Improved changes to the zk tool

[mationorato]

discussion: matter-labs#1015 (comment)

Validium introduces some changes to zk tool (init.ts mainly, but not related to it) that does not follow some common patters.

The new behavior is undocumented, does not follow hierarchical structure of the module.

Reuse the existing configuration subsystem as much as possible (consult ML if feeling stuck); document introduced changes; introduce changes according to the logical domain.