Rename DocumentDiff to DiffMessage

[cycraig]

Description of change

Rename DocumentDiff to DiffMessage which is more accurate and distinguishes it from DiffDocument.

Refactor the identity-iota project layout slightly by moving did/did and did/doc into top-level did and document modules respectively.

Fixes minor linting and formatting issues.

This PR is to reduce the number of changes in anticipation of the metadata refactor PR for #486.

Type of change

• Bug fix (a non-breaking change which fixes an issue)
• Enhancement (a non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation Fix

How the change has been tested

Tests and Wasm Nodejs examples pass locally.

Change checklist

Add an x to the boxes that are relevant to your changes.

• I have followed the contribution guidelines for this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

[PhilippGackstatter]

Looks good!