diff --git a/App/App.pro b/App/App.pro
index f1c70ad043a8a7427af3cddc5882cb153e552042..7edadfe2e8cdf2131f1e884a1c9b5a0995bb339e 100644
--- a/App/App.pro
+++ b/App/App.pro
@@ -171,7 +171,7 @@ DEPENDPATH  += $$PWD/../Fit/Factory/inc
 # generate ROOT dictionaries
 # -----------------------------------------------------------------------------
 BORNAGAIN_ROOT_DICT_FOR_CLASSES =  inc/App.h inc/AppLinkDef.h
-BORNAGAIN_ROOT_DICT_INCLUDES = ../Core/Tools/inc
+BORNAGAIN_ROOT_DICT_INCLUDES = $$PWD/../Core/Tools/inc
 
 # -----------------------------------------------------------------------------
 # general project settings
diff --git a/Doc/UserManual/UserManual.pdf b/Doc/UserManual/UserManual.pdf
index 6a12d251ea653850418f776ba420e83791467f8b..3b19173a0a6bfdfb8f30dd305e70a0c4a22bf9f2 100644
Binary files a/Doc/UserManual/UserManual.pdf and b/Doc/UserManual/UserManual.pdf differ
diff --git a/Doc/UserManual/UserManual.tex b/Doc/UserManual/UserManual.tex
index ea2a15141b0ccce6cd00c6de1b1ba9a66971b344..afcc4514900bb5cfb72de4ca359be17a729cb233 100644
--- a/Doc/UserManual/UserManual.tex
+++ b/Doc/UserManual/UserManual.tex
@@ -157,7 +157,7 @@ keepaspectratio]{results2_2.png}%
 %\chapter{Working with BornAgain}
 \input{Introduction}
 \input{QuickStart}
-%\input{SoftwareArchitecture}
+\input{SoftwareArchitecture}
 %\input{Installation}
 %\input{Fitting}
 %\input{Examples}
diff --git a/cmake/modules/FindFFTW.cmake b/cmake/modules/FindFFTW.cmake
index c4100ff303fe64f983f9183a5c72af26282c44aa..d05ab5ba3c5f1faadf3ba57d8e49eaabf68faa95 100644
--- a/cmake/modules/FindFFTW.cmake
+++ b/cmake/modules/FindFFTW.cmake
@@ -17,7 +17,7 @@ find_path(FFTW_INCLUDE_DIR fftw3.h
   /usr/local/include
   /usr/include
   /opt/fftw3/include
-  HINTS /opt/local/include
+  /opt/local/include
   DOC "Specify the directory containing fftw3.h"
 )
 
@@ -39,6 +39,14 @@ if(FFTW_INCLUDE_DIR AND FFTW_LIBRARY)
   endif()
 endif()
 
+
+if( NOT FFTW_FOUND )
+    if( FFTW_FIND_REQUIRED )
+        message( FATAL_ERROR "FindFFTW: can't find fftw3 header or library" )
+    endif()
+endif()
+
+
 set(FFTW_LIBRARIES ${FFTW_LIBRARY})
 
 mark_as_advanced(FFTW_FOUND FFTW_LIBRARY FFTW_INCLUDE_DIR)
diff --git a/cmake/modules/FindROOT.cmake b/cmake/modules/FindROOT.cmake
index 856a322fe5af86c5e683a263b1b29d7b686904b0..bbbab4ba8ed20170e7568c88f52d1867afed6936 100644
--- a/cmake/modules/FindROOT.cmake
+++ b/cmake/modules/FindROOT.cmake
@@ -78,7 +78,9 @@ function(ROOT_GENERATE_DICTIONARY dictionary)
   get_directory_property(incdirs INCLUDE_DIRECTORIES)
   set(includedirs) 
   foreach( d ${incdirs})    
+   if(NOT ${d} STREQUAL "/usr/include")
    set(includedirs ${includedirs} -I${d})
+   endif()
   endforeach()
   #---Get LinkDef.h file------------------------------------
   set(linkdefs)
diff --git a/cmake/modules/SearchInstalledSoftware.cmake b/cmake/modules/SearchInstalledSoftware.cmake
index 73bf9adc0f08015f868d21034da4bcd8aa638343..443e1e040be88e0e4d0bbfdea644f88cacffe62c 100644
--- a/cmake/modules/SearchInstalledSoftware.cmake
+++ b/cmake/modules/SearchInstalledSoftware.cmake
@@ -8,8 +8,8 @@ endif()
 include_directories(${EIGEN3_INCLUDE_DIR})
 
 # --- FFTW3 ---
-find_package(FFTW)
-include_directories(${FFTW_INCLUDE_DIR} REQUIRED)
+find_package(FFTW REQUIRED)
+include_directories(${FFTW_INCLUDE_DIR})
 
 # --- Boost ---
 set(Boost_USE_STATIC_LIBS OFF)