From 05e876856ef61cbcd063b5440ab6926c40fb98c6 Mon Sep 17 00:00:00 2001
From: Chuck Atkins <chuck.atkins@kitware.com>
Date: Wed, 19 Apr 2017 14:16:14 -0400
Subject: [PATCH] Finish header shuffeling

---
 bindings/python/include/ADIOSPy.h             |  12 +-
 bindings/python/include/EnginePy.h            |  16 +-
 bindings/python/include/MethodPy.h            |   8 +-
 bindings/python/include/VariablePy.h          |   4 +-
 bindings/python/include/adiosPyFunctions.h    |   8 +-
 bindings/python/src/ADIOSPy.cpp               |   4 +-
 bindings/python/src/EnginePy.cpp              |   4 +-
 bindings/python/src/MethodPy.cpp              |   4 +-
 bindings/python/src/VariablePy.cpp            |   2 +-
 bindings/python/src/adiosPyFunctions.cpp      |   2 +-
 bindings/python/src/glueBoostPython.cpp       |  14 +-
 bindings/python/src/gluePyBind11.cpp          |   6 +-
 doc/API_design/API_example_use.cpp            |   2 +-
 examples/globalArray/globalArrayNoXML.cpp     |   2 +-
 examples/globalArray/globalArrayXML.cpp       |   2 +-
 examples/globalArray/globalArrayZeroCopy.cpp  |   2 +-
 examples/heatTransfer/read/PrintData.cpp      |   2 +-
 .../heatTransfer/read/heatRead_adios1.cpp     |   4 +-
 examples/heatTransfer/write/HeatTransfer.cpp  |   2 +-
 examples/heatTransfer/write/HeatTransfer.h    |   2 +-
 examples/heatTransfer/write/IO.h              |   4 +-
 examples/heatTransfer/write/IO_adios1.cpp     |   4 +-
 examples/heatTransfer/write/IO_adios2.cpp     |   2 +-
 examples/heatTransfer/write/IO_ascii.cpp      |   2 +-
 examples/heatTransfer/write/IO_hdf5_a.cpp     |   4 +-
 examples/heatTransfer/write/Settings.cpp      |   2 +-
 examples/heatTransfer/write/main.cpp          |   6 +-
 examples/solidfluid/solidfluid_read.cpp       |   2 +-
 examples/xmlParser/xmlParser.cpp              |   4 +-
 source/adios2/ADIOS.cpp                       |  30 +--
 source/adios2/ADIOS.h                         |  20 +-
 source/adios2/ADIOS.tcc                       |   4 +-
 source/adios2/ADIOSTypes.h                    |   2 +-
 source/adios2/ADIOS_MPI.h                     |   4 +-
 source/adios2/CMakeLists.txt                  |   3 +-
 source/adios2/capsule/heap/STLVector.cpp      |   6 +-
 source/adios2/capsule/heap/STLVector.h        |   4 +-
 source/adios2/capsule/shmem/ShmSystemV.cpp    |   7 +-
 source/adios2/capsule/shmem/ShmSystemV.h      |   4 +-
 source/adios2/core/Attribute.h                |   2 +-
 source/adios2/core/Capsule.cpp                |   4 +-
 source/adios2/core/Capsule.h                  |   2 +-
 source/adios2/core/Engine.cpp                 |   7 +-
 source/adios2/core/Engine.h                   |  20 +-
 source/adios2/core/IOChrono.h                 |   4 +-
 source/adios2/core/Method.cpp                 |   5 +-
 source/adios2/core/Method.h                   |   6 +-
 source/adios2/core/Selection.h                |   2 +-
 source/adios2/core/SelectionBoundingBox.h     |   4 +-
 source/adios2/core/SelectionPoints.h          |   4 +-
 source/adios2/core/Support.cpp                |   5 +-
 source/adios2/core/Support.h                  |   2 +-
 source/adios2/core/Timer.cpp                  |   2 +-
 source/adios2/core/Timer.h                    |   4 +-
 source/adios2/core/Transform.cpp              |   5 +-
 source/adios2/core/Transform.h                |   2 +-
 source/adios2/core/Transport.cpp              |   4 +-
 source/adios2/core/Transport.h                |   6 +-
 source/adios2/core/Variable.h                 |   6 +-
 source/adios2/core/VariableBase.h             |   8 +-
 source/adios2/core/VariableCompound.h         |   4 +-
 source/adios2/core/adiosFunctions.cpp         |  22 +-
 source/adios2/core/adiosFunctions.h           |   6 +-
 source/adios2/core/adiosTemplates.h           |   2 +-
 source/adios2/core/capsuleTemplates.h         |   4 +-
 source/adios2/engine/adios1/ADIOS1Reader.cpp  |  12 +-
 source/adios2/engine/adios1/ADIOS1Reader.h    |  11 +-
 source/adios2/engine/adios1/ADIOS1Writer.cpp  |   4 +-
 source/adios2/engine/adios1/ADIOS1Writer.h    |   6 +-
 source/adios2/engine/bp/BPFileReader.cpp      |  10 +-
 source/adios2/engine/bp/BPFileReader.h        |   6 +-
 source/adios2/engine/bp/BPFileWriter.cpp      |  12 +-
 source/adios2/engine/bp/BPFileWriter.h        |   8 +-
 .../adios2/engine/dataman/DataManReader.cpp   |  15 +-
 source/adios2/engine/dataman/DataManReader.h  |  13 +-
 .../adios2/engine/dataman/DataManWriter.cpp   |  12 +-
 source/adios2/engine/dataman/DataManWriter.h  |  13 +-
 source/adios2/engine/hdf5/HDF5ReaderP.cpp     |   4 +-
 source/adios2/engine/hdf5/HDF5WriterP.cpp     |   8 +-
 source/adios2/engine/hdf5/HDF5WriterP.h       |   8 +-
 source/adios2/external/adios_selection.h      | 240 ------------------
 source/adios2/mpidummy.cpp                    |  17 +-
 source/adios2/mpidummy.h                      |   2 +-
 source/adios2/transform/BZip2.h               |   4 +-
 source/adios2/transport/file/FStream.cpp      |   6 +-
 source/adios2/transport/file/FStream.h        |   4 +-
 .../adios2/transport/file/FileDescriptor.cpp  |   6 +-
 source/adios2/transport/file/FileDescriptor.h |   4 +-
 source/adios2/transport/file/FilePointer.cpp  |   6 +-
 source/adios2/transport/file/FilePointer.h    |   4 +-
 source/adios2/transport/file/MPI_File.h       |   4 +-
 source/adios2/transport/wan/MdtmMan.h         |   8 +-
 source/adios2/utilities/format/bp1/BP1.h      |   8 +-
 .../utilities/format/bp1/BP1Aggregator.cpp    |   2 -
 .../utilities/format/bp1/BP1Aggregator.h      |   4 +-
 .../adios2/utilities/format/bp1/BP1Base.cpp   |   3 +-
 source/adios2/utilities/format/bp1/BP1Base.h  |   6 +-
 .../adios2/utilities/format/bp1/BP1Structs.h  |   4 +-
 .../adios2/utilities/format/bp1/BP1Writer.cpp |   8 +-
 .../adios2/utilities/format/bp1/BP1Writer.h   |  18 +-
 100 files changed, 300 insertions(+), 558 deletions(-)
 delete mode 100644 source/adios2/external/adios_selection.h

diff --git a/bindings/python/include/ADIOSPy.h b/bindings/python/include/ADIOSPy.h
index f6d6ebb74..b1a009370 100644
--- a/bindings/python/include/ADIOSPy.h
+++ b/bindings/python/include/ADIOSPy.h
@@ -16,17 +16,17 @@
 #include <string>
 
 #ifdef HAVE_BOOSTPYTHON
-#include "boost/python.hpp"
+#include "adios2/boost/python.hpp"
 #endif
 
 #ifdef HAVE_PYBIND11
-#include "pybind11/pybind11.h"
+#include "adios2/pybind11/pybind11.h"
 #endif
 
-#include "ADIOS.h"
-#include "MethodPy.h"
-#include "VariablePy.h"
-#include "adiosPyFunctions.h" //ListToVector, VectorToList
+#include "adios2/ADIOS.h"
+#include "adios2/MethodPy.h"
+#include "adios2/VariablePy.h"
+#include "adios2/adiosPyFunctions.h" //ListToVector, VectorToList
 
 namespace adios
 {
diff --git a/bindings/python/include/EnginePy.h b/bindings/python/include/EnginePy.h
index 29d65cb00..8ecb12679 100644
--- a/bindings/python/include/EnginePy.h
+++ b/bindings/python/include/EnginePy.h
@@ -12,19 +12,19 @@
 #define ENGINEPY_H_
 
 #ifdef HAVE_BOOSTPYTHON
-#include "boost/python.hpp"
-#include "boost/python/numpy.hpp"
+#include "adios2/boost/python.hpp"
+#include "adios2/boost/python/numpy.hpp"
 #endif
 
 #ifdef HAVE_PYBIND11
-#include "pybind11/numpy.h"
-#include "pybind11/pybind11.h"
+#include "adios2/pybind11/numpy.h"
+#include "adios2/pybind11/pybind11.h"
 #endif
 
-#include "ADIOSPy.h"
-#include "VariablePy.h"
-#include "adiosPyFunctions.h"
-#include "core/Engine.h"
+#include "adios2/ADIOSPy.h"
+#include "adios2/VariablePy.h"
+#include "adios2/adiosPyFunctions.h"
+#include "adios2/core/Engine.h"
 
 namespace adios
 {
diff --git a/bindings/python/include/MethodPy.h b/bindings/python/include/MethodPy.h
index 5bdb9a3aa..3b012f566 100644
--- a/bindings/python/include/MethodPy.h
+++ b/bindings/python/include/MethodPy.h
@@ -12,15 +12,15 @@
 #define METHODPY_H_
 
 #ifdef HAVE_BOOSTPYTHON
-#include "boost/python.hpp"
+#include "adios2/boost/python.hpp"
 #endif
 
