part 2 of the reorganization. Benefits/changes:

1) Eigen2 co-installable with Eigen1 without conflict, without affecting programs including either.
2) #include<Eigen/Core> without the .h without conflict with the Core/ directory
3) Uniformize coding style of the CMakeLists.

doc/Doxyfile.in

@@ -89,49 +89,9 @@ WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 INPUT                  = ${CMAKE_SOURCE_DIR}/doc ${CMAKE_SOURCE_DIR}/Eigen
 INPUT_ENCODING         = UTF-8
-FILE_PATTERNS          = *.c \
-                         *.cc \
-                         *.cxx \
-                         *.cpp \
-                         *.c++ \
-                         *.d \
-                         *.java \
-                         *.ii \
-                         *.ixx \
-                         *.ipp \
-                         *.i++ \
-                         *.inl \
-                         *.h \
-                         *.hh \
-                         *.hxx \
-                         *.hpp \
-                         *.h++ \
-                         *.idl \
-                         *.odl \
-                         *.cs \
-                         *.php \
-                         *.php3 \
-                         *.inc \
-                         *.m \
-                         *.mm \
-                         *.dox \
-                         *.py \
-                         *.C \
-                         *.CC \
-                         *.C++ \
-                         *.II \
-                         *.I++ \
-                         *.H \
-                         *.HH \
-                         *.H++ \
-                         *.CS \
-                         *.PHP \
-                         *.PHP3 \
-                         *.M \
-                         *.MM \
-                         *.PY
+FILE_PATTERNS          = *
 RECURSIVE              = NO
-EXCLUDE                = 
+EXCLUDE                = CMake* *.txt
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       = 
 EXCLUDE_SYMBOLS        = 

doc/benchmark.cpp

@@ -1,6 +1,6 @@
 // g++ -O3 -DNDEBUG benchmark.cpp -o benchmark && time ./benchmark
 
-#include <Eigen/Core.h>
+#include <Eigen/Core>
 
 using namespace std;
 USING_PART_OF_NAMESPACE_EIGEN

doc/example.cpp

@@ -1,4 +1,4 @@
-#include <Eigen/Core.h>
+#include <Eigen/Core>
 
 USING_PART_OF_NAMESPACE_EIGEN
 

doc/examples/class_Block.cpp

@@ -1,4 +1,4 @@
-#include <Eigen/Core.h>
+#include <Eigen/Core>
 USING_PART_OF_NAMESPACE_EIGEN
 using namespace std;
 

doc/examples/class_Cast.cpp

@@ -1,4 +1,4 @@
-#include <Eigen/Core.h>
+#include <Eigen/Core>
 USING_PART_OF_NAMESPACE_EIGEN
 using namespace std;
 

doc/examples/class_Column.cpp

@@ -1,4 +1,4 @@
-#include <Eigen/Core.h>
+#include <Eigen/Core>
 USING_PART_OF_NAMESPACE_EIGEN
 using namespace std;
 

doc/examples/class_DynBlock.cpp

@@ -1,4 +1,4 @@
-#include <Eigen/Core.h>
+#include <Eigen/Core>
 USING_PART_OF_NAMESPACE_EIGEN
 using namespace std;
 

doc/examples/class_Eval.cpp

@@ -1,4 +1,4 @@
-#include <Eigen/Core.h>
+#include <Eigen/Core>
 USING_PART_OF_NAMESPACE_EIGEN
 using namespace std;
 

doc/examples/class_Row.cpp

@@ -1,4 +1,4 @@
-#include <Eigen/Core.h>
+#include <Eigen/Core>
 USING_PART_OF_NAMESPACE_EIGEN
 using namespace std;
 

doc/snippets/compile_snippet.cpp.in

@@ -1,4 +1,4 @@
-#include <Eigen/Core.h>
+#include <Eigen/Core>
 USING_PART_OF_NAMESPACE_EIGEN
 using namespace std;
 int main(int, char**)

doc/tutorial.cpp

@@ -1,4 +1,4 @@
-#include <Eigen/Core.h>
+#include <Eigen/Core>
 
 USING_PART_OF_NAMESPACE_EIGEN