/afl-as.c b/src/afl-as.c
similarity index 99%
rename from afl-as.c
rename to src/afl-as.c
index 94595f24..063e3bcd 100644
--- a/afl-as.c
+++ b/src/afl-as.c
@@ -35,7 +35,7 @@
 #include "debug.h"
 #include "alloc-inl.h"
 
-#include "afl-as.h"
+#include "as.h"
 
 #include <stdio.h>
 #include <unistd.h>
diff --git a/afl-common.c b/src/afl-common.c
similarity index 100%
rename from afl-common.c
rename to src/afl-common.c
diff --git a/afl-forkserver.c b/src/afl-forkserver.c
similarity index 99%
rename from afl-forkserver.c
rename to src/afl-forkserver.c
index 226175e1..0051f6b0 100644
--- a/afl-forkserver.c
+++ b/src/afl-forkserver.c
@@ -1,7 +1,7 @@
 #include "config.h"
 #include "types.h"
 #include "debug.h"
-#include "afl-forkserver.h"
+#include "forkserver.h"
 
 #include <stdio.h>
 #include <unistd.h>
diff --git a/afl-fuzz.c b/src/afl-fuzz.c
similarity index 99%
rename from afl-fuzz.c
rename to src/afl-fuzz.c
index ec54cc85..0285a242 100644
--- a/afl-fuzz.c
+++ b/src/afl-fuzz.c
@@ -33,9 +33,9 @@
 #include "debug.h"
 #include "alloc-inl.h"
 #include "hash.h"
-#include "afl-sharedmem.h"
-#include "afl-forkserver.h"
-#include "afl-common.h"
+#include "sharedmem.h"
+#include "forkserver.h"
+#include "common.h"
 
 #include <stdio.h>
 #include <unistd.h>
diff --git a/afl-gcc.c b/src/afl-gcc.c
similarity index 100%
rename from afl-gcc.c
rename to src/afl-gcc.c
diff --git a/afl-gotcpu.c b/src/afl-gotcpu.c
similarity index 100%
rename from afl-gotcpu.c
rename to src/afl-gotcpu.c
diff --git a/afl-sharedmem.c b/src/afl-sharedmem.c
similarity index 99%
rename from afl-sharedmem.c
rename to src/afl-sharedmem.c
index 400a0a46..3fd38444 100644
--- a/afl-sharedmem.c
+++ b/src/afl-sharedmem.c
@@ -9,7 +9,7 @@
 #include "debug.h"
 #include "alloc-inl.h"
 #include "hash.h"
-#include "afl-sharedmem.h"
+#include "sharedmem.h"
 
 #include <stdio.h>
 #include <unistd.h>
diff --git a/afl-showmap.c b/src/afl-showmap.c
similarity index 99%
rename from afl-showmap.c
rename to src/afl-showmap.c
index 96b7b5e0..66c77094 100644
--- a/afl-showmap.c
+++ b/src/afl-showmap.c
@@ -28,8 +28,8 @@
 #include "debug.h"
 #include "alloc-inl.h"
 #include "hash.h"
-#include "afl-sharedmem.h"
-#include "afl-common.h"
+#include "sharedmem.h"
+#include "common.h"
 
 #include <stdio.h>
 #include <unistd.h>
diff --git a/afl-tmin.c b/src/afl-tmin.c
similarity index 99%
rename from afl-tmin.c
rename to src/afl-tmin.c
index e83b217d..663bb510 100644
--- a/afl-tmin.c
+++ b/src/afl-tmin.c
@@ -27,9 +27,9 @@
 #include "debug.h"
 #include "alloc-inl.h"
 #include "hash.h"
-#include "afl-forkserver.h"
-#include "afl-sharedmem.h"
-#include "afl-common.h"
+#include "forkserver.h"
+#include "sharedmem.h"
+#include "common.h"
 
 #include <stdio.h>
 #include <unistd.h>
diff --git a/test-instr.c b/src/test-instr.c
similarity index 100%
rename from test-instr.c
rename to src/test-instr.c