Relaxing tolerances slightly after consultation with David, in response to a
slight change in the test result on Ubuntu Trusty. Note that this may be a
change from gmsh - the test passed fine on 2.5/2.6, failed intermittently with
2.8.3, and fails consistently with 2.8.4.
BUG FIX: p%mesh should be p_theta%mesh.  This was only a problem when using the viscous fs while testing the divergence using cv.  This is tested but apparently not in parallel when you can't get away with using the wrong global node numbering.
Obvious copy and paste bug.

I think this may fix the intel flredecomp bug for the cx1 tests, as I get the following 
backtrace (only for non-debugging build):
gdb) bt
#0  0x0000000000659f0b in state_module_mp_aliased_scalar_ ()
#1  0x000000000050950c in checkpoint_mp_checkpoint_fields_ ()
#2  0x00000000005072cb in checkpoint_mp_checkpoint_state_ ()
#3  0x0000000000507116 in checkpoint_mp_checkpoint_simulation_ ()
#4  0x0000000000503c5e in flredecomp ()
#5  0x000000000050419b in main ()
As per discussion at:
http://lists.gnu.org/archive/html/bug-libtool/2012-03/msg00004.html

libtool generation breaks for wrapped gfortran >=4.6 in some cases. This is
a different fix to the one proposed in the link above but seems to work. I'm
applying this directly to Fluidity to get a quick fix for Archer but will also
propose it as a fix to spud.
The current hack for building on ARCHER only works on the master node; 
rather than extending the hack to work on the slave nodes (which have far
more generic hostnames) this changes the behaviour to require a variable
to be set by the user, ARCHER.
Mea culpa; correcting an autoconf syntax error in my previous commit.
Expanding variables in the test XML command section as in some cases the 
variable assignment failed leading to a test failure.
Use git (rather than bzr) commands to determine the branch name and revision number (in the form of a SHA-1 commit hash).
Use a colon instead of a dot to separate the branch name and SHA-1 hash.
Git-migration fixes

Deleting files that crept in during git-migration
Add AM_MAINTAINER_MODE([enable]) to spatialindex' configure.ac

This adds the options --enable/--disable-maintainer-mode to configure.
With --disable spatialindex' Makefiles will no longer try to reconfigure/
autoreconf/automake when it thinks intermediate files (like Makefile.in
and configure) are out of date. This prevents random regeneration of these
when timestamps are messed up by switching branches in git.

This commit probably undoes the following two previous commits:

skramer@skramer-laptop:~/git/fluidity$ git log -n2 spatialindex-1.8.0
commit 51948d2533b43952f8916c58df2f6ca71324b8cd
Author: Gerard Gorman <g.gorman@imperial.ac.uk>
Date:   Thu Jan 31 17:43:38 2013 +0000

    Removed spaces from PACAKGE_STRING in spatialindex as it causes the intel compiler to choke.

commit 8a8fe4cad7dd9ac29c6f6208b17fbbbc466c8421
Author: Gerard Gorman <g.gorman@imperial.ac.uk>
Date:   Tue Jan 29 11:07:31 2013 +0000

    Stop spatialindex from executing make test; this fixes compilation on Cray and other systems where we compile statically.

If we hit these issues again I'd rather look for a proper fix instead
of creating an inconsistent set of build files (these were fixes
were done in configure instead of configure.ac).
Following Stephan's fixes to spatialindex to enable
AM_MAINTAINER_MODE, the regeneration of configure
introduced a perfectly valid space in PACKAGE_STRING
which a bug in the Intel compiler results in a misparse
of, as per commit 51948d2533b43952f8916c58df2f6ca71324b8cd
from Gerard Gorman. This change reinstates Gerard's edit
of configure to fix Intel.

Since this is entirely an Intel bug and valid behaviour
on the part of autoconf, it was considered reasonable to
continue with the hack of editing configure even though
this does result in an inconsisten set of configure* files
in the spatialindex directory.
Merge pull request #1 from FluidityProject/git-version-info

Use git (rather than bzr) commands to determine the branch name and revision number.
General manual overhaul in the system sections, including:

* Updates to the Ubuntu install procedures
* Introduction of sections for installing on other Linux variants
* General overhaul of the build-from-source method including a new
    section for gmsh.
* Updated recommended petsc configuration options.
* Updates for the migration from bzr+launchpad to git+github
Merge pull request #4 from FluidityProject/fluidity-core/manualoverhaul201406

General manual overhaul in the system sections, including:
Put all petsc-legacy redefinitions in one header file.

This cleans up some repeated #if PETSC_VERSION stuff in the modules that use fortran.

Using petsc in any of our fortran modules is simplified to:

  module foo
    ...

  #ifdef HAVE_PETSC_MODULES
    use petsc
  #endif
    implicit none

  #include "petsc_legacy.h"
    ...
    contains
    ...

It also adds supports for building Fluidity linked with petsc-dev master. Since a few
people are now reliant on using petsc master I suggest we keep fluidity up-to-date with
it, i.e. as soon as an API change hits petsc master we push fixes for it to fluidity's
master (pull request if necessary), obviously without breaking support for previous release
versions of petsc.

Where API changes between petsc versions can be handled via #define macros, our
fortran code should read as if it is using the latest stable release (currently 3.4). When
linked against other petsc versions (including petsc-dev master) the macros,
defined in petsc_legacy.h, should then adapt this to match the API of that version.
Merge branch 'master' into fluidity-core/slope_limiter_boundary