Force InputFld to update fielddef

This forces InputFld to update fielddef after loading the expansions, instead of only doing this when range is specified. This is necessary because the number of partitions from the original file might not be the same as the number of processes being used in FieldConvert, causing the fielddef obtained from Import to contain extra elements.

For example, when converting a serial fld to a parallel format using
```
mpirun -np 8 FieldConvert file.xml file_serial.fld file_par.fld
```
the current implementation causes all 8 partition files from file_par.fld to contain the whole field.

See merge request !611

Fix for assembly map array initialisation bug.

This MR fixes a bug in the CG assembly map which incorrectly initialises the local coefficient array if performing an in-place assembly.

See merge request !598

Initial instructions on how to build the documentation and tutorials.

This MR expands the user guide to describe how to build the user guide, doxygen and tutorials.

See merge request !596

Fix for clang 7.3 in compiling metis

This MR fixes an issue in compiling METIS on Clang 7.3, which ships with the latest OS X Xcode.

See merge request !603

Fix some LaTeX errors in doxygen.

This MR fixes some compile errors in the doxygen documentation which were not picked up on the release of 4.3.

See merge request !586

Fix eps image path for some versions of epstopdf.

This MR updates an EPS image in the developer guide to use the full path to avoid a bug in some versions of epstopdf.

See merge request !593

Fix namespace pollution

This MR removes occurrences `using namespace` in header files. This causes problems when using the library with external tools as it conflicts with other libraries (e.g. VTK).

See merge request !601

fix/meshing_TPURL

Small fix to third party urls as pointed out by spencer for the meshing side of things.
Turns out using the ae-nektar public html doesnt agree with some machines.

See merge request !606

Fix bug in DriverModifiedArnoldi

This fixes a bug in ModifiedArnoldi, which may cause the solver to exit with
```
Fatal   : Level 0 assertion violation
Unrecognised value.
```
as recently reported in nektar-users.

The problem happens because the iteration could be marked as converged when the number of vectors available is lower than `nvec`.

See merge request !608

Fix bug in Homogeneous1DTrans

This fixes a small bug in `ExpListHomogeneous1D::Homogeneous1DTrans`.

I think the particular case where this was wrong is not used anywhere, so it is very likely that nothing will change.

See merge request !599

Updated to extract directory of libccmio.a

Updated the ThirdPartyCCM.cmake file to add in Link directory and use the get_Filename_component to obtain the directory path if the library is found. This therefore allows the libccmio.a to be correctly linked from a third party location where as previous it was only compiling if the .a files were copied to the dist/lib directory. 

See merge request !600