Update GitHub code to ensure everything is working

[Jennit07]

The code on GitHub has not been updated for some time and there have been many changes making this now out of date. I have spent some time updating these changes and summarise below:

• New working directories - Outputs will go to /conf/dementia/A&I/Outputs which will allow us to have one consistent area which will be the master copy for releasing outputs.
• Updates to redundant code e.g. changes to functions in PHSmethods
• Lookups updated
• Redundant code removed (this could have further review of functions not needed and librarys not longer being used)
• MI report RMD files updated - this is a huge part of the changes with new improvements
• Publication RMD files updated - another huge part of the changes which include using the newest PHStemplates

Still to do but i will open issues for:

• check code for 04-create-excel-tables and get this working
• check code for 05-create-discovery-data and get this working
• review functions which may not be needed. e.g. i identified we no longer use the function create_report.R and removed this
• review librarys which are no longer being used and remove them

Overall, at this stage, i am happy the code is working and it will produce a working MI report and working Publication report and summary document. At this stage i would like to merge into master