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fix multiple cut

meshPartitionOptions::partitionByExtrusion assigns all extruded elements to the same partition as the source element

* issue error for zero volume elements in FEA export
* reset element number between 2D/3D in FEA export

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free to improve...)

pretty please do not just "throw;" when you don't know what to do

+ constify MElement some more

single file IO)

TWO BIG WARNINGS:

1) The MSH file version has been bumped from 2.1 to 2.2 because if a
mesh has partitions, the meaning of the tags has changed. Tag 3 used
to be the partition id; now tag 3 contains the number of partitions
(self+ghosts, if necessary), and the next tag(s) contain(s) the
partition(s) id(s). Ghost partitions have < 0 ids. The (new) default
behaviour is to not save partition numbers by default if there are
none.

2) There is an issue for split-file IO (one file per partition), due
to our on-the-fly renumbering of the elements (we would need a global
pass+store an inverse multimap to have the correct ghost element
numbers in a split-file scheme). The problem comes from the multiple
physicals -> multiple copies of the same MElement* in the MSH file +
our refusal to store an index in MElement. We need to discuss this
before we implement split-file IO in parallel...



PS -- I also changed the way we write binary files. We now save blobs
of single elements. This is fully compatible with old versions, but
might slow down reading large files. I did not see any performance hit
on my machine, but this should be tested more thoroughly. Third party
codes can still write larger binary blobs if they want to, but Gmsh
itself now writes small blobs, which makes the writeMSH routine much
simpler.

- renamed functionSpace into polynomialBasis (functionSpace will be much higher level)

renamed most gmsh* classes

make MElement and MVertex thread-safe by guarding _globalNum

- moved GUI to FlGui + added experimental QGui to test Qt

- fixed most MSVC and gcc compiler warnings

- converted some remaining tabs to whitespace (that's why the patch is
  so large; please try to remember to indent with 2 spaces and not
  tabs when you commit stuff to CVS)

- merged modified patch from Konstantinos Poulios to allow saving
  physical/partition as element tags in mesh formats that don't
  support them natively

call setVolumePositive() in all ::writeXXX() functions

too hard to maintain

added createtopologyFromMSH to create Topology from list of triangles

* point not found should NOT be an error in the octree

HAVE_XXX defines.

This fixes three longstanding problems:

- the API was hard to use because some headers had HAVE_XXX ifdefs, so
  that cient codes had to know how the lib was compiled to compile
  themselves

- we had to do make clean after each ./configure, which erased too
  much (e.g. most of contrib)

- make depend could include unwanted stuff since it redefined FLAGS