Reorganise source code

[SamuelBrand1]

This DRAFT PR is aimed at addressing #125.

Goals

Reorganise the source code into sub-directories for

• utilities
• epi models
• latent models
• observation models
• inference methods

With only abstract types and back-stop dispatches on them in /src. Each implementation of a model indicated by type (e.g direct infection epi model) should have its own file.

Closes #125

EDIT: actually I think this is better scoped to just reorganise, but it will make it easier to sub-task docstrings so therefore contribute to #35 and other issues.

[SamuelBrand1]

Only effect on documentation is to change the doc template here.

Reason for change is that we are trying to (possibly loosely) follow SciML documentation convention here, and this change to template better matches their style.

[seabbs]

LGTM. I think we should go oone step further here and use submodules so will propose a PR for this.