build(all projects): gradle updates, now works with vscode

[holmeso]

Description

Small changes to gradle build files that allows users to use vscode. Use implementation rather that api in most projects when declaring dependencies.

How Has This Been Tested?

Existing tests pass, existing build processes work

Are WDL Updates Required?

no

Checklist:

• [X] My code follows the style guidelines of this project
• [X] I have performed a self-review of my own code
• [X] I have commented my code, particularly in hard-to-understand areas
• [X] I have made corresponding changes to the documentation
• [X] My changes generate no new warnings
• [X] I have added tests that prove my fix is effective or that my feature works
• [X] New and existing unit tests pass locally with my changes