More consistent and better structured directory/file layout

[holgerd77]

Currently file naming is pretty inconsistent within the source directory of the library and it's relatively hard to grasp for newcomers what the code within different files do and how task/responsibility areas are structured.

File/directory structure should be updated - with respect (or at least considering) to API changes which would occur when moving certain files (e.g. src/secure.js). The following is a proposal which came out of discussion within PR #74:

• main directory
  • base.js
  • checkpoint.js
  • index.js
  • secure.js
  • node.js
  • proof.js
• util directory
  • async.js
  • hex.js
  • nibbles.js
  • tasks.js (or eventually merge with async.js)
• db directory
  • index.js
  • scratch.js
• readStream directory
  • index.js
  • scratch.js

[holgerd77]

Note: eventually we can rename DB file and source occurences to Storage or something similar, to better prepare for a future backend exchange possibility.

[holgerd77]

Addressed along several follow-up (and at least partially unrelated) refactoring PRs, will close.