refactor: re-organize charts in the viewer code and minor improvements

[donghaoren]

Cleanup and re-organize the code for the Embedding Atlas view to a better structure, including:

• Move charts to a dedicated folder.
• Move layouts to a dedicated folder.
• Move utility functions to a separate "utils" module and a "utils" folder, and separate them into files.

Let the root view own the chart states, instead of individual charts own their states and "sync" with the root view.