diff --git a/cdatapack/cdatapack.h b/cdatapack/cdatapack.h
--- a/cdatapack/cdatapack.h
+++ b/cdatapack/cdatapack.h
@@ -7,12 +7,12 @@
 #ifndef CDATAPACK_CDATAPACK_H
 #define CDATAPACK_CDATAPACK_H
 
-#include <stdint.h>
+#include <stdbool.h>
 #include <stddef.h>
-#include <stdbool.h>
+#include <stdint.h>
 #include <sys/types.h>
 
-#include "portability/portability.h"
+#include "clib/portability/portability.h"
 
 #define NODE_SZ 20
 
diff --git a/cdatapack/cdatapack.c b/cdatapack/cdatapack.c
--- a/cdatapack/cdatapack.c
+++ b/cdatapack/cdatapack.c
@@ -4,6 +4,8 @@
 //
 // no-check-code
 
+#include "cdatapack/cdatapack.h"
+
 // be64toh is only available if _DEFAULT_SOURCE is defined for glibc >= 2.19,
 // or _BSD_SOURCE is defined for glibc < 2.19. These have to be defined before
 // #include <features.h>. Macros testing glibc version are defined by
@@ -36,11 +38,10 @@
 #endif /* #if defined(__APPLE__) */
 
 #include <lz4.h>
-#include "portability/inet.h"
-#include "portability/unistd.h"
 
-#include "cdatapack.h"
-#include "buffer.h"
+#include "clib/buffer.h"
+#include "clib/portability/inet.h"
+#include "clib/portability/unistd.h"
 
 #define MAX_PAGED_IN_DATAPACK  (1024 * 1024 * 1024)
 
diff --git a/cdatapack/cdatapack_dump.c b/cdatapack/cdatapack_dump.c
--- a/cdatapack/cdatapack_dump.c
+++ b/cdatapack/cdatapack_dump.c
@@ -5,12 +5,13 @@
 //
 // no-check-code
 
+#include <inttypes.h>
 #include <memory.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <inttypes.h>
-#include "convert.h"
-#include "cdatapack.h"
+
+#include "cdatapack/cdatapack.h"
+#include "clib/convert.h"
 
 #define DATAIDX_EXT  ".dataidx"
 #define DATAPACK_EXT ".datapack"
diff --git a/cdatapack/cdatapack_get.c b/cdatapack/cdatapack_get.c
--- a/cdatapack/cdatapack_get.c
+++ b/cdatapack/cdatapack_get.c
@@ -9,9 +9,9 @@
 #include <stdio.h>
 #include <stdlib.h>
 
-#include "cdatapack.h"
+#include "cdatapack/cdatapack.h"
+#include "clib/convert.h"
 #include "clib/sha1.h"
-#include "convert.h"
 
 #define DATAIDX_EXT  ".dataidx"
 #define DATAPACK_EXT ".datapack"
diff --git a/clib/buffer.c b/clib/buffer.c
--- a/clib/buffer.c
+++ b/clib/buffer.c
@@ -8,7 +8,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "buffer.h"
+#include "clib/buffer.h"
 
 bool buffer_append(
     char **buffer, size_t *buffer_idx, size_t *buffer_sz,
diff --git a/cstore/bitmanipulation.h b/cstore/bitmanipulation.h
--- a/cstore/bitmanipulation.h
+++ b/cstore/bitmanipulation.h
@@ -1,7 +1,7 @@
 #ifndef _HG_BITMANIPULATION_H_
 #define _HG_BITMANIPULATION_H_
 
-#include "compat.h"
+#include "cstore/compat.h"
 
 static inline uint32_t getbe32(const char *c)
 {
diff --git a/cstore/datapackstore.h b/cstore/datapackstore.h
--- a/cstore/datapackstore.h
+++ b/cstore/datapackstore.h
@@ -11,16 +11,16 @@
 #define DATAPACKSTORE_H
 
 extern "C" {
-#include "cdatapack.h"
+#include "cdatapack/cdatapack.h"
 }
 
+#include <ctime>
 #include <string>
-#include <ctime>
 #include <unordered_set>
 #include <vector>
 
-#include "key.h"
-#include "portability/portability.h"
+#include "clib/portability/portability.h"
+#include "cstore/key.h"
 
 const clock_t PACK_REFRESH_RATE = 0.1 * CLOCKS_PER_SEC;
 
diff --git a/cstore/datapackstore.cpp b/cstore/datapackstore.cpp
--- a/cstore/datapackstore.cpp
+++ b/cstore/datapackstore.cpp
@@ -7,14 +7,15 @@
 //
 // no-check-code
 