 #ifdef HAVE_PYBIND11
-#include "pybind11/cast.h"
-#include "pybind11/pybind11.h"
+#include "adios2/pybind11/cast.h"
+#include "adios2/pybind11/pybind11.h"
 #endif
 
-#include "core/Method.h"
+#include "adios2/core/Method.h"
 
 namespace adios
 {
diff --git a/bindings/python/include/VariablePy.h b/bindings/python/include/VariablePy.h
index 91b71be59..86143dca5 100644
--- a/bindings/python/include/VariablePy.h
+++ b/bindings/python/include/VariablePy.h
@@ -11,8 +11,8 @@
 #ifndef VARIABLEPY_H_
 #define VARIABLEPY_H_
 
-#include "adiosPyFunctions.h"
-#include "core/Variable.h"
+#include "adios2/adiosPyFunctions.h"
+#include "adios2/core/Variable.h"
 
 namespace adios
 {
diff --git a/bindings/python/include/adiosPyFunctions.h b/bindings/python/include/adiosPyFunctions.h
index b47e02d7b..4751fe804 100644
--- a/bindings/python/include/adiosPyFunctions.h
+++ b/bindings/python/include/adiosPyFunctions.h
@@ -16,13 +16,13 @@
 #include <vector>
 
 #ifdef HAVE_BOOSTPYTHON
-#include "boost/python.hpp"
-#include "boost/python/numpy.hpp"
+#include "adios2/boost/python.hpp"
+#include "adios2/boost/python/numpy.hpp"
 #endif
 
 #ifdef HAVE_PYBIND11
-#include "pybind11/numpy.h"
-#include "pybind11/pybind11.h"
+#include "adios2/pybind11/numpy.h"
+#include "adios2/pybind11/pybind11.h"
 #endif
 
 namespace adios
diff --git a/bindings/python/src/ADIOSPy.cpp b/bindings/python/src/ADIOSPy.cpp
index 6e45ce397..9f8a6ac83 100644
--- a/bindings/python/src/ADIOSPy.cpp
+++ b/bindings/python/src/ADIOSPy.cpp
@@ -12,8 +12,8 @@
 
 #include <mpi4py/mpi4py.h>
 
-#include "ADIOSPy.h"
-#include "EnginePy.h"
+#include "adios2/ADIOSPy.h"
+#include "adios2/EnginePy.h"
 
 namespace adios
 {
diff --git a/bindings/python/src/EnginePy.cpp b/bindings/python/src/EnginePy.cpp
index 20826731f..91310f2a7 100644
--- a/bindings/python/src/EnginePy.cpp
+++ b/bindings/python/src/EnginePy.cpp
@@ -10,9 +10,9 @@
 
 #include <string>
 
-#include "EnginePy.h"
+#include "adios2/EnginePy.h"
 
-#include "adiosPyFunctions.h"
+#include "adios2/adiosPyFunctions.h"
 
 namespace adios
 {
diff --git a/bindings/python/src/MethodPy.cpp b/bindings/python/src/MethodPy.cpp
index 937df58fb..6545ca363 100644
--- a/bindings/python/src/MethodPy.cpp
+++ b/bindings/python/src/MethodPy.cpp
@@ -10,8 +10,8 @@
 
 #include <iostream>
 
-#include "MethodPy.h"
-#include "adiosPyFunctions.h"
+#include "adios2/MethodPy.h"
+#include "adios2/adiosPyFunctions.h"
 
 namespace adios
 {
diff --git a/bindings/python/src/VariablePy.cpp b/bindings/python/src/VariablePy.cpp
index 09d92899e..e7dc4034d 100644
--- a/bindings/python/src/VariablePy.cpp
+++ b/bindings/python/src/VariablePy.cpp
@@ -8,7 +8,7 @@
  *      Author: wfg
  */
 
-#include "VariablePy.h"
+#include "adios2/VariablePy.h"
 
 namespace adios
 {
diff --git a/bindings/python/src/adiosPyFunctions.cpp b/bindings/python/src/adiosPyFunctions.cpp
index 92d18b4c0..f9396e05b 100644
--- a/bindings/python/src/adiosPyFunctions.cpp
+++ b/bindings/python/src/adiosPyFunctions.cpp
@@ -9,7 +9,7 @@
  */
 #include <iostream>
 
-#include "adiosPyFunctions.h"
+#include "adios2/adiosPyFunctions.h"
 
 namespace adios
 {
diff --git a/bindings/python/src/glueBoostPython.cpp b/bindings/python/src/glueBoostPython.cpp
index 1718700b4..a1e2988b0 100644
--- a/bindings/python/src/glueBoostPython.cpp
+++ b/bindings/python/src/glueBoostPython.cpp
@@ -10,14 +10,14 @@
 
 #include <mpi4py/mpi4py.h>
 
-#include "boost/python.hpp"
-#include "boost/python/numpy.hpp"
-#include "boost/python/raw_function.hpp"
-#include "boost/python/suite/indexing/vector_indexing_suite.hpp"
+#include "adios2/boost/python.hpp"
+#include "adios2/boost/python/numpy.hpp"
+#include "adios2/boost/python/raw_function.hpp"
+#include "adios2/boost/python/suite/indexing/vector_indexing_suite.hpp"
 
-#include "ADIOSPy.h"
-#include "EnginePy.h"
-#include "adiosPyFunctions.h"
+#include "adios2/ADIOSPy.h"
+#include "adios2/EnginePy.h"
+#include "adios2/adiosPyFunctions.h"
 
 namespace py = boost::python;
 namespace np = boost::python::numpy;
diff --git a/bindings/python/src/gluePyBind11.cpp b/bindings/python/src/gluePyBind11.cpp
index dd76c295c..15adfd967 100644
--- a/bindings/python/src/gluePyBind11.cpp
+++ b/bindings/python/src/gluePyBind11.cpp
@@ -12,10 +12,10 @@
 
 #include <mpi4py/mpi4py.h>
 
-#include "pybind11/pybind11.h"
+#include "adios2/pybind11/pybind11.h"
 
-#include "ADIOSPy.h"
-#include "EnginePy.h"
+#include "adios2/ADIOSPy.h"
+#include "adios2/EnginePy.h"
 
 namespace py = pybind11;
 
diff --git a/doc/API_design/API_example_use.cpp b/doc/API_design/API_example_use.cpp
index 701bb8994..bc1c00fc8 100644
--- a/doc/API_design/API_example_use.cpp
+++ b/doc/API_design/API_example_use.cpp
@@ -2,7 +2,7 @@
  * of the ideas */
 #include <mpi.h>
 
-#include "ADIOS.h"
+#include "adios2/ADIOS.h"
 
 void cb_AsyncWriteAdvanceCompleted(std::shared_ptr<adios::Engine> writer)
 {
diff --git a/examples/globalArray/globalArrayNoXML.cpp b/examples/globalArray/globalArrayNoXML.cpp
index 64f33e42d..aa4a3d5c6 100644
--- a/examples/globalArray/globalArrayNoXML.cpp
+++ b/examples/globalArray/globalArrayNoXML.cpp
@@ -15,7 +15,7 @@
 #include <string>
 #include <vector>
 
-#include "../../include/ADIOS.h"
+#include "adios2/../../include/ADIOS.h"
 
 int main(int argc, char *argv[])
 {
diff --git a/examples/globalArray/globalArrayXML.cpp b/examples/globalArray/globalArrayXML.cpp
index c25d046e3..9ab202767 100644
--- a/examples/globalArray/globalArrayXML.cpp
+++ b/examples/globalArray/globalArrayXML.cpp
@@ -15,7 +15,7 @@
 #include <string>
 #include <vector>
 
-#include "../../include/ADIOS.h"
+#include "adios2/../../include/ADIOS.h"
 
 int main(int argc, char *argv[])
 {
diff --git a/examples/globalArray/globalArrayZeroCopy.cpp b/examples/globalArray/globalArrayZeroCopy.cpp
index a85b5dc56..7b7506eb9 100644
--- a/examples/globalArray/globalArrayZeroCopy.cpp
+++ b/examples/globalArray/globalArrayZeroCopy.cpp
@@ -15,7 +15,7 @@
 #include <string>
 #include <vector>
 
-#include "../../include/ADIOS.h"
+#include "adios2/../../include/ADIOS.h"
 
 int main(int argc, char *argv[])
 {
diff --git a/examples/heatTransfer/read/PrintData.cpp b/examples/heatTransfer/read/PrintData.cpp
index 030fa561f..67090a2e9 100644
--- a/examples/heatTransfer/read/PrintData.cpp
+++ b/examples/heatTransfer/read/PrintData.cpp
@@ -8,7 +8,7 @@
  *      Author: Norbert Podhorszki
  */
 
-#include "PrintData.h"
+#include "adios2/PrintData.h"
 #include <fstream>
 #include <iomanip>
 #include <iostream>
diff --git a/examples/heatTransfer/read/heatRead_adios1.cpp b/examples/heatTransfer/read/heatRead_adios1.cpp
index bcedac6d5..47b69b2b6 100644
--- a/examples/heatTransfer/read/heatRead_adios1.cpp
+++ b/examples/heatTransfer/read/heatRead_adios1.cpp
@@ -1,7 +1,7 @@
 
 #include <mpi.h>
 
-#include "adios_read.h"
+#include "adios2/adios_read.h"
 #include <cstdint>
 #include <iomanip>
 #include <iostream>
@@ -10,7 +10,7 @@
 #include <stdexcept>
 #include <string>
 
-#include "PrintData.h"
+#include "adios2/PrintData.h"
 
 int main(int argc, char *argv[])
 {
diff --git a/examples/heatTransfer/write/HeatTransfer.cpp b/examples/heatTransfer/write/HeatTransfer.cpp
index 29283fa77..eb37cadc5 100644
--- a/examples/heatTransfer/write/HeatTransfer.cpp
+++ b/examples/heatTransfer/write/HeatTransfer.cpp
@@ -18,7 +18,7 @@
 #include <stdexcept>
 #include <string>
 
-#include "HeatTransfer.h"
+#include "adios2/HeatTransfer.h"
 
