Rename generated files and classes

[cdcarson]

While writing the docs I realized that the filenames are not really friendly.

• It's not obvious that schema-definition.d.ts is where you edit the schema, plus it kinda conflicts with generated/schema-definition.js
• The *-db names are not adequately grouped
• There are too many files on this level. The only file that really needs to be at the top of generated if models.d.ts. (Since it's the only one that deals with type imports.
• Everything should be exported from index.js. There's a potential gotcha -- do we then need to have more d.ts files? Need to check that.
• While we're at it, change the class names to be ApplicationDatabase, ModelsDatabase and TransactionDatabase, with matching filenames.

So, new structure:

• [outputPath]
  • model-types.d.ts
  • generated
    • index.js
    • models.d.ts
    • database-classes
      • application-database.js
      • models-database.js
      • transaction-database.js
    • schema
      • schema-definition.js
      • schema-cast-map.js
    • search
      • search-indexes.js