Code tagging and some usefull methods for debugging and the begining of a true accumulator for time series (for any sampling rates).

Overall all include statements within in the library have been replaced by angle brackets, the default install path for the include file is $CMAKE_INSTALL_DIR/include/meteoio, the meteoio libraries (static and shared) will be installed in $CMAKE_INSTALL_DIR/lib per default.

The plugins will be installed in the subdirectory $CMAKE_INSTALL_DIR/lib/meteoio/plugins

The types TYPE_DOUBLE2D, TYPE_DOUBLE3D and TYPE_INT2D have been removed (and replaced by another, internal name because POPC does not accept templates and needs an alias for them). A variable that was used only within two private methods with a local scope in IOHandler has been removed from the class scope and is now a local variable.

LegacyIO has now finally been removed!! (Hurrah! Freedom!). This version has also a few hacks so that it successfully compiles with POPC (there were still issues with the namespaces)

Then, the remaining namespace issues with doxygen have been fixed, by enclosing the full class implementation in the namespace (as seen for the libstdc++). This removes all these irritating issues. But the popc version has been broken by the change (as seen in LegacyIO).

The POPC compilation issue has been fixed (work around a POPC bug). These work arounds have been tagged as "HACK for POPC" in DEMObject, Date, Grid2/3DObject, IOHandler.ph, LegacyIO.ph and marshall_meteoio.cc.

The SNIO plugin that was forgotten at the last commit is now here and has been improved so that it correctly formats its output (it does not read yet).

Cosmetic fix in Date.h and some namespace additions for the POPC version (.ph and marshalling). But the marshalling is not working yet...

The plugin's interface (IOInterface) has been slightly modified: readSpecialPoints now returns a vector of Coords. This means that a plugin can provide coordinates as (lat,long) or (easting, northing) or (grid_i, grid_j). All the plugins have been modified accordingly and POINTS and POINTSArray have been removed from Array.h

The new Coords object is now used by all grids (Grid2DObject, Grid3DObject, DEMObject) as well as by all plugins (but checking proper operation was not possible for GSNIO because of missing libraries on my system...). The documentation has been updated as well as the code examples. A few extra methods have been added when usage has shown the need/convenience of having them (specially for standardazing some processing called by the plugins). A few small bugs have been fixed (possibility of not updating or improperly updating the coordinates in some rare cases).

The proper marshalling for Grid3DObject has been implemented (it was more or less a dummy method until now). One bug has been fixed for Proj4 support. The code of most of the plugins has been cleaned up in order to get rid of the few remaining "using namespace" in header files. 

The class Stationdata now properly uses the new Coords class. All usual dependencies have been fixed (A3DIO.cc) but not (yet) the optional plugins. The Coords class has been modified so that it computes the matching coordinates as soon as possible instead of the previous implementation that was delaying it as much as possible (thus making "const Coords..." impossible).

The includes have been cleaned up (compilation was failing because of multiple "using namespace" in header files) and all "using namespace" have been removed from header files (please don't put any of these back!!). The doxygen comments has been updated.

The MapProj class has been renamed in Coords. It now contains the coordinates (lat,long) and (xcoord, ycoord) and should therefore be used as a storage and conversion class. The necessary changes have been made to the rest of the code so it uses this class, but it still does NOT use it as a storage of coordinates (which will have to be done in the future). This addressed partially issue 35.

The Special_PTS and CSpecialPointsArray structures have been renamed in "POINT" and "POINTSArray" (there was no reason to call them "special points"). 

A few new methods have been added to DEMObject: getPointsBetween that returns a vector containing the indices of all points located on the line between two points (given by their real world (x,y) coordinates), horizontalDistance that returns the horizontal distance between two points and terrainDistance that returns the distance between two point accros the terrain as described by the DEM (ie: going up and down the terrain).

The parallelization was lagging behind, so this has been fixed: One internal variable was not serialized in DEMObject, there was no serialization at all in Meteo2DInterpolator and some marshalling methods had to be written (in marshall_meteoio). The serialization of Meteo2DInterpolator should be tested however!

The marshalling code has been cleaned up and some missing "std::" added in FilterAlgorithms (doxygen was complaining).

The successfull call of MeteoIO from Java has been implemented by Cyril Perot but needed a few adjustments in MeteoIO. This commit makes the said adjustments: a few more "#ifdef _POPC_", a missing ConfgReader.addKey(key, section, value) and some previously private members of Meteo2DInterpolator now exposed. 

The plugin unloading sections have been protected by ifndef _METEOIO_JNI because the current implementation of such Java integration uses JNI and does its own plugin loading/unloading.

A new slope computation algorithm has bee added: CARD It computes the slope using Corripio and then discretizes the azimuth along 8 cardinal directions and the slope by degrees. This should be all that GEOtop needs for its drainage direction (then simply calling a dem.update("CARDINAL")).

The copyright notices have been put in place in all files (headers and cc) with proper attribution of copyright.

The documentation has been improved, specially fixing issue 22. Warning messages of doxygen have been fixed. An example subdirectory has been created in /doc and contains (currently) 2 examples of code using MeteoIO.

	* Changed method call to readDEM so that polymorphism is not used anymore.

Modif for parallel version. Dynamic libraries are now compiled separately to avoid a huge bug due to differences in some headers files.

The popc version now works (thanks Laurent for your help!!). A small warning has been removed (base class instantiation).

The autotools configuration has been slightly improved (checking for pkg-config only if needed).

The meteoio_demo demo program has been fixed so that it works with the newest version of the library.

Another round of fixes for the popc version. A few tricks have been implemented (using typedefs to make popc's parser accept some inputs, making ConfigReader more flexible so it would be easier to implement some possibily necessary tricks later on, etc).

A warning (unused parameter) have been removed from A3DIO

Some more fixes for the popc version... Implementing missing marshaling functions, and a few tricks to make it work with popc...

A new file has been added, IOPlugin.h, so that this definition is common to popc and regular c++.

Trying to make the popc version work again... by adjusting the popc code to the latest changes. It does not work yet.

Ok, this is the correct implementation of what I tried to do in the previous commit... Now, the Meteo2DInterpolator can take either Array2D<double> or Grid2DObjects as tables to fill. The overloading of the Write2DGrid has therefore been suppressed: since Grid2DObjects are geography-friendly, they should be used in our applications instead of Array2D (that should be reserved for internal implementation of objects).

So, this is mostly reverting to the code before the last commit, with a few extra lines of code to do the magic...

* renamed functions in Array.h
	SetSize() to resize()
	RemoveAll() to clear()
	RemoveAt() to removeAt()
	InsertAt() to insertAt()
* had to propagate these changes into all files that use class Array

* Changed nomenclature in CArray2D<T> to reflect STL conventions:
	GetSize() renamed to size()
	Create() renamed to resize()
	Destroy() renamed to clear()

A small warning has been fixed in the Inverse Vincenty calculation (possibly uninitialized value, but extremely remote possibility).

The warnings for the marshalling functions have been fixed. Please check that it makes sense!