 HeatTransfer::HeatTransfer(const Settings &settings) : m_s{settings}
 {
diff --git a/examples/heatTransfer/write/HeatTransfer.h b/examples/heatTransfer/write/HeatTransfer.h
index a52acbb74..c1efc5fdf 100644
--- a/examples/heatTransfer/write/HeatTransfer.h
+++ b/examples/heatTransfer/write/HeatTransfer.h
@@ -15,7 +15,7 @@
 
 #include <vector>
 
-#include "Settings.h"
+#include "adios2/Settings.h"
 
 class HeatTransfer
 {
diff --git a/examples/heatTransfer/write/IO.h b/examples/heatTransfer/write/IO.h
index 53caaf599..8c888d26e 100644
--- a/examples/heatTransfer/write/IO.h
+++ b/examples/heatTransfer/write/IO.h
@@ -11,8 +11,8 @@
 #ifndef IO_H_
 #define IO_H_
 
-#include "HeatTransfer.h"
-#include "Settings.h"
+#include "adios2/HeatTransfer.h"
+#include "adios2/Settings.h"
 
 #include <mpi.h>
 
diff --git a/examples/heatTransfer/write/IO_adios1.cpp b/examples/heatTransfer/write/IO_adios1.cpp
index 8bc8753c2..c858c07d9 100644
--- a/examples/heatTransfer/write/IO_adios1.cpp
+++ b/examples/heatTransfer/write/IO_adios1.cpp
@@ -12,8 +12,8 @@
 #include <iostream>
 #include <string>
 
-#include "IO.h"
-#include "adios.h"
+#include "adios2/IO.h"
+#include "adios2/adios.h"
 
 static int64_t group;
 static int rank_saved;
diff --git a/examples/heatTransfer/write/IO_adios2.cpp b/examples/heatTransfer/write/IO_adios2.cpp
index ee3e1b0d8..9eb19b2ec 100644
--- a/examples/heatTransfer/write/IO_adios2.cpp
+++ b/examples/heatTransfer/write/IO_adios2.cpp
@@ -8,7 +8,7 @@
  *      Author: Norbert Podhorszki
  */
 
-#include "IO.h"
+#include "adios2/IO.h"
 #include <adios2.h>
 
 #include <string>
diff --git a/examples/heatTransfer/write/IO_ascii.cpp b/examples/heatTransfer/write/IO_ascii.cpp
index 5f16aa05f..a83e11512 100644
--- a/examples/heatTransfer/write/IO_ascii.cpp
+++ b/examples/heatTransfer/write/IO_ascii.cpp
@@ -12,7 +12,7 @@
 #include <iomanip>
 #include <iostream>
 
-#include "IO.h"
+#include "adios2/IO.h"
 
 static std::ofstream of;
 static std::streambuf *buf;
diff --git a/examples/heatTransfer/write/IO_hdf5_a.cpp b/examples/heatTransfer/write/IO_hdf5_a.cpp
index c0514b803..b63553ebd 100644
--- a/examples/heatTransfer/write/IO_hdf5_a.cpp
+++ b/examples/heatTransfer/write/IO_hdf5_a.cpp
@@ -16,8 +16,8 @@
 #include <iostream>
 #include <string>
 
-#include "IO.h"
-#include "hdf5.h"
+#include "adios2/IO.h"
+#include "adios2/hdf5.h"
 
 IO::IO(const Settings &s, MPI_Comm comm) : m_outputfilename{s.outputfile} {}
 
diff --git a/examples/heatTransfer/write/Settings.cpp b/examples/heatTransfer/write/Settings.cpp
index 4922afd5f..7e5631809 100644
--- a/examples/heatTransfer/write/Settings.cpp
+++ b/examples/heatTransfer/write/Settings.cpp
@@ -13,7 +13,7 @@
 
 #include <stdexcept>
 
-#include "Settings.h"
+#include "adios2/Settings.h"
 
 static unsigned int convertToUint(std::string varName, char *arg)
 {
diff --git a/examples/heatTransfer/write/main.cpp b/examples/heatTransfer/write/main.cpp
index 657348f1d..34b10ca2e 100644
--- a/examples/heatTransfer/write/main.cpp
+++ b/examples/heatTransfer/write/main.cpp
@@ -17,9 +17,9 @@
 #include <stdexcept>
 #include <string>
 
-#include "HeatTransfer.h"
-#include "IO.h"
-#include "Settings.h"
+#include "adios2/HeatTransfer.h"
+#include "adios2/IO.h"
+#include "adios2/Settings.h"
 
 void printUsage()
 {
diff --git a/examples/solidfluid/solidfluid_read.cpp b/examples/solidfluid/solidfluid_read.cpp
index 028590601..f451ff12d 100644
--- a/examples/solidfluid/solidfluid_read.cpp
+++ b/examples/solidfluid/solidfluid_read.cpp
@@ -15,7 +15,7 @@
 #include <string>
 #include <vector>
 
-#include "ADIOS_OOP.h"
+#include "adios2/ADIOS_OOP.h"
 
 struct MYDATA
 {
diff --git a/examples/xmlParser/xmlParser.cpp b/examples/xmlParser/xmlParser.cpp
index 98624de22..e19295e5d 100644
--- a/examples/xmlParser/xmlParser.cpp
+++ b/examples/xmlParser/xmlParser.cpp
@@ -12,12 +12,12 @@
 #include <stdexcept>
 #include <string>
 
-#include "../../include/ADIOS.h"
+#include "adios2/../../include/ADIOS.h"
 
 #ifdef HAVE_MPI
 #include <mpi.h>
 #else
-#include "../../include/mpidummy.h"
+#include "adios2/../../include/mpidummy.h"
 using namespace adios;
 #endif
 
diff --git a/source/adios2/ADIOS.cpp b/source/adios2/ADIOS.cpp
index 19e0e54cf..15676f532 100644
--- a/source/adios2/ADIOS.cpp
+++ b/source/adios2/ADIOS.cpp
@@ -8,37 +8,33 @@
  *      Author: William F Godoy
  */
 
-/// \cond EXCLUDE_FROM_DOXYGEN
+#include "ADIOS.h"
+#include "ADIOS.tcc"
+
 #include <fstream>
 #include <ios> //std::ios_base::failure
 #include <iostream>
 #include <sstream>
 #include <utility>
-/// \endcond
-
-#include "ADIOS.h"
-#include "ADIOS.tcc"
-#include "ADIOSMacros.h"
-
-#include "core/adiosFunctions.h"
 
-// Engines
-#include "engine/bp/BPFileReader.h"
-#include "engine/bp/BPFileWriter.h"
+#include "adios2/ADIOSMacros.h"
+#include "adios2/core/adiosFunctions.h"
+#include "adios2/engine/bp/BPFileReader.h"
+#include "adios2/engine/bp/BPFileWriter.h"
 
 #ifdef ADIOS2_HAVE_DATAMAN // external dependencies
-#include "engine/dataman/DataManReader.h"
-#include "engine/dataman/DataManWriter.h"
+#include "adios2/engine/dataman/DataManReader.h"
+#include "adios2/engine/dataman/DataManWriter.h"
 #endif
 
 #ifdef ADIOS2_HAVE_ADIOS1 // external dependencies
-#include "engine/adios1/ADIOS1Reader.h"
-#include "engine/adios1/ADIOS1Writer.h"
+#include "adios2/engine/adios1/ADIOS1Reader.h"
+#include "adios2/engine/adios1/ADIOS1Writer.h"
 #endif
 
 #ifdef ADIOS2_HAVE_HDF5 // external dependencies
-#include "engine/hdf5/HDF5ReaderP.h"
-#include "engine/hdf5/HDF5WriterP.h"
+#include "adios2/engine/hdf5/HDF5ReaderP.h"
+#include "adios2/engine/hdf5/HDF5WriterP.h"
 #endif
 
 namespace adios
diff --git a/source/adios2/ADIOS.h b/source/adios2/ADIOS.h
index 8b7ac1e11..8a72294b4 100644
--- a/source/adios2/ADIOS.h
+++ b/source/adios2/ADIOS.h
@@ -20,15 +20,15 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "ADIOSMacros.h"
-#include "ADIOS_MPI.h"
-#include "ADIOSTypes.h"
-#include "core/Method.h"
-#include "core/Support.h"
-#include "core/Transform.h"
-#include "core/Variable.h"
-#include "core/VariableCompound.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOSMacros.h"
+#include "adios2/ADIOSTypes.h"
+#include "adios2/ADIOS_MPI.h"
+#include "adios2/core/Method.h"
+#include "adios2/core/Support.h"
+#include "adios2/core/Transform.h"
+#include "adios2/core/Variable.h"
+#include "adios2/core/VariableCompound.h"
 
 namespace adios
 {
@@ -359,6 +359,6 @@ extern template unsigned int ADIOS::GetVariableIndex<void>(const std::string &);
 } // end namespace adios
 
 // Include the inline implementations for the public interface
-#include "ADIOS.inl"
+#include "adios2/ADIOS.inl"
 
 #endif /* ADIOS_H_ */
diff --git a/source/adios2/ADIOS.tcc b/source/adios2/ADIOS.tcc
index 44d95a9fd..b75b163dd 100644
--- a/source/adios2/ADIOS.tcc
+++ b/source/adios2/ADIOS.tcc
@@ -9,8 +9,8 @@
 #ifndef ADIOS_TCC_
 #define ADIOS_TCC_
 
-#include "ADIOS.h"
-#include "ADIOSMacros.h"
+#include "adios2/ADIOS.h"
+#include "adios2/ADIOSMacros.h"
 
 namespace adios
 {
diff --git a/source/adios2/ADIOSTypes.h b/source/adios2/ADIOSTypes.h
index a2d52421b..1412bdfce 100644
--- a/source/adios2/ADIOSTypes.h
+++ b/source/adios2/ADIOSTypes.h
@@ -16,7 +16,7 @@
 #include <cstdint>
 #include <type_traits>
 
