1. Replace includes {lib,pkg}-* with {lib,pkg}/*; compiles (no full compilation tested)

SConstruct

@@ -510,9 +510,15 @@ if not env.GetOption('clean'):
 	#installHeaders() # install to buildDir always
 	#if 0: # do not install headers
 	#	installHeaders(env.subst('$PREFIX')) # install to $PREFIX if specifically requested: like "scons /usr/local/include"
+	def mkSymlink(link,target):
+		if exists(link) and not islink(link): os.remove(link)
+		if not exists(link):
+			if lexists(link): os.remove(link) # remove dangling symlink
+			os.symlink(relpath(link,target),link)
 
 	yadeInc=join(buildDir,'include/yade')
-	if not os.path.exists(yadeInc): os.makedirs(yadeInc)
+	mkSymlink(yadeInc,'.')
+	#if not os.path.exists(yadeInc): os.makedirs(yadeInc)
 	import glob
 	# old compat paths
 	#for p in ['core','extra']+glob.glob('lib/*')+glob.glob('pkg/*')+glob.glob('gui'):
@@ -522,10 +528,6 @@ if not env.GetOption('clean'):
 	#		os.symlink(relpath(link,p),link)
 	boostDir=buildDir+'/include/boost'
 	if not exists(boostDir): os.makedirs(boostDir)
-	def mkSymlink(link,target):
-		if not exists(link):
-			if lexists(link): os.remove(link) # remove dangling symlink
-			os.symlink(relpath(link,target),link)
 	if not env['haveForeach']:
 		mkSymlink(boostDir+'/foreach.hpp','extra/foreach.hpp_local')
 	#mkSymlink(boostDir+'/python','py/3rd-party/boost-python-indexing-suite-v2-noSymlinkHeaders')

core/Body.hpp

@@ -15,9 +15,9 @@
 #include"State.hpp"
 #include"Material.hpp"
 
-#include<yade/lib-base/Math.hpp>
-#include<yade/lib-serialization/Serializable.hpp>
-#include<yade/lib-multimethods/Indexable.hpp>
+#include<yade/lib/base/Math.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
+#include<yade/lib/multimethods/Indexable.hpp>
 
 class Scene;
 

core/BodyContainer.hpp

@@ -4,7 +4,7 @@
 
 #pragma once
 
-#include<yade/lib-serialization/Serializable.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
 
 #include<boost/foreach.hpp>
 #ifndef FOREACH

core/Bound.hpp

@@ -7,9 +7,9 @@
 *************************************************************************/
 #pragma once
 
-#include<yade/lib-base/Math.hpp>
-#include<yade/lib-serialization/Serializable.hpp>
-#include<yade/lib-multimethods/Indexable.hpp>
+#include<yade/lib/base/Math.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
+#include<yade/lib/multimethods/Indexable.hpp>
 #include<yade/core/Dispatcher.hpp>
 
 /*! Interface for approximate body locations in space

core/Cell.hpp

@@ -14,8 +14,8 @@ The transformation has normal part and rotation/shear part. the shearPt, unshear
 
 #pragma once
 
-#include<yade/lib-serialization/Serializable.hpp>
-#include<yade/lib-base/Math.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
+#include<yade/lib/base/Math.hpp>
 
 class Cell: public Serializable{
 	public:

core/Dispatcher.hpp

@@ -13,7 +13,7 @@
 #include<yade/core/Engine.hpp>
 #include<yade/core/Functor.hpp>
 #include<yade/core/Omega.hpp>
-#include<yade/lib-multimethods/DynLibDispatcher.hpp>
+#include<yade/lib/multimethods/DynLibDispatcher.hpp>
 
 #include<boost/preprocessor/cat.hpp>
 

core/EnergyTracker.hpp

@@ -2,8 +2,8 @@
 #include<boost/python.hpp>
 #include<boost/foreach.hpp>
 #include<string>
-#include<yade/lib-base/openmp-accu.hpp>
-#include<yade/lib-serialization/Serializable.hpp>
+#include<yade/lib/base/openmp-accu.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
 
 #ifndef FOREACH
 	#define FOREACH BOOST_FOREACH

core/Engine.hpp

@@ -10,10 +10,10 @@
 
 #pragma once
 
-#include<yade/lib-serialization/Serializable.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
 #include<yade/core/Omega.hpp>
 #include<yade/core/Timing.hpp>
-#include<yade/lib-base/Logging.hpp>
+#include<yade/lib/base/Logging.hpp>
 #include<stdexcept>
 
