Remove depracated extended source stuff from configure.
Revert "Remove depracated extended source stuff from configure."

This reverts commit 9a85c0d7638f524e1f31e7853bc54aa34c63d41f.
Fix make install on archer.

This fixes make bin/burgers_equation which is a prerequisite for make
install.
Reorder modules and other hacks for intel 14 build.

Usual intel voodoo.
Fixes in gmsh reading with intel.

This should fix gmsh ascii reading for intel 11 as well (which was
previously broken/unsupported).

This is based on the new understanding (from Ben at NCI, Canberra)
 of the intel bug/feature where it disagrees with gcc about the file positioning. Basically after a

  read(unit, '(I1)', advance='no')

(Note there's nothing actually read since there are no variables on the right) - intel
decides that the advance='no' must apply to the next read(), whereas gcc simply applies
the default in the next read. Have now moved the intel specific code to directly after
the read following a call to ascii_formatting() call (which has the above read statement), instead
at a random place in the next subroutine along.
Adjust tolerances in a few tests to pass with intel.
Sort indentation to see if this placates intel.
Changes in configure to enable intel 14 build.

* Pass on optimisation flags to CFLAGS and CXXFLAGS. Previously these
  were only in FCFLAGS to hide bugs in libvtkfortran and libjudy.
* The bug in libvtkfortran consisted of a non-standard way of using a single char as the
last member of a struct to store a longer string by mallocing the struct
with the extra bytes needed. There seems a variety of ways to define
this last member: 1) char name 2) char name[1] 3) char name[]. 1) is
what was used here but is non-standard. According to various source 2)
is also non-standard but used in so many places that it "works in
practice on all known compilers". 3) is c99 standard that has not been
incorporated in c++ standard. 1) proved not to work with -O3 which is
probably why we never passed these optimisation flags on. Instead of
using these variable length struct hacks, we now simply allocate a
separate buffer to store the field name.
* Switch off aggr. loop optimisations in libjudy.  This is to workaround
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=755099 when passing on
optimisation flags to libjudy.
* Some other improvements in our fortran wrapper around libjudy (using
* bind(c)). Not strictly necessary but an improvement nonetheless.
* Add -ip -Xhost optimisation flags for intel build.
Merge branch 'Fluidity-intel-build'

This allows Fluidity to be build with intel 14. It also fixes gmsh ascii
reading with older intel versions (only intel 11.1 is currently known to
work).
Only pass -fno-aggressive-loop-optimisation to libjudy when using gcc >= 4.8.

Fixes #23. Option didn't exist before 4.8 - so presumably not necessary.
Makefiles changed after intel 14 fixes.

This is due to "use module" reorderings.
Make fluidity build with petsc master again.

MatGetVecs() has been renamed to MatCreateVecs().
Xhost --> xHost.
Xhost --> xHost in libadaptivity.
Merge branch 'master' into fluidity-core/lift-velocity-bcs