[Docs] Updating section Using an External Mesh

[castelletto1]

With PR #1992 we switched to using VTK external meshes for all input file examples provided in the repo. Ultimately, VTK meshes will become the default and we would ditch PAMELA (including stop linking to it). When the transition is completed, actions needed will be:

• updating section Using an External Mesh in the User Guide
• updating tutorial 2
• removing PAMELA tests located here