Clean up the core/base model stuff

[ld-archer]

The core model replaced all the baseline stuff a long time ago, but there are still remnants of the base model in the code (e.g. in the Makefile, covariate_definitions files amongst others). Just for my sanity I need to clean all this up, and remove any mentions of base and core. Core will become the new normal, and base will be removed entirely as we haven't run it in forever.

This would be a good opportunity to add some of the variables back that were not included in the core model, such as lnly, hipe, psyche, parkine, srh, mstat etc.

Also can include some of the variables that have been included in the harmonised ELSA data from wave 9, which I already opened some issues for but got buried somewhere in the list (osteoporosis, heart attack and related vars, etc.).

[ld-archer]

Mentioning #71 & #72 to be completed alongside this.

[ld-archer]

Best way to find everything that needs to be changed is a big dirty grep for 'core'.

• [ ] Rename files & their mentions
  • [ ] covariate_definitions
  • [ ] debug documents (FEM_R)
  • [ ] detailed_appends
  • [ ] crossvalidation (T-tests)
  • [ ] simulation
  • [ ] summary_output_gen
  • [ ] estimates (save_est_cpp)
  • [ ] Transitions (suffix changes) (ELSA_init_transitions)
• [ ] Makefile