 #include<boost/foreach.hpp>

core/FileGenerator.cpp

@@ -7,8 +7,8 @@
 #include<boost/date_time/posix_time/posix_time.hpp>
 
 #include<yade/core/Omega.hpp>
-#include<yade/lib-pyutil/gil.hpp>
-#include<yade/lib-serialization/ObjectIO.hpp>
+#include<yade/lib/pyutil/gil.hpp>
+#include<yade/lib/serialization/ObjectIO.hpp>
 
 #include"FileGenerator.hpp"
 

core/FileGenerator.hpp

@@ -8,8 +8,8 @@
 
 #pragma once
 
-#include<yade/lib-serialization/Serializable.hpp>
-#include<yade/lib-base/Logging.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
+#include<yade/lib/base/Logging.hpp>
 
 #include "Scene.hpp"
 #include "ThreadWorker.hpp"

core/ForceContainer.hpp

@@ -3,7 +3,7 @@
 
 #include<string.h>
 #include<vector>
-#include<yade/lib-base/Math.hpp>
+#include<yade/lib/base/Math.hpp>
 // for Body::id_t
 #include<yade/core/Body.hpp>
 

core/FrontEnd.hpp

@@ -10,7 +10,7 @@
 
 #include "Omega.hpp"
 
-#include<yade/lib-factory/Factorable.hpp>
+#include<yade/lib/factory/Factorable.hpp>
 
 class FrontEnd : public Factorable
 {	

core/Functor.hpp

@@ -10,8 +10,8 @@
 
 #pragma once
 
-#include<yade/lib-serialization/Serializable.hpp>
-#include<yade/lib-multimethods/FunctorWrapper.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
+#include<yade/lib/multimethods/FunctorWrapper.hpp>
 
 class TimingDeltas;
 class Scene;

core/GroupRelationData.hpp

@@ -15,7 +15,7 @@
 #define YADE_GROUP_RELATION_DATA
 
 
-#include<yade/lib-serialization/Serializable.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
 
 #include <iostream>
 #include <sstream>

core/IGeom.hpp

@@ -8,9 +8,9 @@
 
 #pragma once
 
-#include<yade/lib-base/Math.hpp>
-#include<yade/lib-serialization/Serializable.hpp>
-#include<yade/lib-multimethods/Indexable.hpp>
+#include<yade/lib/base/Math.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
+#include<yade/lib/multimethods/Indexable.hpp>
 #include<yade/core/Dispatcher.hpp>
 
 class IGeom : public Serializable, public Indexable

core/IPhys.hpp

@@ -8,9 +8,9 @@
 
 #pragma once
 
-#include<yade/lib-base/Math.hpp>
-#include<yade/lib-serialization/Serializable.hpp>
-#include<yade/lib-multimethods/Indexable.hpp>
+#include<yade/lib/base/Math.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
+#include<yade/lib/multimethods/Indexable.hpp>
 #include<yade/core/Dispatcher.hpp>
 
 class IPhys : public Serializable, public Indexable

core/Interaction.hpp

@@ -2,7 +2,7 @@
 //  Copyright (C) 2004 by Janek Kozicki <cosurgi@berlios.de>
 //
 #pragma once
-#include<yade/lib-serialization/Serializable.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
 // keep those two here, template instantiation & boost::python gets broken otherwise, e.g. https://bugs.launchpad.net/bugs/618766
 #include<yade/core/IGeom.hpp> 
 #include<yade/core/IPhys.hpp>

core/InteractionContainer.hpp

@@ -4,7 +4,7 @@
 
 #pragma once
 
-#include<yade/lib-serialization/Serializable.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
 #include<boost/thread/mutex.hpp>
 
 #ifdef YADE_OPENMP

core/Material.hpp

 // 2009 © Václav Šmilauer <eudoxos@arcig.cz>
 #pragma once
 #include<string>
-#include<yade/lib-serialization/Serializable.hpp>
-#include<yade/lib-multimethods/Indexable.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
+#include<yade/lib/multimethods/Indexable.hpp>
 #include<yade/core/State.hpp>
 #include<yade/core/Dispatcher.hpp>
 

core/Omega.cpp

@@ -12,9 +12,9 @@
 #include"Scene.hpp"
 #include"TimeStepper.hpp"
 #include"ThreadRunner.hpp"
-#include<yade/lib-base/Math.hpp>
-#include<yade/lib-multimethods/FunctorWrapper.hpp>
-#include<yade/lib-multimethods/Indexable.hpp>
+#include<yade/lib/base/Math.hpp>
+#include<yade/lib/multimethods/FunctorWrapper.hpp>
+#include<yade/lib/multimethods/Indexable.hpp>
 #include<cstdlib>
 #include<boost/filesystem/operations.hpp>
 #include<boost/filesystem/convenience.hpp>
@@ -24,7 +24,7 @@
 #include<boost/version.hpp>
 #include<boost/python.hpp>
 
