Merge tools/ and src/ and reorganize pipeline components

[khughitt]

Based on our current architecture, it is no longer necessary to have a separate tools and src folders.

A better approach might be to put everything in src and have the structure mirror that of the data, e.g.:

• data_processing/
  • raw/
  • filtered/
  • combined/
  • final/
• visualization/
• prediction/

Or something to that effect...

[khughitt]

@daler Since you have already done a lot of the organizational work for the pipeline, do you want to handle this issue as well?