Refactor all collection files to use same structure

[brylie]

Audit all project collection files and make sure they have similar structure:

• files are organized by component
  • /component/collection/index.js
  • /component/collection/schema.js
  • /component/collection/permissions.js
  • /component/collection/server/publications.js
• all collections index.js files contain only the collection definition and export
• colletions are imported correctly into any file where they are used