-#include<yade/lib-serialization/ObjectIO.hpp>
+#include<yade/lib/serialization/ObjectIO.hpp>
 
 
 #include<cxxabi.h>

core/Omega.hpp

@@ -33,10 +33,10 @@
 #include <boost/thread/thread.hpp>
 #include <iostream>
 
-#include<yade/lib-base/Math.hpp>
-#include<yade/lib-factory/ClassFactory.hpp>
+#include<yade/lib/base/Math.hpp>
+#include<yade/lib/factory/ClassFactory.hpp>
 
-#include<yade/lib-base/Singleton.hpp>
+#include<yade/lib/base/Singleton.hpp>
 
 #include "SimulationFlow.hpp"
 

core/Scene.cpp

@@ -13,7 +13,7 @@
 #include<yade/core/Timing.hpp>
 #include<yade/core/TimeStepper.hpp>
 
-#include<yade/lib-base/Math.hpp>
+#include<yade/lib/base/Math.hpp>
 #include<boost/foreach.hpp>
 #include<boost/date_time/posix_time/posix_time.hpp>
 #include<boost/algorithm/string.hpp>

core/Shape.hpp

@@ -8,8 +8,8 @@
 
 #pragma once
 
-#include<yade/lib-serialization/Serializable.hpp>
-#include<yade/lib-multimethods/Indexable.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
+#include<yade/lib/multimethods/Indexable.hpp>
 #include<yade/core/Dispatcher.hpp>
 
 #define BV_FUNCTOR_CACHE

core/State.hpp

 // 2009 © Václav Šmilauer <eudoxos@arcig.cz>
 #pragma once
-#include<yade/lib-serialization/Serializable.hpp>
-#include<yade/lib-multimethods/Indexable.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
+#include<yade/lib/multimethods/Indexable.hpp>
 #include<yade/core/Dispatcher.hpp>
 /*! State (internal & spatial variables) of a body.
 

core/corePlugins.cpp

-#include<yade/lib-factory/ClassFactory.hpp>
+#include<yade/lib/factory/ClassFactory.hpp>
 // make core classes known to the class factory
 #include<yade/core/Body.hpp>
 #include<yade/core/BodyContainer.hpp>

core/main/pyboot.cpp

 #include<yade/core/Omega.hpp>
-#include<yade/lib-base/Logging.hpp>
+#include<yade/lib/base/Logging.hpp>
 
 #include<signal.h>
 #include<cstdlib>

gui/qt4/GLViewer.cpp

@@ -11,7 +11,7 @@
 #include"GLViewer.hpp"
 #include"OpenGLManager.hpp"
 
-#include<yade/lib-opengl/OpenGLWrapper.hpp>
+#include<yade/lib/opengl/OpenGLWrapper.hpp>
 #include<yade/core/Body.hpp>
 #include<yade/core/Scene.hpp>
 #include<yade/core/Interaction.hpp>
@@ -23,7 +23,7 @@
 #include<sstream>
 #include<iomanip>
 #include<boost/algorithm/string/case_conv.hpp>
-#include<yade/lib-serialization/ObjectIO.hpp>
+#include<yade/lib/serialization/ObjectIO.hpp>
 
 #include<QtGui/qevent.h>
 

gui/qt4/GLViewer.hpp

@@ -3,7 +3,7 @@
 #pragma once
 
 #include<yade/core/Omega.hpp>
-#include<yade/pkg-common/OpenGLRenderer.hpp>
+#include<yade/pkg/common/OpenGLRenderer.hpp>
 
 #include<QGLViewer/qglviewer.h>
 #include<QGLViewer/constraint.h>
@@ -11,7 +11,7 @@
 #include<boost/date_time/posix_time/posix_time.hpp>
 #include<set>
 
-#include<yade/pkg-common/PeriodicEngines.hpp>
+#include<yade/pkg/common/PeriodicEngines.hpp>
 