-#include "ADIOSConfig.h"
+#include "adios2/ADIOSConfig.h"
 
 namespace adios
 {
diff --git a/source/adios2/ADIOS_MPI.h b/source/adios2/ADIOS_MPI.h
index 83b5a212c..d06557fd0 100644
--- a/source/adios2/ADIOS_MPI.h
+++ b/source/adios2/ADIOS_MPI.h
@@ -6,12 +6,12 @@
 #ifndef ADIOS_MPI_H_
 #define ADIOS_MPI_H_
 
-#include "ADIOSConfig.h"
+#include "adios2/ADIOSConfig.h"
 
 #ifdef ADIOS2_HAVE_MPI
 #include <mpi.h>
 #else
-#include "mpidummy.h"
+#include "adios2/mpidummy.h"
 #endif
 
 #endif /* ADIOS_MPI_H_ */
diff --git a/source/adios2/CMakeLists.txt b/source/adios2/CMakeLists.txt
index 36f7d71c6..e24b486a1 100644
--- a/source/adios2/CMakeLists.txt
+++ b/source/adios2/CMakeLists.txt
@@ -36,6 +36,7 @@ add_library(adios2
 )
 target_include_directories(adios2
   PUBLIC
+    $<BUILD_INTERFACE:${ADIOS_SOURCE_DIR}/source>
     $<BUILD_INTERFACE:${ADIOS_BINARY_DIR}>
     $<INSTALL_INTERFACE:include>
   PRIVATE ${ADIOS_SOURCE_DIR}/source
@@ -102,7 +103,7 @@ endif()
 
 install(
   FILES
-    ADIOS.h ADIOS.inl ADIOSMacros.h ADIOS_MPI.h ADIOSTypes.h mpidummy.h adios2.h
+    ADIOS.h ADIOS.inl ADIOSMacros.h ADIOS_MPI.h ADIOSTypes.h mpidummy.h
   DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/adios2
 )
 install(
diff --git a/source/adios2/capsule/heap/STLVector.cpp b/source/adios2/capsule/heap/STLVector.cpp
index 31a9e1845..2b6b9a289 100644
--- a/source/adios2/capsule/heap/STLVector.cpp
+++ b/source/adios2/capsule/heap/STLVector.cpp
@@ -8,12 +8,10 @@
  *      Author: wfg
  */
 
-/// \cond EXCLUDE_FROM_DOXYGEN
+#include "STLVector.h"
+
 #include <new>       //std::bad_alloc
 #include <stdexcept> //std::runtime_error
-/// \endcond
-
-#include "STLVector.h"
 
 namespace adios
 {
diff --git a/source/adios2/capsule/heap/STLVector.h b/source/adios2/capsule/heap/STLVector.h
index 019e92a59..20b70de67 100644
--- a/source/adios2/capsule/heap/STLVector.h
+++ b/source/adios2/capsule/heap/STLVector.h
@@ -15,8 +15,8 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "core/Capsule.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Capsule.h"
 
 namespace adios
 {
diff --git a/source/adios2/capsule/shmem/ShmSystemV.cpp b/source/adios2/capsule/shmem/ShmSystemV.cpp
index 4bd56810c..c241b6eab 100644
--- a/source/adios2/capsule/shmem/ShmSystemV.cpp
+++ b/source/adios2/capsule/shmem/ShmSystemV.cpp
@@ -7,14 +7,13 @@
  *  Created on: Dec 22, 2016
  *      Author: wfg
  */
-/// \cond EXCLUDE_FROM_DOXYGEN
+
+#include "ShmSystemV.h"
+
 #include <sys/shm.h>
 
 #include <ios> //std::ios_base::failure
 #include <utility>
-/// \endcond
-
-#include "ShmSystemV.h"
 
 namespace adios
 {
diff --git a/source/adios2/capsule/shmem/ShmSystemV.h b/source/adios2/capsule/shmem/ShmSystemV.h
index cceac2266..2b58ea5f5 100644
--- a/source/adios2/capsule/shmem/ShmSystemV.h
+++ b/source/adios2/capsule/shmem/ShmSystemV.h
@@ -5,8 +5,8 @@
 #include <sys/ipc.h>
 #include <sys/types.h>
 
-#include "ADIOSConfig.h"
-#include "core/Capsule.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Capsule.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Attribute.h b/source/adios2/core/Attribute.h
index fea3b0bed..d732a26d6 100644
--- a/source/adios2/core/Attribute.h
+++ b/source/adios2/core/Attribute.h
@@ -15,7 +15,7 @@
 #include <string>
 /// \endcond
 
-#include "ADIOSConfig.h"
+#include "adios2/ADIOSConfig.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Capsule.cpp b/source/adios2/core/Capsule.cpp
index b30603ab4..60888e8f8 100644
--- a/source/adios2/core/Capsule.cpp
+++ b/source/adios2/core/Capsule.cpp
@@ -8,9 +8,9 @@
  *      Author: wfg
  */
 
-#include <utility>
+#include "Capsule.h"
 
-#include "core/Capsule.h"
+#include <utility>
 
 namespace adios
 {
diff --git a/source/adios2/core/Capsule.h b/source/adios2/core/Capsule.h
index 896ddbaf4..7d1b8cd3e 100644
--- a/source/adios2/core/Capsule.h
+++ b/source/adios2/core/Capsule.h
@@ -15,7 +15,7 @@
 #include <string>
 /// \endcond
 
-#include "ADIOSConfig.h"
+#include "adios2/ADIOSConfig.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Engine.cpp b/source/adios2/core/Engine.cpp
index bbfe5a978..76ded52fa 100644
--- a/source/adios2/core/Engine.cpp
+++ b/source/adios2/core/Engine.cpp
@@ -8,11 +8,12 @@
  *      Author: wfg
  */
 
+#include "Engine.h"
+
 #include <ios> //std::ios_base::failure
 
-#include "core/Engine.h"
-#include "core/Support.h"
-#include "core/adiosFunctions.h"
+#include "adios2/core/Support.h"
+#include "adios2/core/adiosFunctions.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Engine.h b/source/adios2/core/Engine.h
index 6d9bc8c20..783c8939c 100644
--- a/source/adios2/core/Engine.h
+++ b/source/adios2/core/Engine.h
@@ -21,16 +21,16 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "ADIOS_MPI.h"
-#include "ADIOS.h"
-#include "ADIOSTypes.h"
-#include "core/Capsule.h"
-#include "core/Method.h"
-#include "core/Transform.h"
-#include "core/Transport.h"
-#include "core/Variable.h"
-#include "core/VariableCompound.h"
+#include "adios2/ADIOS.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOSTypes.h"
+#include "adios2/ADIOS_MPI.h"
+#include "adios2/core/Capsule.h"
+#include "adios2/core/Method.h"
+#include "adios2/core/Transform.h"
+#include "adios2/core/Transport.h"
+#include "adios2/core/Variable.h"
+#include "adios2/core/VariableCompound.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/IOChrono.h b/source/adios2/core/IOChrono.h
index 489c214aa..7f1ac8e56 100644
--- a/source/adios2/core/IOChrono.h
+++ b/source/adios2/core/IOChrono.h
@@ -15,8 +15,8 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "core/Timer.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Timer.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Method.cpp b/source/adios2/core/Method.cpp
index 25b7af4ad..083e19135 100644
--- a/source/adios2/core/Method.cpp
+++ b/source/adios2/core/Method.cpp
@@ -8,10 +8,11 @@
  *      Author: wfg
  */
 
+#include "Method.h"
+
 #include <utility>
 
-#include "core/Method.h"
-#include "core/adiosFunctions.h"
+#include "adios2/core/adiosFunctions.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Method.h b/source/adios2/core/Method.h
index 9c415e9d6..676f857e5 100644
--- a/source/adios2/core/Method.h
+++ b/source/adios2/core/Method.h
@@ -17,9 +17,9 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "ADIOSTypes.h"
-#include "core/adiosFunctions.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOSTypes.h"
+#include "adios2/core/adiosFunctions.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Selection.h b/source/adios2/core/Selection.h
index e6c8ac2ff..17091c91d 100644
--- a/source/adios2/core/Selection.h
+++ b/source/adios2/core/Selection.h
@@ -33,7 +33,7 @@
 #ifndef __ADIOS_SELECTION_H__
 #define __ADIOS_SELECTION_H__
 
-#include "ADIOSConfig.h"
+#include "adios2/ADIOSConfig.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/SelectionBoundingBox.h b/source/adios2/core/SelectionBoundingBox.h
index f9fec44d2..4e0f2fdcf 100644
--- a/source/adios2/core/SelectionBoundingBox.h
+++ b/source/adios2/core/SelectionBoundingBox.h
@@ -12,8 +12,8 @@
 
 #include <vector>
 
-#include "ADIOSConfig.h"
-#include "core/Selection.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Selection.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/SelectionPoints.h b/source/adios2/core/SelectionPoints.h
index f0da44f3b..463c4d9ce 100644
--- a/source/adios2/core/SelectionPoints.h
+++ b/source/adios2/core/SelectionPoints.h
@@ -12,8 +12,8 @@
 
 #include <vector>
 
-#include "ADIOSConfig.h"
-#include "core/Selection.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Selection.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Support.cpp b/source/adios2/core/Support.cpp
index 7a7785efb..c1db02342 100644
--- a/source/adios2/core/Support.cpp
+++ b/source/adios2/core/Support.cpp
@@ -8,8 +8,9 @@
  *      Author: wfg
  */
 
-#include "core/Support.h"
-#include "core/adiosTemplates.h"
+#include "Support.h"
+
+#include "adios2/core/adiosTemplates.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Support.h b/source/adios2/core/Support.h
index 51efeb1b2..bdb494e90 100644
--- a/source/adios2/core/Support.h
+++ b/source/adios2/core/Support.h
@@ -17,7 +17,7 @@
 #include <string>
 /// \endcond
 
-#include "ADIOSConfig.h"
+#include "adios2/ADIOSConfig.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Timer.cpp b/source/adios2/core/Timer.cpp
index 731714489..2ae983fe8 100644
--- a/source/adios2/core/Timer.cpp
+++ b/source/adios2/core/Timer.cpp
@@ -8,7 +8,7 @@
  *      Author: wfg
  */
 
