#2597 Implement the changes from Shameer's patch

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22745 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2597 Working on todos:  averaged phi method coverage and the [min, max] summary reporting.

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22748 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2585 Some changes to command line arguments, mainly so that GetNumberOfArgumentsForOption is allowed to return 0 if the flag does exist but has no arguments (needed so adding -citations flag prints to screen, and -citations foo.txt prints to disk).
Also couldn't help myself and moved the exceptions around a bit!

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22749 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2585 Citations!

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22750 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2597 Working on todos:  removed unnecessary loops which were needed to convert between V and phi.

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22752 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2565 Typo, and revert `TestCommandLineArgumentsParrotting`.

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22753 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2597 Tolerances for optimised build

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22754 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2597 Tolerances for optimised build

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22755 b5f69653-2bf5-0310-8201-b0dafb8e1405
Replace all PetscTruth (pre-PETSc 3.2) with PetscBool (PETSc 3.2 and newer).

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22756 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2565 I don't think Louie made a failing test!

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22759 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2565 Example use of the new -citations flag

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22760 b5f69653-2bf5-0310-8201-b0dafb8e1405
Fix parallel continuous. #2597 (There were more warnings in parallel)

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22763 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2565 Doxygen

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22768 b5f69653-2bf5-0310-8201-b0dafb8e1405
#2597 valid the new/old formulation in the graph metric

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22769 b5f69653-2bf5-0310-8201-b0dafb8e1405
Preparatory to #2332, fix output directory names in test.

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22770 b5f69653-2bf5-0310-8201-b0dafb8e1405
Tidy up doxygen (c.f. r22768, #2565).

git-svn-id: https://chaste.cs.ox.ac.uk/svn/chaste/trunk@22771 b5f69653-2bf5-0310-8201-b0dafb8e1405