V2 : Fix core packaging

[z3dev]

These changes correct the core package, and enhance the package into a true library.

• source has been moved to 'src' directory
• indexes have been created for each sub-part, i.e. code-evaluation, utils, etc.
• packaging has been improved to meet NPM standards

NOTE: The core package was only repackaged. No restructuring of code was performed.

There are two areas of change in the core package:

• rebuildGeometry has been changed; improving the documentation, and correcting default options
• walkFileTree has been moved from the web package into the core package, as this is fundamental for other applications

In addition to the core package changes, the cli and the web packages were corrected to use the core package properly, i.e. require().

All Submissions:

• Have you followed the guidelines in our Contributing document?
• Have you checked to ensure there aren't other open Pull Requests for the same update/change?
• Does your submission pass tests?

[z3dev]

Changes as expected. TIme for review.

[z3dev]

Changes as expected. Time for a review.