 /*****************************************************************************
 *********************************** SnapshotEngine ***************************

gui/qt4/_GLViewer.cpp

 #include"GLViewer.hpp"
 #include"OpenGLManager.hpp"
 #include<boost/python.hpp>
-#include<yade/pkg-common/OpenGLRenderer.hpp>
-#include<yade/lib-pyutil/doc_opts.hpp>
+#include<yade/pkg/common/OpenGLRenderer.hpp>
+#include<yade/lib/pyutil/doc_opts.hpp>
 
 #include<QApplication>
 #include<QCloseEvent>

lib/base/Math.cpp

-#include<yade/lib-base/Math.hpp>
+#include<yade/lib/base/Math.hpp>
 template<> const Real Math<Real>::EPSILON = DBL_EPSILON;
 template<> const Real Math<Real>::ZERO_TOLERANCE = 1e-20;
 template<> const Real Math<Real>::MAX_REAL = DBL_MAX;

lib/base/openmp-accu.hpp

@@ -2,7 +2,7 @@
 #pragma once 
 
 // for ZeroInitializer template
-#include<yade/lib-base/Math.hpp>
+#include<yade/lib/base/Math.hpp>
 
 #include<boost/serialization/split_free.hpp>
 #include<boost/lexical_cast.hpp>

lib/factory/ClassFactory.cpp

@@ -11,7 +11,7 @@
 #include "ClassFactory.hpp"
 
 #include<boost/algorithm/string/regex.hpp>
-#include<yade/lib-base/Logging.hpp>
+#include<yade/lib/base/Logging.hpp>
 
 CREATE_LOGGER(ClassFactory);
 SINGLETON_SELF(ClassFactory);

lib/factory/ClassFactory.hpp

@@ -26,7 +26,7 @@
 #endif
 
 
-#include<yade/lib-base/Singleton.hpp>
+#include<yade/lib/base/Singleton.hpp>
 
 #include<boost/preprocessor.hpp>
 

lib/factory/DynLibManager.hpp

@@ -16,7 +16,7 @@
 #include <map>
 #include <vector>
 
-#include<yade/lib-base/Logging.hpp>
+#include<yade/lib/base/Logging.hpp>
 
 using namespace std;
 

lib/multimethods/DynLibDispatcher.hpp

@@ -12,8 +12,8 @@
 #include "Indexable.hpp"
 
 
-#include<yade/lib-factory/ClassFactory.hpp>
-#include<yade/lib-serialization/Serializable.hpp>
+#include<yade/lib/factory/ClassFactory.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
 
 #include<loki/Functor.h>
 #include<loki/Typelist.h>

lib/multimethods/FunctorWrapper.hpp

@@ -9,7 +9,7 @@
 #pragma once
 
 
-#include<yade/lib-serialization/Serializable.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
 
 #include<loki/Typelist.h>
 #include<loki/Functor.h>

lib/opengl/GLUtils.hpp

@@ -4,7 +4,7 @@
 //
 #pragma once
 
-#include<yade/lib-opengl/OpenGLWrapper.hpp>
+#include<yade/lib/opengl/OpenGLWrapper.hpp>
 #include<boost/lexical_cast.hpp>
 #include<sstream>
 #include<iomanip>

lib/opengl/OpenGLWrapper.hpp

@@ -12,7 +12,7 @@
 #error "This build doesn't support openGL. Therefore, this header must not be used."
 #endif
 
-#include<yade/lib-base/Math.hpp>
+#include<yade/lib/base/Math.hpp>
 
 
 // disable temporarily

lib/pyutil/gil.cpp

-#include<yade/lib-pyutil/gil.hpp>
+#include<yade/lib/pyutil/gil.hpp>
 void pyRunString(const std::string& cmd){
 	gilLock lock; PyRun_SimpleString(cmd.c_str());
 };

lib/serialization/Serializable.hpp

@@ -30,11 +30,11 @@
 #include<string>
 #include<vector>
 #include<iostream>
-#include<yade/lib-factory/Factorable.hpp>
-#include<yade/lib-pyutil/raw_constructor.hpp>
-#include<yade/lib-pyutil/doc_opts.hpp>
+#include<yade/lib/factory/Factorable.hpp>
+#include<yade/lib/pyutil/raw_constructor.hpp>
+#include<yade/lib/pyutil/doc_opts.hpp>
 
-#include<yade/lib-base/Math.hpp>
+#include<yade/lib/base/Math.hpp>
 
 using namespace boost;
 using namespace std;

lib/smoothing/WeightedAverage2d.hpp

@@ -30,7 +30,7 @@
 using namespace std;
 using namespace boost;
 
