Re-organise folder structure

[TomBearpark]

We want to make the folder structure match the 5 steps outlined in the methods section of the paper.

[TomBearpark]

@aarode

[TomBearpark]

@aarode and I chatted and agreed this should be a task done later in the process by any RA, and also that there is some benefit to a fresh pair of eyes doing this since they will be able to do a final check that everything runs nicely.

This task has a few parts:

• Update the folder structure of the codes

• Make sure that all codes correctly reference each other (ie when one code calls another). This will require going through each code in the repo, and updating the paths that are referenced

• Going through all readmes in the repo, and updating github links as necessary

[aarode]

Updating the folder structure of the codes will involve making the folders correspond to the steps in the overall readme.

• Numbering of folders should start with 1 instead of 0.

• The SCC folder should be pulled outside of the "post-projection" folder and named to be step 5.