Update waves

Created by: acrovato

Context

This pull request brings the last developments from the flow module as well as some upgrade to waves.

Major changes in flow

• flow is now able to compute 3D flows
• The Jacobian (tangent) matrix for the Netwton method is now fully analytical
• The adjacent elements identification is now based on ```std::unordered_set````

Major changes in waves

• tbox and fwk are now included in a namespace
• waves is now fully included in a namespace
• All elements now have a private memory (Mem) which can be publicly accessed
• All elements now have a cache including Gauss points (Gauss) which can be publicly accessed
• MshDeformation now uses a linear elasticity solver
• MshCrack class implemented (creates duplicate internal boundaries in meshes)

Test

The ctest battery has been run on gaston, 100% tests passed under 110s.

Future work

• Use automated indentation rules for the whole code
• Move methods using VTK outside of MshData
• Clean tbox (mainly MshData, Tri3, Tera4 and Hex8)

Doxyfile.in

@@ -781,8 +781,14 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = @PROJECT_SOURCE_DIR@/exe \
-                         @PROJECT_SOURCE_DIR@/vtl \
+INPUT                  = @PROJECT_SOURCE_DIR@/fdtd \
+                         @PROJECT_SOURCE_DIR@/flow \
+                         @PROJECT_SOURCE_DIR@/fwk \
+                         @PROJECT_SOURCE_DIR@/heat \
+                         @PROJECT_SOURCE_DIR@/mirrors \
+                         @PROJECT_SOURCE_DIR@/sph \
+                         @PROJECT_SOURCE_DIR@/tbox \
+                         @PROJECT_SOURCE_DIR@/waves \
                          @PROJECT_SOURCE_DIR@/doxygen/pages