Main bulk of stuff needed to update strain rate in momentum diagnostics. I've tested that the code compiles and runs, but need to tidy the code and verify that it also work in sync with the viscosity, as planned.
Minor comment clarification.
Some tidying up following my chat to Dr. Wilson. Need to test this next in a non-linear run, to verify that things are being updates as I think they are.
Merge trunk into branch.
Merge in trunk.
Merge in trunk.
Merge in trunk.
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and configure) are out of date.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.
Add P0-support to project_vtu and fix output ordering

project_vtu now also projects cell-based (P0) fields from the input vtu.
If the vtu is piecewise linear and continuous, maintain the node ordering
of the donor triangle mesh in the output vtu. This is useful if the output
vtu is used for further analysis with for instance vtudiff.
Add gmsh support to project_vtu.

Use .msh filenames directly on the commandline (identified by .msh extension)
instead of triangle file basename.
Fix galerkin projection of CG tensor fields.

Option path was not passed on in extract_scalar_field_from_tensor.
This should fix both galerkin_projection in fluidity and tensor fields
in project_vtu.
Make project_vtu work for the case of having both cell-based and point-based fields in one vtu.
Add a test case for project_vtu.
Update usage message and manual for project_vtu.

This is to reflect it now handles gmsh meshes.