-#include "core/Timer.h"
+#include "Timer.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Timer.h b/source/adios2/core/Timer.h
index 6c371fa27..90656079d 100644
--- a/source/adios2/core/Timer.h
+++ b/source/adios2/core/Timer.h
@@ -16,8 +16,8 @@
 #include <string>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "core/Support.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Support.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Transform.cpp b/source/adios2/core/Transform.cpp
index 7549342b2..ac75b66ad 100644
--- a/source/adios2/core/Transform.cpp
+++ b/source/adios2/core/Transform.cpp
@@ -7,9 +7,10 @@
  *  Created on: Dec 5, 2016
  *      Author: wfg
  */
-#include <utility>
 
-#include "core/Transform.h"
+#include "Transform.h"
+
+#include <utility>
 
 namespace adios
 {
diff --git a/source/adios2/core/Transform.h b/source/adios2/core/Transform.h
index d98bbd975..ffb00d142 100644
--- a/source/adios2/core/Transform.h
+++ b/source/adios2/core/Transform.h
@@ -16,7 +16,7 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
+#include "adios2/ADIOSConfig.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Transport.cpp b/source/adios2/core/Transport.cpp
index 1fde211ae..808b5c933 100644
--- a/source/adios2/core/Transport.cpp
+++ b/source/adios2/core/Transport.cpp
@@ -8,9 +8,9 @@
  *      Author: wfg
  */
 
-#include <utility>
+#include "Transport.h"
 
-#include "core/Transport.h"
+#include <utility>
 
 namespace adios
 {
diff --git a/source/adios2/core/Transport.h b/source/adios2/core/Transport.h
index ae55dc71f..03c8d62a4 100644
--- a/source/adios2/core/Transport.h
+++ b/source/adios2/core/Transport.h
@@ -16,9 +16,9 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "ADIOS_MPI.h"
-#include "core/IOChrono.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOS_MPI.h"
+#include "adios2/core/IOChrono.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/Variable.h b/source/adios2/core/Variable.h
index 30abdff35..4839297bf 100644
--- a/source/adios2/core/Variable.h
+++ b/source/adios2/core/Variable.h
@@ -18,9 +18,9 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "core/Transform.h"
-#include "core/VariableBase.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Transform.h"
+#include "adios2/core/VariableBase.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/VariableBase.h b/source/adios2/core/VariableBase.h
index 6f84e6003..eba000148 100644
--- a/source/adios2/core/VariableBase.h
+++ b/source/adios2/core/VariableBase.h
@@ -19,10 +19,10 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "core/SelectionBoundingBox.h"
-#include "core/adiosFunctions.h"
-#include "core/adiosTemplates.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/SelectionBoundingBox.h"
+#include "adios2/core/adiosFunctions.h"
+#include "adios2/core/adiosTemplates.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/VariableCompound.h b/source/adios2/core/VariableCompound.h
index 4df5344d3..d40c8ae21 100644
--- a/source/adios2/core/VariableCompound.h
+++ b/source/adios2/core/VariableCompound.h
@@ -11,8 +11,8 @@
 #ifndef VARIABLECOMPOUND_H_
 #define VARIABLECOMPOUND_H_
 
-#include "ADIOSConfig.h"
-#include "core/VariableBase.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/VariableBase.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/adiosFunctions.cpp b/source/adios2/core/adiosFunctions.cpp
index 965967852..ffb5c81f4 100644
--- a/source/adios2/core/adiosFunctions.cpp
+++ b/source/adios2/core/adiosFunctions.cpp
@@ -8,26 +8,26 @@
  *      Author: wfg
  */
 
-/// \cond EXCLUDED_FROM_DOXYGEN
+#include "adiosFunctions.h"
+
+#include <sys/stat.h>  //stat
+#include <sys/types.h> //CreateDirectory
+#include <unistd.h>    //CreateDirectory
+
+#include <cmath>   // std::ceil, std::pow, std::log
+#include <cstring> //std::memcpy
+
 #include <algorithm> //std::count
-#include <cmath>     // std::ceil, std::pow, std::log
-#include <cstring>   //std::memcpy
 #include <fstream>
 #include <ios> //std::ios_base::failure
 #include <sstream>
 #include <stdexcept>
 #include <thread> //std::thread
 
-#include <sys/stat.h>  //stat
-#include <sys/types.h> //CreateDirectory
-#include <unistd.h>    //CreateDirectory
-/// \endcond
-
-#include "core/Support.h"
-#include "core/adiosFunctions.h"
+#include "adios2/core/Support.h"
 
 #ifdef ADIOS2_HAVE_BZIP2
-#include "transform/BZip2.h"
+#include "adios2/transform/BZip2.h"
 #endif
 
 namespace adios
diff --git a/source/adios2/core/adiosFunctions.h b/source/adios2/core/adiosFunctions.h
index 963563347..1c267000e 100644
--- a/source/adios2/core/adiosFunctions.h
+++ b/source/adios2/core/adiosFunctions.h
@@ -19,9 +19,9 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "ADIOS_MPI.h"
-#include "core/Transform.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOS_MPI.h"
+#include "adios2/core/Transform.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/adiosTemplates.h b/source/adios2/core/adiosTemplates.h
index 90c8b66b9..570e31f48 100644
--- a/source/adios2/core/adiosTemplates.h
+++ b/source/adios2/core/adiosTemplates.h
@@ -21,7 +21,7 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
+#include "adios2/ADIOSConfig.h"
 
 namespace adios
 {
diff --git a/source/adios2/core/capsuleTemplates.h b/source/adios2/core/capsuleTemplates.h
index f88a3aaca..7fe230bca 100644
--- a/source/adios2/core/capsuleTemplates.h
+++ b/source/adios2/core/capsuleTemplates.h
@@ -17,8 +17,8 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "core/Transport.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Transport.h"
 
 namespace adios
 {
diff --git a/source/adios2/engine/adios1/ADIOS1Reader.cpp b/source/adios2/engine/adios1/ADIOS1Reader.cpp
index 376927bc0..daf4a418f 100644
--- a/source/adios2/engine/adios1/ADIOS1Reader.cpp
+++ b/source/adios2/engine/adios1/ADIOS1Reader.cpp
@@ -8,14 +8,14 @@
  *      Author: wfg
  */
 
-#include "core/Support.h"
-#include "core/adiosFunctions.h"           // CSVToVector
-#include "transport/file/FStream.h"        // uses C++ fstream
-#include "transport/file/FileDescriptor.h" // uses POSIX
-#include "transport/file/FilePointer.h"    // uses C FILE*
-
 #include "ADIOS1Reader.h"
 
+#include "adios2/core/Support.h"
+#include "adios2/core/adiosFunctions.h"           // CSVToVector
+#include "adios2/transport/file/FStream.h"        // uses C++ fstream
+#include "adios2/transport/file/FileDescriptor.h" // uses POSIX
+#include "adios2/transport/file/FilePointer.h"    // uses C FILE*
+
 namespace adios
 {
 
diff --git a/source/adios2/engine/adios1/ADIOS1Reader.h b/source/adios2/engine/adios1/ADIOS1Reader.h
index aa8059d7a..584ddf778 100644
--- a/source/adios2/engine/adios1/ADIOS1Reader.h
+++ b/source/adios2/engine/adios1/ADIOS1Reader.h
@@ -15,18 +15,17 @@
 
 #include <iostream> //this must go away
 
-#include "ADIOSConfig.h"
-#include "core/Engine.h"
-#include "capsule/heap/STLVector.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/capsule/heap/STLVector.h"
+#include "adios2/core/Engine.h"
+
+#include <adios_read_v2.h>
 
 namespace adios
 {
 
-#include "adios_read_v2.h" // this is adios 1.x header file
-
 class ADIOS1Reader : public Engine
 {
-
 public:
     /**
      * Constructor for single BP capsule engine, writes in BP format into a
diff --git a/source/adios2/engine/adios1/ADIOS1Writer.cpp b/source/adios2/engine/adios1/ADIOS1Writer.cpp
index d66714bed..9dff8ee98 100644
--- a/source/adios2/engine/adios1/ADIOS1Writer.cpp
+++ b/source/adios2/engine/adios1/ADIOS1Writer.cpp
@@ -10,10 +10,10 @@
  *      Author: pnb
  */
 
-#include "core/adiosFunctions.h"
-
 #include "ADIOS1Writer.h"
 
+#include "adios2/core/adiosFunctions.h"
+
 extern int adios_verbose_level;
 extern int adios_errno;
 
diff --git a/source/adios2/engine/adios1/ADIOS1Writer.h b/source/adios2/engine/adios1/ADIOS1Writer.h
index 407605d37..759a5d102 100644
--- a/source/adios2/engine/adios1/ADIOS1Writer.h
+++ b/source/adios2/engine/adios1/ADIOS1Writer.h
@@ -13,13 +13,13 @@
 #ifndef ADIOS1WRITER_H_
 #define ADIOS1WRITER_H_
 
-#include "ADIOSConfig.h"
-#include "core/Engine.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Engine.h"
 
 namespace adios
 {
 
-#include "adios.h" // this is adios 1.x header file
+#include <adios.h> // this is adios 1.x header file
 
 class ADIOS1Writer : public Engine
 {
diff --git a/source/adios2/engine/bp/BPFileReader.cpp b/source/adios2/engine/bp/BPFileReader.cpp
index 265ab95bf..ef4951a0a 100644
--- a/source/adios2/engine/bp/BPFileReader.cpp
+++ b/source/adios2/engine/bp/BPFileReader.cpp
@@ -10,11 +10,11 @@
 
 #include "BPFileReader.h"
 
-#include "core/Support.h"
-#include "core/adiosFunctions.h"           // CSVToVector
-#include "transport/file/FStream.h"        // uses C++ fstream
-#include "transport/file/FileDescriptor.h" // uses POSIX
-#include "transport/file/FilePointer.h"    // uses C FILE*
+#include "adios2/core/Support.h"
+#include "adios2/core/adiosFunctions.h"           // CSVToVector
+#include "adios2/transport/file/FStream.h"        // uses C++ fstream
+#include "adios2/transport/file/FileDescriptor.h" // uses POSIX
+#include "adios2/transport/file/FilePointer.h"    // uses C FILE*
 
 namespace adios
 {
diff --git a/source/adios2/engine/bp/BPFileReader.h b/source/adios2/engine/bp/BPFileReader.h
index 4142e724b..3f09cb36c 100644
--- a/source/adios2/engine/bp/BPFileReader.h
+++ b/source/adios2/engine/bp/BPFileReader.h
@@ -13,9 +13,9 @@
 