-#include<yade/lib-base/Math.hpp>
+#include<yade/lib/base/Math.hpp>
 
 
 template<typename T>

pkg/common/Bo1_Box_Aabb.cpp

@@ -7,8 +7,8 @@
 *************************************************************************/
  
 #include "Bo1_Box_Aabb.hpp"
-#include<yade/pkg-common/Box.hpp>
-#include<yade/pkg-common/Aabb.hpp>
+#include<yade/pkg/common/Box.hpp>
+#include<yade/pkg/common/Aabb.hpp>
 
 
 void Bo1_Box_Aabb::go(	const shared_ptr<Shape>& cm,

pkg/common/Bo1_Box_Aabb.hpp

@@ -9,7 +9,7 @@
 #pragma once
 
 
-#include<yade/pkg-common/Dispatching.hpp>
+#include<yade/pkg/common/Dispatching.hpp>
 
 
 class Bo1_Box_Aabb : public BoundFunctor{

pkg/common/Bo1_Sphere_Aabb.cpp

@@ -7,8 +7,8 @@
 *************************************************************************/
  
 #include "Bo1_Sphere_Aabb.hpp"
-#include<yade/pkg-common/Sphere.hpp>
-#include<yade/pkg-common/Aabb.hpp>
+#include<yade/pkg/common/Sphere.hpp>
+#include<yade/pkg/common/Aabb.hpp>
 
 void Bo1_Sphere_Aabb::go(const shared_ptr<Shape>& cm, shared_ptr<Bound>& bv, const Se3r& se3, const Body* b){
 	Sphere* sphere = static_cast<Sphere*>(cm.get());

pkg/common/Bo1_Sphere_Aabb.hpp

@@ -8,7 +8,7 @@
  
 #pragma once
 
-#include<yade/pkg-common/Dispatching.hpp>
+#include<yade/pkg/common/Dispatching.hpp>
 
 class Bo1_Sphere_Aabb : public BoundFunctor
 {

pkg/common/BoundaryController.cpp

-#include<yade/pkg-common/BoundaryController.hpp>
+#include<yade/pkg/common/BoundaryController.hpp>
 #include<stdexcept>
 void BoundaryController::action(){ throw std::runtime_error("BoundaryController must not be used in simulations directly (BoundaryController::action called)."); }
 YADE_PLUGIN((BoundaryController));

pkg/common/Callbacks.cpp

-#include<yade/pkg-common/Callbacks.hpp>
+#include<yade/pkg/common/Callbacks.hpp>
 BodyCallback::~BodyCallback(){};
 IntrCallback::~IntrCallback(){};
 YADE_PLUGIN((IntrCallback)(BodyCallback));

pkg/common/Callbacks.hpp

@@ -2,7 +2,7 @@
 #pragma once 
 
 #include<stdexcept>
-#include<yade/lib-serialization/Serializable.hpp>
+#include<yade/lib/serialization/Serializable.hpp>
 
 class Interaction;
 class Body;

pkg/common/Collider.cpp

@@ -6,7 +6,7 @@
 *  GNU General Public License v2 or later. See file LICENSE for details. *
 *************************************************************************/
 
-#include<yade/pkg-common/Collider.hpp>
+#include<yade/pkg/common/Collider.hpp>
 
 YADE_PLUGIN((Collider));
 

pkg/common/Collider.hpp

@@ -12,7 +12,7 @@
 #include<yade/core/Interaction.hpp>
 #include<yade/core/GlobalEngine.hpp>
 
-#include<yade/pkg-common/Dispatching.hpp>
+#include<yade/pkg/common/Dispatching.hpp>
 
 class Collider: public GlobalEngine {
 	public:

pkg/common/Cylinder.cpp

 #include "Cylinder.hpp"
-#include<yade/pkg-common/Sphere.hpp>
+#include<yade/pkg/common/Sphere.hpp>
 #ifdef YADE_OPENGL
-	#include<yade/lib-opengl/OpenGLWrapper.hpp>
+	#include<yade/lib/opengl/OpenGLWrapper.hpp>
 #endif
-#include<yade/pkg-common/Aabb.hpp>
+#include<yade/pkg/common/Aabb.hpp>
 
 Cylinder::~Cylinder(){}
 ChainedCylinder::~ChainedCylinder(){}

pkg/common/Cylinder.hpp

@@ -2,12 +2,12 @@
 #include<yade/core/Shape.hpp>
 #include<yade/core/State.hpp>
 #include<yade/core/Body.hpp>