-#include "datapackstore.h"
-#include "key.h"
+#include "cstore/datapackstore.h"
 
 #include <sys/types.h>
 #include <dirent.h>
 #include <stdexcept>
 #include <stdlib.h>
 
+#include "cstore/key.h"
+
 std::vector<std::string> getAvailablePackFiles(const std::string &path) {
   std::vector<std::string> results;
 
diff --git a/cstore/key.h b/cstore/key.h
--- a/cstore/key.h
+++ b/cstore/key.h
@@ -11,11 +11,10 @@
 #define KEY_H
 
 #include <cstring>
+#include <stdexcept>
 #include <vector>
-#include <stdexcept>
 
-#include "convert.h"
-#include "convert.h"
+#include "clib/convert.h"
 
 /* Represents a key into the Mercurial store. Each key is a (name, node) pair,
  * though store implementations can choose to ignore the name in some cases. */
diff --git a/cstore/mpatch.h b/cstore/mpatch.h
--- a/cstore/mpatch.h
+++ b/cstore/mpatch.h
@@ -5,6 +5,8 @@
 #define MPATCH_ERR_CANNOT_BE_DECODED -2
 #define MPATCH_ERR_INVALID_PATCH -1
 
+#include "clib/portability/unistd.h"
+
 struct mpatch_frag {
 	int start, end, len;
 	const char *data;
diff --git a/cstore/mpatch.c b/cstore/mpatch.c
--- a/cstore/mpatch.c
+++ b/cstore/mpatch.c
@@ -19,13 +19,13 @@
  This software may be used and distributed according to the terms
  of the GNU General Public License, incorporated herein by reference.
 */
+#include "cstore/mpatch.h"
 
 #include <stdlib.h>
 #include <string.h>
 
-#include "bitmanipulation.h"
-#include "compat.h"
-#include "mpatch.h"
+#include "cstore/bitmanipulation.h"
+#include "cstore/compat.h"
 
 static struct mpatch_flist *lalloc(ssize_t size)
 {
diff --git a/cstore/py-cdatapack.h b/cstore/py-cdatapack.h
--- a/cstore/py-cdatapack.h
+++ b/cstore/py-cdatapack.h
@@ -15,7 +15,7 @@
 #include <Python.h>
 
 extern "C" {
-#include "cdatapack.h"
+#include "cdatapack/cdatapack.h"
 }
 
 // ====  py_cdatapack PyObject declaration ====
diff --git a/cstore/py-cstore.cpp b/cstore/py-cstore.cpp
--- a/cstore/py-cstore.cpp
+++ b/cstore/py-cstore.cpp
@@ -13,9 +13,9 @@
 
 #include <Python.h>
 
-#include "py-cdatapack.h"
-#include "py-datapackstore.h"
-#include "py-treemanifest.h"
+#include "cstore/py-cdatapack.h"
+#include "cstore/py-datapackstore.h"
+#include "cstore/py-treemanifest.h"
 
 static PyMethodDef mod_methods[] = {
   {NULL, NULL}
diff --git a/cstore/py-datapackstore.h b/cstore/py-datapackstore.h
--- a/cstore/py-datapackstore.h
+++ b/cstore/py-datapackstore.h
@@ -15,14 +15,14 @@
 #include <string>
 
 extern "C" {
-#include "cdatapack.h"
+#include "cdatapack/cdatapack.h"
 }
 
-#include "pythonutil.h"
-#include "datapackstore.h"
-#include "key.h"
-#include "py-structs.h"
-#include "uniondatapackstore.h"
+#include "cstore/datapackstore.h"
+#include "cstore/key.h"
+#include "cstore/py-structs.h"
+#include "cstore/pythonutil.h"
+#include "cstore/uniondatapackstore.h"
 
 // --------- DatapackStore Implementation ---------
 
diff --git a/cstore/py-structs.h b/cstore/py-structs.h
--- a/cstore/py-structs.h
+++ b/cstore/py-structs.h
@@ -12,8 +12,9 @@
 
 #include <memory>
 
-#include "datapackstore.h"
-#include "uniondatapackstore.h"
+#include "cstore/datapackstore.h"
+#include "cstore/pythonutil.h"
+#include "cstore/uniondatapackstore.h"
 
 struct py_datapackstore {
   PyObject_HEAD;
diff --git a/cstore/py-treemanifest.h b/cstore/py-treemanifest.h
--- a/cstore/py-treemanifest.h
+++ b/cstore/py-treemanifest.h
@@ -14,12 +14,12 @@
 #include <memory>
 #include <string>
 