 #include <iostream> //this must go away
 
-#include "ADIOSConfig.h"
-#include "core/Engine.h"
-#include "capsule/heap/STLVector.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/capsule/heap/STLVector.h"
+#include "adios2/core/Engine.h"
 
 namespace adios
 {
diff --git a/source/adios2/engine/bp/BPFileWriter.cpp b/source/adios2/engine/bp/BPFileWriter.cpp
index b83f4052f..013a19ec0 100644
--- a/source/adios2/engine/bp/BPFileWriter.cpp
+++ b/source/adios2/engine/bp/BPFileWriter.cpp
@@ -7,15 +7,15 @@
  *  Created on: Dec 19, 2016
  *      Author: wfg
  */
-#include <utility>
 
-#include "ADIOS.h"
 #include "BPFileWriter.h"
 
-// supported transports
-#include "transport/file/FStream.h"
-#include "transport/file/FileDescriptor.h"
-#include "transport/file/FilePointer.h"
+#include <utility>
+
+#include "adios2/ADIOS.h"
+#include "adios2/transport/file/FStream.h"
+#include "adios2/transport/file/FileDescriptor.h"
+#include "adios2/transport/file/FilePointer.h"
 
 namespace adios
 {
diff --git a/source/adios2/engine/bp/BPFileWriter.h b/source/adios2/engine/bp/BPFileWriter.h
index 5e338f043..5c0551b96 100644
--- a/source/adios2/engine/bp/BPFileWriter.h
+++ b/source/adios2/engine/bp/BPFileWriter.h
@@ -11,10 +11,10 @@
 #ifndef BPFILEWRITER_H_
 #define BPFILEWRITER_H_
 
-#include "ADIOSConfig.h"
-#include "core/Engine.h"
-#include "capsule/heap/STLVector.h"
-#include "utilities/format/bp1/BP1.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/capsule/heap/STLVector.h"
+#include "adios2/core/Engine.h"
+#include "adios2/utilities/format/bp1/BP1.h"
 
 namespace adios
 {
diff --git a/source/adios2/engine/dataman/DataManReader.cpp b/source/adios2/engine/dataman/DataManReader.cpp
index 32cfdb967..bb520b501 100644
--- a/source/adios2/engine/dataman/DataManReader.cpp
+++ b/source/adios2/engine/dataman/DataManReader.cpp
@@ -10,15 +10,12 @@
 
 #include "DataManReader.h"
 
-#include "core/Support.h"
-#include "core/adiosFunctions.h" //CSVToVector
-#include "external/json.hpp"
-
-// supported transports
-#include "transport/file/FStream.h"        // uses C++ fstream
-#include "transport/file/FileDescriptor.h" // uses POSIX
-#include "transport/file/FilePointer.h"    // uses C FILE*
-#include "transport/wan/MdtmMan.h"         //uses Mdtm library
+#include "adios2/core/Support.h"
+#include "adios2/core/adiosFunctions.h"           //CSVToVector
+#include "adios2/transport/file/FStream.h"        // uses C++ fstream
+#include "adios2/transport/file/FileDescriptor.h" // uses POSIX
+#include "adios2/transport/file/FilePointer.h"    // uses C FILE*
+#include "adios2/transport/wan/MdtmMan.h"         //uses Mdtm library
 
 namespace adios
 {
diff --git a/source/adios2/engine/dataman/DataManReader.h b/source/adios2/engine/dataman/DataManReader.h
index a163890d3..cc367825a 100644
--- a/source/adios2/engine/dataman/DataManReader.h
+++ b/source/adios2/engine/dataman/DataManReader.h
@@ -13,11 +13,12 @@
 
 #include <iostream> //std::cout << Needs to go
 
-#include "ADIOSConfig.h"
-#include "core/Engine.h"
-#include "utilities/format/bp1/BP1Writer.h"
-#include "utilities/realtime/dataman/DataMan.h"
-#include "capsule/heap/STLVector.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/capsule/heap/STLVector.h"
+#include "adios2/core/Engine.h"
+#include "adios2/utilities/format/bp1/BP1Writer.h"
+
+#include <DataMan.h>
 
 namespace adios
 {
@@ -107,7 +108,7 @@ private:
     /// m_Transports
 
     bool m_DoRealTime = false;
-    realtime::DataMan m_Man;
+    DataMan m_Man;
     std::function<void(const void *, std::string, std::string, std::string,
                        Dims)>
         m_CallBack; ///< call back function
diff --git a/source/adios2/engine/dataman/DataManWriter.cpp b/source/adios2/engine/dataman/DataManWriter.cpp
index bd2ef126d..c125c10cb 100644
--- a/source/adios2/engine/dataman/DataManWriter.cpp
+++ b/source/adios2/engine/dataman/DataManWriter.cpp
@@ -8,16 +8,14 @@
  *      Author: wfg
  */
 
-#include <iostream> //needs to go away, this is just for demo purposes
-
 #include "DataManWriter.h"
 
-#include "core/Support.h"
-#include "core/adiosFunctions.h" //CSVToVector
+#include <iostream> //needs to go away, this is just for demo purposes
 
-// supported transports
-#include "transport/file/FStream.h" // uses C++ fstream
-#include "transport/wan/MdtmMan.h"  //uses Mdtm library
+#include "adios2/core/Support.h"
+#include "adios2/core/adiosFunctions.h"    //CSVToVector
+#include "adios2/transport/file/FStream.h" // uses C++ fstream
+#include "adios2/transport/wan/MdtmMan.h"  //uses Mdtm library
 
 namespace adios
 {
diff --git a/source/adios2/engine/dataman/DataManWriter.h b/source/adios2/engine/dataman/DataManWriter.h
index 2e1b4c220..95cfefb3e 100644
--- a/source/adios2/engine/dataman/DataManWriter.h
+++ b/source/adios2/engine/dataman/DataManWriter.h
@@ -14,11 +14,12 @@
 #include <iostream> //std::cout must be removed, only used for hello example
 #include <unistd.h> //sleep must be removed
 
-#include "ADIOSConfig.h"
-#include "core/Engine.h"
-#include "utilities/format/bp1/BP1Writer.h"
-#include "utilities/realtime/dataman/DataMan.h"
-#include "capsule/heap/STLVector.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/capsule/heap/STLVector.h"
+#include "adios2/core/Engine.h"
+#include "adios2/utilities/format/bp1/BP1Writer.h"
+
+#include <DataMan.h>
 
 namespace adios
 {
@@ -105,7 +106,7 @@ private:
 
     bool m_DoRealTime = false;
     bool m_DoMonitor = false;
-    realtime::DataMan m_Man;
+    DataMan m_Man;
     std::function<void(const void *, std::string, std::string, std::string,
                        Dims)>
         m_CallBack; ///< call back function
diff --git a/source/adios2/engine/hdf5/HDF5ReaderP.cpp b/source/adios2/engine/hdf5/HDF5ReaderP.cpp
index 5b706030e..9ed3135d0 100644
--- a/source/adios2/engine/hdf5/HDF5ReaderP.cpp
+++ b/source/adios2/engine/hdf5/HDF5ReaderP.cpp
@@ -8,6 +8,6 @@
  *      Author: Junmin
  */
 
-#include <iostream> //needs to go away, this is just for demo purposes
+#include "adios2/HDF5ReaderP.h"
 
-#include "HDF5ReaderP.h"
+#include <iostream> //needs to go away, this is just for demo purposes
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.cpp b/source/adios2/engine/hdf5/HDF5WriterP.cpp
index cec8d43a4..9377560b8 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.cpp
+++ b/source/adios2/engine/hdf5/HDF5WriterP.cpp
@@ -8,12 +8,12 @@
  *      Author: Junmin
  */
 
-#include <iostream> //needs to go away, this is just for demo purposes
+#include "adios2/HDF5WriterP.h"
 
-#include "HDF5WriterP.h"
+#include <iostream> //needs to go away, this is just for demo purposes
 
-#include "core/Support.h"
-#include "core/adiosFunctions.h" //CSVToVector
+#include "adios2/core/Support.h"
+#include "adios2/core/adiosFunctions.h" //CSVToVector
 
 namespace adios
 {
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.h b/source/adios2/engine/hdf5/HDF5WriterP.h
index 9975fe526..d581ace08 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.h
+++ b/source/adios2/engine/hdf5/HDF5WriterP.h
@@ -12,10 +12,10 @@
 #ifndef HDF5_WRITER_P_H_
 #define HDF5_WRITER_P_H_
 
-#include "ADIOSConfig.h"
-#include "ADIOS_MPI.h"
-#include "core/Engine.h"
-#include "capsule/heap/STLVector.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOS_MPI.h"
+#include "adios2/capsule/heap/STLVector.h"
+#include "adios2/core/Engine.h"
 
