docs: rewrite README for clarity and educational depth

Restructure around three core ideas (attention=memory, FFN=instructions,
trace=witness) as distinct teachable concepts. Tighten the opening hook,
add example output, consolidate engine docs into tables, and cut
redundant sections.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: AbdelStark