Clean up repo

[mfutey]

I wanted to make a suggestion that we clean up the repo as it is public facing and might be confusing for users. Removing, organizing or renaming files could help make it easier to navigate.

[dosumis]

AFAIK, the only unused files are

• general_schema.md
• anndata_file_general.md

We could organise the top level a bit better - pushing content down into subdirectories.

There is also a long-standing ticket on providing better automated documentation: https://github.com/cellannotation/cell-annotation-schema/issues/48 . Having this at the top level would make it easier for users to understand. We can also link to some notebooks on CAS-Tools now that code for working between CAS and AnnData is nearly ready.

[evanbiederstedt]

We could organise the top level a bit better - pushing content down into subdirectories.

This would be nice

[hkir-dev]

Basic clean up completed:

• Folder structure improved
• Markup files moved to https://github.com/cellannotation/cell-annotation-schema/tree/main/docs folder