 #include <hdf5.h>
 
diff --git a/source/adios2/external/adios_selection.h b/source/adios2/external/adios_selection.h
deleted file mode 100644
index 551d72ee5..000000000
--- a/source/adios2/external/adios_selection.h
+++ /dev/null
@@ -1,240 +0,0 @@
-/*
- * Distributed under the OSI-approved Apache License, Version 2.0.  See
- * accompanying file Copyright.txt for details.
- *
- */
-
-/*
- *   Streaming/Chunking/Selection Read API in C for ADIOS BP format
- *
- *   A SELECTION is the data ranges resulting from a QUERY over a file and
- * variable(s).
- *
- *   A SELECTION can be a list of bounding boxes and point-sets. Other data
- * structures
- *   are not supported. Any query will result in such a selection.
- *   Other selections are the write-block and auto.
- *
- *   Write block is a block of data written
- *   by a writer process, it is identified by an index. If each writer outputs
- * one block
- *   then the index equals to the rank of the write process. With multi-var
- * writing and
- *   multiple steps in a file, index runs from 0 as rank 0 process' first block.
- *
- *   Auto selection lets the read method to automatically choose what to return.
- * It will
- *   be a block / blocks of selected writers.
- *
- *   If a query is a simple bounding box, the selection is the bounding box
- * itself, so
- *   the application does not need to retrieve the selection to work on the read
- * data.
- */
-#ifndef __ADIOS_SELECTION_C_H__
-#define __ADIOS_SELECTION_C_H__
-
-#include <stdint.h>
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/*************************/
-/* Types used in the API */
-/*************************/
-
-typedef struct ADIOS_SELECTION_STRUCT ADIOS_SELECTION;
-
-/* Type of selection */
-enum ADIOS_SELECTION_TYPE
-{
-    ADIOS_SELECTION_BOUNDINGBOX = 0, /* Contiguous block of data defined by
-                                        offsets and counts in each dimension */
-    ADIOS_SELECTION_POINTS = 1,      /* List of individual points */
-    ADIOS_SELECTION_WRITEBLOCK =
-        2, /* Selection of an individual block written by a writer process */
-    ADIOS_SELECTION_AUTO = 3 /* Let the method decide what to return */
-};
-
-/* A Bounding Box */
-typedef struct
-{
-    int ndim;
-    uint64_t *start;
-    uint64_t *count;
-} ADIOS_SELECTION_BOUNDINGBOX_STRUCT;
-
-/* A list of points.
- * It is a 1D array of indices, linearized for all dimension
- *     (e.g.  [i1,j1,k1,i2,j2,k2,...,in,jn,kn] for n points in a 3D space.
- * If a container selection is given, points are relative coordinates/offsets in
- * the
- * container box/writeblock.
- * 1D offsets in N-dimensional container are allowed. Such selections are
- * returned by
- * FASTBIT and ALACRITY query method. File reading is supported for such
- * selections.
- * adios_selection_points_1DtoND() can be used to convert 1D to N-D points.
- */
-typedef struct
-{
-    int ndim;
-    int _free_points_on_delete; // user provided points are not copied, won't
-                                // free either
-    uint64_t npoints;
-    uint64_t *points;
-    ADIOS_SELECTION
-    *container_selection; // a writeblock, a bounding box, or NULL
-} ADIOS_SELECTION_POINTS_STRUCT;
-
-/* A selected block produced by a writer
- * Identified with an index in current versions.
- */
-typedef struct
-{
-    int index;
-
-    /* NCSU ALACRITY-ADIOS:
-     *     Adding timestep-relative vs. absolute writeblock selections, as
-     *     well as sub-PG selection support. Both of these are currently only
-     *     used by the transform layer
-     */
-    int is_absolute_index; /* 0 if 'index' is relative to the current timestep,
-                              != 0
-                              otherwise (i.e., absolute index) */
-    int is_sub_pg_selection; /* Whether this writeblock selection contains
-                                sub-PG bounds.
-                                The following fields only matter if this is != 0
-                                */
-
-    /* Reads the linear range of elements in [element_offset, element_offset +
-     * nelements) */
-    uint64_t element_offset;
-    uint64_t nelements;
-} ADIOS_SELECTION_WRITEBLOCK_STRUCT;
-
-/* Let the read method decide what to return to each reading client.
- * Hints are method-dependent parameters to influence what and how to
- * return (e.g. the ordering of returned chunks, decomposition among
- * read processes, etc.)
- */
-typedef struct
-{
-    char *hints;
-} ADIOS_SELECTION_AUTO_STRUCT;
-
-/** Selection for reading a subset of a variable.
- *   A selection is an additive list of bounding boxes and point-sets
- */
-struct ADIOS_SELECTION_STRUCT
-{
-    enum ADIOS_SELECTION_TYPE type; /* Type of selection */
-    union {
-        ADIOS_SELECTION_BOUNDINGBOX_STRUCT bb;
-        ADIOS_SELECTION_POINTS_STRUCT points;
-        ADIOS_SELECTION_WRITEBLOCK_STRUCT block;
-        ADIOS_SELECTION_AUTO_STRUCT autosel;
-    } u;
-    // ADIOS_SELECTION             *next;
-};
-
-#ifndef __INCLUDED_FROM_FORTRAN_API__
-
-/** Boundingbox selection to read a subset of a non-scalar variable.
- *  IN:
- *       ndim      Number of dimensions
- *       start     array of offsets to start reading in each dimension
- *       count     number of data elements to read in each dimension
- *  RETURN:        A selection which can be used to read variables
- */
-ADIOS_SELECTION *adios_selection_boundingbox(int ndim, const uint64_t *start,
-                                             const uint64_t *count);
-
-/** Selection for a selection of an enumeration of positions.
- *  IN:
- *       ndim      Number of dimensions
- *       npoints   Number of points of the selection
- *       points    1D array of indices, compacted for all dimension
- *                 (e.g.  [i1,j1,k1,i2,j2,k2,...,in,jn,kn] for
- *                 n points in a 3D space.
- */
-ADIOS_SELECTION *adios_selection_points(int ndim, uint64_t npoints,
-                                        const uint64_t *points);
-
-/** Selection for a block of data coming from a certain producer.
- *
- *  IN:
- *       index      Identifier of the written block, starting from 0 for the
- * first block
- *                  written by producer rank 0. If each writer outputs one block
- *                  then the index equals to the rank of the write process.
- *                  With multi-var writing and multiple steps in a file, index
- * should be
- *                  calculated by the reading application using outside
- * information beyond
- *                  what is provided by the ADIOS Read API.
- */
-ADIOS_SELECTION *adios_selection_writeblock(int index);
-
-/** Let the method decide what data gets to what reader process.
- *  This selection enables each reading method to provide an 'optimal'
- *  data transfer from writers to readers. It depends on the method and the
- *  circumstances, what this selection actually means.
- *
- *  E.g. in situ processing: readers on a compute node will receive all data
- *       from the writers on the same compute node.
- *
- *  IN:
- *       hints    Method dependent parameters to influence what and how to
- *                return (e.g. decomposition; ordering of returned chunks)
- */
-ADIOS_SELECTION *adios_selection_auto(char *hints);
-
-/** Make a strided hyperslab selection the same way as in HDF5.
- *  IN:
- *       ndim      Number of dimentsions
- *       start     array of offsets to start reading in each dimension
- *       strides   striding steps, NULL=1 in all dimensions (= boundingbox)
- *       count     number of data elements to read in each dimension
- *       blocks    block size at each stride, NULL=1 in all dimensions
- */
-/*
-   No support: Klasky, Podhorszki
-   Support:
-
-ADIOS_SELECTION* adios_selection_hyperslab (uint64_t ndim, uint64_t *start,
-uint64_t *strides,
-                                    uint64_t *count, uint64_t *blocks);
-*/
-
-/** Delete a selection and free up memory used by the selection.
-  * IN: selection
-  * RESULT: None
-  * The ADIOS_SELECTION object can be simply freed by free(), too.
-  */
-void adios_selection_delete(ADIOS_SELECTION *selection);
-
-/* Convert one selection of 1D point offsets in a bounding box,
- * returned by FASTBIT and ALACRITY query methods, to N-dimensional points.
- * This function works only if there is a bounding box in
- * pointsinbox1D->u.points.container!
- * It allocates memory for the result selection, after which the original can be
- * freed.
- * Return:
- * If global==0, the points will be relative to the container, if not, the
- * points will be
- * global coordinates (container's starting offsets added to each point) and
- * result's container
- * will be NULL.
- */
-ADIOS_SELECTION *adios_selection_points_1DtoND(ADIOS_SELECTION *pointsinbox1D,
-                                               int global);
-
-#endif /*__INCLUDED_FROM_FORTRAN_API__*/
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /*__ADIOS_SELECTION_C_H__*/
diff --git a/source/adios2/mpidummy.cpp b/source/adios2/mpidummy.cpp
index c70ae74e0..44baae4a0 100644
--- a/source/adios2/mpidummy.cpp
+++ b/source/adios2/mpidummy.cpp
@@ -12,21 +12,18 @@
    A dummy MPI implementation for the BP READ API, to have an MPI-free version
    of the API
 */
-/// \cond EXCLUDE_FROM_DOXYGEN
-#define __STDC_FORMAT_MACROS
-#include <cinttypes>
-#include <cstdint>
-#include <cstdio>
-#include <cstring>
 
-//#define _LARGEFILE64_SOURCE
-#include <unistd.h>
+#include "mpidummy.h"
 
 #include <sys/time.h>
 #include <sys/types.h>
-/// \endcond
+#include <unistd.h>
 
-#include "mpidummy.h"
+#define __STDC_FORMAT_MACROS
+#include <cinttypes>
+#include <cstdint>
+#include <cstdio>
+#include <cstring>
 
 #if defined(__APPLE__) || defined(__WIN32__) || defined(__CYGWIN__)
 #define lseek64 lseek
diff --git a/source/adios2/mpidummy.h b/source/adios2/mpidummy.h
index 3803925bc..3025f38ef 100644
--- a/source/adios2/mpidummy.h
+++ b/source/adios2/mpidummy.h
@@ -19,7 +19,7 @@
 #include <sys/types.h>
 /// \endcond
 
-#include "ADIOSConfig.h"
+#include "adios2/ADIOSConfig.h"
 
 namespace adios
 {
diff --git a/source/adios2/transform/BZip2.h b/source/adios2/transform/BZip2.h
index bf2110880..3fc726ba3 100644
--- a/source/adios2/transform/BZip2.h
+++ b/source/adios2/transform/BZip2.h
@@ -11,8 +11,8 @@
 #ifndef BZIP2_H_
 #define BZIP2_H_
 
-#include "ADIOSConfig.h"
-#include "core/Transform.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Transform.h"
 
 namespace adios
 {
diff --git a/source/adios2/transport/file/FStream.cpp b/source/adios2/transport/file/FStream.cpp
index 69b603e63..a22f83da1 100644
--- a/source/adios2/transport/file/FStream.cpp
+++ b/source/adios2/transport/file/FStream.cpp
@@ -8,12 +8,10 @@
  *      Author: wfg
  */
 