-#include "convert.h"
-#include "manifest.h"
-#include "pythonutil.h"
-#include "treemanifest.h"
-#include "uniondatapackstore.h"
-#include "py-structs.h"
+#include "clib/convert.h"
+#include "cstore/py-structs.h"
+#include "cstore/pythonutil.h"
+#include "cstore/uniondatapackstore.h"
+#include "ctreemanifest/manifest.h"
+#include "ctreemanifest/treemanifest.h"
 
 #define FILENAME_BUFFER_SIZE 16348
 #define FLAG_SIZE 1
diff --git a/cstore/pythonutil.h b/cstore/pythonutil.h
--- a/cstore/pythonutil.h
+++ b/cstore/pythonutil.h
@@ -20,10 +20,10 @@
 // Py_BuildValue treats NULL as NONE, so we have to have a non-null pointer.
 #define MAGIC_EMPTY_STRING ""
 
-#include "store.h"
-#include "key.h"
-#include "match.h"
-#include "treemanifest.h"
+#include "cstore/key.h"
+#include "cstore/match.h"
+#include "cstore/store.h"
+#include "ctreemanifest/treemanifest.h"
 
 /**
  * C++ exception that represents an issue at the python C api level.
diff --git a/cstore/store.h b/cstore/store.h
--- a/cstore/store.h
+++ b/cstore/store.h
@@ -10,9 +10,10 @@
 #ifndef STORE_H
 #define STORE_H
 
-#include "key.h"
+#include <cstddef>
 #include <memory>
-#include <cstddef>
+
+#include "cstore/key.h"
 
 class ConstantStringRef {
   private:
diff --git a/cstore/uniondatapackstore.h b/cstore/uniondatapackstore.h
--- a/cstore/uniondatapackstore.h
+++ b/cstore/uniondatapackstore.h
@@ -10,17 +10,17 @@
 #ifndef UNIONDATAPACKSTORE_H
 #define UNIONDATAPACKSTORE_H
 
+#include <cstring>
+#include <stdexcept>
+#include <vector>
+
 extern "C" {
-#include "cdatapack.h"
+#include "cdatapack/cdatapack.h"
 }
 
-#include "key.h"
-#include "datapackstore.h"
-#include "store.h"
-
-#include <cstring>
-#include <vector>
-#include <stdexcept>
+#include "cstore/key.h"
+#include "cstore/datapackstore.h"
+#include "cstore/store.h"
 
 class UnionDatapackStore;
 class UnionDatapackStoreKeyIterator : public KeyIterator {
diff --git a/cstore/uniondatapackstore.cpp b/cstore/uniondatapackstore.cpp
--- a/cstore/uniondatapackstore.cpp
+++ b/cstore/uniondatapackstore.cpp
@@ -7,13 +7,13 @@
 //
 // no-check-code
 
+#include "cstore/uniondatapackstore.h"
+
 #include <algorithm>
 #include <memory>
 
-#include "uniondatapackstore.h"
-
 extern "C" {
-#include "mpatch.h"
+#include "cstore/mpatch.h"
 }
 
 UnionDatapackStore::UnionDatapackStore(std::vector<DatapackStore*> stores) :
diff --git a/ctreemanifest/manifest.h b/ctreemanifest/manifest.h
--- a/ctreemanifest/manifest.h
+++ b/ctreemanifest/manifest.h
@@ -14,7 +14,7 @@
 #include <list>
 #include <stdexcept>
 
-#include "convert.h"
+#include "clib/convert.h"
 
 class Manifest;
 class ManifestIterator;
@@ -41,15 +41,17 @@
     bool isnull() const;
 };
 
-#include "manifest_entry.h"
-#include "store.h"
-
 enum FindResultType {
   RESULT_FILE,
   RESULT_DIRECTORY,
   RESULT_FILE_OR_DIRECTORY,
 };
 
+class ManifestEntry;
+
+#include "cstore/store.h"
+#include "ctreemanifest/manifest_entry.h"
+
 /**
  * This class represents a view on a particular Manifest instance. It provides
  * access to the list of files/directories at one level of the tree, not the
diff --git a/ctreemanifest/manifest.cpp b/ctreemanifest/manifest.cpp
--- a/ctreemanifest/manifest.cpp
+++ b/ctreemanifest/manifest.cpp
@@ -7,7 +7,8 @@
 //
 // no-check-code
 
-#include "manifest.h"
+#include "ctreemanifest/manifest.h"
+
 #include "clib/sha1.h"
 
 Manifest::Manifest(ConstantStringRef &rawobj, const char *node) :
diff --git a/ctreemanifest/manifest_entry.h b/ctreemanifest/manifest_entry.h
--- a/ctreemanifest/manifest_entry.h
+++ b/ctreemanifest/manifest_entry.h
@@ -14,11 +14,9 @@
 #include <cstring>
 #include <string>
 
