Fix/manual

Just fixed one line describing how to clone git repository using SSH key: URL was outdated.

See merge request !406

Switch Timing classes to use Timer

This MR switches the Timer classes from using `gettimeofday` to `Timer` inside `LibUtilities`.

See merge request !402

Fix/ape tests

this fixes the APE-related tests

See merge request !404

This reverts commit 44cc095e.

fix typo in APEUpwind Riemann Solverthat broke 3D problems with baseflow

See merge request !399

Fix/arnoldi parallel

See merge request !384

Fix/singular parallel

Fixes a unique choice of vertex to pin when enumerating a singular system. The maximum vertex ID across all boundaries is selected to ensure consistency in the parallel implementation.

See merge request !398

Conflicts:
	solvers/IncNavierStokesSolver/Tests/bfs_tg.tst

Fix/extract surface3 dcfs

See merge request !394

Conflicts:
	solvers/IncNavierStokesSolver/Tests/bfs_tg.tst

Updated test values due to change in vertex in singular systems.

Fix/threshold max filter variable

Update this filter to support thresholding on any variable rather than hard-coded to the first variable. Also added a default filename and updated the doc.

See merge request !395

Feature/ape improvements

Various improvements to the APESolver.

Note that this also changes the copyright statement of the files i contributed to. As i am not part of any of the organisations mentioned in the previous statement, i cant publish anything under their names. Therefore, i added myself to the copyright holders for the specific files. This is how most open source projects i have contributed to handle this. Please get in touch with me if you are not OK with that so we can figure something out.

See merge request !379

Fix/cmake warnings

This MR adds some helpful warnings when some boost libraries are not found.

See merge request !392

Restructure energy filter to support CFS

This MR:

- Restructures the energy filter into an abstract class so that only specific solvers are supported (i.e. those that support the concept of kinetic energy/enstrophy)
- Adds implementations for the incompressible and compressible solvers
- Adds appropriate documentation and tidies existing filter documentation
- Removes uses of `\checkmark` in the docs in deference to `\cmark` which is already used elsewhere and has a corresponding `\xmark`.

See merge request !388

Fix/field convert interppoints

See merge request !387

Various fixes for Windows 7

This MR fixes a bunch of stuff for Windows 7 with Visual Studio 2013.

See merge request !391