-/// \cond EXCLUDED_FROM_DOXYGEN
+#include "FStream.h"
+
 #include <ios> // std::ios_base::failure
 #include <stdexcept>
-/// \endcond
-
-#include "FStream.h"
 
 namespace adios
 {
diff --git a/source/adios2/transport/file/FStream.h b/source/adios2/transport/file/FStream.h
index 4bfe0111d..23816ec32 100644
--- a/source/adios2/transport/file/FStream.h
+++ b/source/adios2/transport/file/FStream.h
@@ -15,8 +15,8 @@
 #include <fstream>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "core/Transport.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Transport.h"
 
 namespace adios
 {
diff --git a/source/adios2/transport/file/FileDescriptor.cpp b/source/adios2/transport/file/FileDescriptor.cpp
index 29959987a..c64d6a4cf 100644
--- a/source/adios2/transport/file/FileDescriptor.cpp
+++ b/source/adios2/transport/file/FileDescriptor.cpp
@@ -8,16 +8,14 @@
  *      Author: wfg
  */
 
-/// \cond EXCLUDE_FROM_DOXYGEN
+#include "FileDescriptor.h"
+
 #include <fcntl.h>     // open
 #include <ios>         // std::ios_base::failure
 #include <stddef.h>    // write output
 #include <sys/stat.h>  // open
 #include <sys/types.h> // open
 #include <unistd.h>    // write, close
-/// \endcond
-
-#include "FileDescriptor.h"
 
 namespace adios
 {
diff --git a/source/adios2/transport/file/FileDescriptor.h b/source/adios2/transport/file/FileDescriptor.h
index f326f6ddd..1668aa07b 100644
--- a/source/adios2/transport/file/FileDescriptor.h
+++ b/source/adios2/transport/file/FileDescriptor.h
@@ -11,8 +11,8 @@
 #ifndef FILEDESCRIPTOR_H_
 #define FILEDESCRIPTOR_H_
 
-#include "ADIOSConfig.h"
-#include "core/Transport.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Transport.h"
 
 namespace adios
 {
diff --git a/source/adios2/transport/file/FilePointer.cpp b/source/adios2/transport/file/FilePointer.cpp
index 8348d80ea..3e889420b 100644
--- a/source/adios2/transport/file/FilePointer.cpp
+++ b/source/adios2/transport/file/FilePointer.cpp
@@ -8,12 +8,10 @@
  *      Author: wfg
  */
 
-/// \cond EXCLUDE_FROM_DOXYGEN
-#include <ios> //std::ios_base::failure
-/// \endcond
-
 #include "FilePointer.h"
 
+#include <ios> //std::ios_base::failure
+
 namespace adios
 {
 namespace transport
diff --git a/source/adios2/transport/file/FilePointer.h b/source/adios2/transport/file/FilePointer.h
index 28cd2f911..26ea22e24 100644
--- a/source/adios2/transport/file/FilePointer.h
+++ b/source/adios2/transport/file/FilePointer.h
@@ -15,8 +15,8 @@
 #include <stdio.h> // FILE*
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "core/Transport.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Transport.h"
 
 namespace adios
 {
diff --git a/source/adios2/transport/file/MPI_File.h b/source/adios2/transport/file/MPI_File.h
index 5cfdd16d6..8380736e5 100644
--- a/source/adios2/transport/file/MPI_File.h
+++ b/source/adios2/transport/file/MPI_File.h
@@ -11,8 +11,8 @@
 #ifndef MPI_FILE_H_
 #define MPI_FILE_H_
 
-#include "ADIOSConfig.h"
-#include "ADIOS_MPI.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOS_MPI.h"
 
 namespace adios
 {
diff --git a/source/adios2/transport/wan/MdtmMan.h b/source/adios2/transport/wan/MdtmMan.h
index 6f718bc36..3b0a0c4fa 100644
--- a/source/adios2/transport/wan/MdtmMan.h
+++ b/source/adios2/transport/wan/MdtmMan.h
@@ -11,10 +11,10 @@
 #ifndef MDTMMAN_H_
 #define MDTMMAN_H_
 
-#include "ADIOSConfig.h"
-#include "core/Transport.h"
-#include "external/json.hpp"
-#include "utilities/realtime/dataman/DataManBase.h"
+#include <json.hpp>
+
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/Transport.h"
 
 namespace adios
 {
diff --git a/source/adios2/utilities/format/bp1/BP1.h b/source/adios2/utilities/format/bp1/BP1.h
index ed447f8e4..dc070be1f 100644
--- a/source/adios2/utilities/format/bp1/BP1.h
+++ b/source/adios2/utilities/format/bp1/BP1.h
@@ -11,9 +11,9 @@
 #ifndef BP1_H_
 #define BP1_H_
 
-#include "ADIOSConfig.h"
-#include "utilities/format/bp1/BP1Aggregator.h"
-#include "utilities/format/bp1/BP1Structs.h"
-#include "utilities/format/bp1/BP1Writer.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/utilities/format/bp1/BP1Aggregator.h"
+#include "adios2/utilities/format/bp1/BP1Structs.h"
+#include "adios2/utilities/format/bp1/BP1Writer.h"
 
 #endif /* BP1_H_ */
diff --git a/source/adios2/utilities/format/bp1/BP1Aggregator.cpp b/source/adios2/utilities/format/bp1/BP1Aggregator.cpp
index 7cb585ed8..b26215f18 100644
--- a/source/adios2/utilities/format/bp1/BP1Aggregator.cpp
+++ b/source/adios2/utilities/format/bp1/BP1Aggregator.cpp
@@ -8,13 +8,11 @@
  *      Author: wfg
  */
 
-/// \cond EXCLUDE_FROM_DOXYGEN
 #include "BP1Aggregator.h"
 
 #include <fstream>
 #include <stdexcept>
 #include <vector>
-/// \endcond
 
 namespace adios
 {
diff --git a/source/adios2/utilities/format/bp1/BP1Aggregator.h b/source/adios2/utilities/format/bp1/BP1Aggregator.h
index 23d2736a5..e68fad5b6 100644
--- a/source/adios2/utilities/format/bp1/BP1Aggregator.h
+++ b/source/adios2/utilities/format/bp1/BP1Aggregator.h
@@ -15,8 +15,8 @@
 #include <string>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "ADIOS_MPI.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOS_MPI.h"
 
 namespace adios
 {
diff --git a/source/adios2/utilities/format/bp1/BP1Base.cpp b/source/adios2/utilities/format/bp1/BP1Base.cpp
index c31d5dec1..86da561c7 100644
--- a/source/adios2/utilities/format/bp1/BP1Base.cpp
+++ b/source/adios2/utilities/format/bp1/BP1Base.cpp
@@ -9,7 +9,8 @@
  */
 
 #include "BP1Base.h"
-#include "core/adiosFunctions.h"
+
+#include "adios2/core/adiosFunctions.h"
 
 namespace adios
 {
diff --git a/source/adios2/utilities/format/bp1/BP1Base.h b/source/adios2/utilities/format/bp1/BP1Base.h
index 7f709e4b0..a4defb631 100644
--- a/source/adios2/utilities/format/bp1/BP1Base.h
+++ b/source/adios2/utilities/format/bp1/BP1Base.h
@@ -18,9 +18,9 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "ADIOS_MPI.h"
-#include "core/Transport.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOS_MPI.h"
+#include "adios2/core/Transport.h"
 
 namespace adios
 {
diff --git a/source/adios2/utilities/format/bp1/BP1Structs.h b/source/adios2/utilities/format/bp1/BP1Structs.h
index ce2721288..e385b3a25 100644
--- a/source/adios2/utilities/format/bp1/BP1Structs.h
+++ b/source/adios2/utilities/format/bp1/BP1Structs.h
@@ -18,8 +18,8 @@
 #include <vector>
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "core/IOChrono.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/core/IOChrono.h"
 
 namespace adios
 {
diff --git a/source/adios2/utilities/format/bp1/BP1Writer.cpp b/source/adios2/utilities/format/bp1/BP1Writer.cpp
index 12b3139a4..6f42bc968 100644
--- a/source/adios2/utilities/format/bp1/BP1Writer.cpp
+++ b/source/adios2/utilities/format/bp1/BP1Writer.cpp
@@ -8,14 +8,12 @@
  *      Author: wfg
  */
 
-/// \cond EXCLUDE_FROM_DOXYGEN
-#include <string>
-#include <vector>
-/// \endcond
-
 #include "BP1Writer.h"
 #include "BP1Writer.tcc"
 
+#include <string>
+#include <vector>
+
 namespace adios
 {
 namespace format
diff --git a/source/adios2/utilities/format/bp1/BP1Writer.h b/source/adios2/utilities/format/bp1/BP1Writer.h
index aff0b9890..eaa81659e 100644
--- a/source/adios2/utilities/format/bp1/BP1Writer.h
+++ b/source/adios2/utilities/format/bp1/BP1Writer.h
@@ -17,15 +17,15 @@
 #include <cstring>   //std::memcpy
 /// \endcond
 
-#include "ADIOSConfig.h"
-#include "ADIOSMacros.h"
-#include "ADIOSTypes.h"
-#include "utilities/format/bp1/BP1Base.h"
-#include "utilities/format/bp1/BP1Structs.h"
-#include "capsule/heap/STLVector.h"
-#include "core/Variable.h"
-#include "core/adiosFunctions.h"
-#include "core/adiosTemplates.h"
+#include "adios2/ADIOSConfig.h"
+#include "adios2/ADIOSMacros.h"
+#include "adios2/ADIOSTypes.h"
+#include "adios2/capsule/heap/STLVector.h"
+#include "adios2/core/Variable.h"
+#include "adios2/core/adiosFunctions.h"
+#include "adios2/core/adiosTemplates.h"
+#include "adios2/utilities/format/bp1/BP1Base.h"
+#include "adios2/utilities/format/bp1/BP1Structs.h"
 
 namespace adios
 {
-- 
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