-class ManifestEntry;
-
-#include "convert.h"
-#include "manifest.h"
-#include "manifest_fetcher.h"
+#include "clib/convert.h"
+#include "ctreemanifest/manifest.h"
+#include "ctreemanifest/manifest_fetcher.h"
 
 #define MANIFEST_DIRECTORY_FLAG 't'
 #define MANIFEST_DIRECTORY_FLAGPTR (&"t"[0])
diff --git a/ctreemanifest/manifest_entry.cpp b/ctreemanifest/manifest_entry.cpp
--- a/ctreemanifest/manifest_entry.cpp
+++ b/ctreemanifest/manifest_entry.cpp
@@ -7,7 +7,8 @@
 //
 // no-check-code
 
-#include "manifest_entry.h"
+#include "ctreemanifest/manifest_entry.h"
+
 #include <cassert>
 
 ManifestEntry::ManifestEntry()
diff --git a/ctreemanifest/manifest_fetcher.h b/ctreemanifest/manifest_fetcher.h
--- a/ctreemanifest/manifest_fetcher.h
+++ b/ctreemanifest/manifest_fetcher.h
@@ -15,8 +15,8 @@
 
 class ManifestFetcher;
 
-#include "manifest.h"
-#include "store.h"
+#include "cstore/store.h"
+#include "ctreemanifest/manifest.h"
 
 /**
  * Class used to obtain Manifests, given a path and node.
diff --git a/ctreemanifest/manifest_fetcher.cpp b/ctreemanifest/manifest_fetcher.cpp
--- a/ctreemanifest/manifest_fetcher.cpp
+++ b/ctreemanifest/manifest_fetcher.cpp
@@ -7,7 +7,7 @@
 //
 // no-check-code
 
-#include "manifest_fetcher.h"
+#include "ctreemanifest/manifest_fetcher.h"
 
 ManifestFetcher::ManifestFetcher(std::shared_ptr<Store> store) :
   _store(store) {
diff --git a/ctreemanifest/treemanifest.h b/ctreemanifest/treemanifest.h
--- a/ctreemanifest/treemanifest.h
+++ b/ctreemanifest/treemanifest.h
@@ -14,9 +14,10 @@
 #include <string>
 #include <vector>
 
-#include "manifest.h"
-#include "manifest_fetcher.h"
-#include "match.h"
+#include "cstore/match.h"
+#include "ctreemanifest/manifest.h"
+#include "ctreemanifest/manifest_entry.h"
+#include "ctreemanifest/manifest_fetcher.h"
 
 enum FindResult {
   FIND_PATH_OK,
diff --git a/ctreemanifest/treemanifest.cpp b/ctreemanifest/treemanifest.cpp
--- a/ctreemanifest/treemanifest.cpp
+++ b/ctreemanifest/treemanifest.cpp
@@ -7,7 +7,8 @@
 //
 // no-check-code
 
-#include "treemanifest.h"
+#include "ctreemanifest/treemanifest.h"
+
 #include <cassert>
 
 /**
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -161,13 +161,14 @@
     availablelibraries = {
         'datapack': {
             "sources" : ["cdatapack/cdatapack.c"],
-            "include_dirs" : ["clib"] + include_dirs,
+            "include_dirs" : ["."] + include_dirs,
             "libraries" : ["lz4", SHA1_LIBRARY],
             "extra_args" : filter(None,
                 [STDC99, WALL, WERROR, WSTRICTPROTOTYPES] + cflags),
         },
         'mpatch': {
-            'sources': ['cstore/mpatch.c']
+            "sources": ["cstore/mpatch.c"],
+            "include_dirs" : ["."] + include_dirs,
         },
         "sha1detectcoll": {
             "sources" : [
@@ -248,10 +249,6 @@
                 ],
                 include_dirs=[
                     '.',
-                    'ctreemanifest',
-                    'cdatapack',
-                    'clib',
-                    'cstore',
                     'third-party',
                 ] + include_dirs,
                 library_dirs=[
@@ -316,7 +313,7 @@
         'traceprof': [
             Extension('hgext3rd.traceprof',
                 sources=['hgext3rd/traceprof.pyx'],
-                include_dirs=['hgext3rd/'],
+                include_dirs=['hgext3rd'],
                 extra_compile_args=filter(None, [
                     OPTIMIZATION, STDCPP0X, WALL, WEXTRA, WCONVERSION, PEDANTIC,
                     PRODUCEDEBUGSYMBOLS