docs: consolidate overview, reference, and miscellaneous documentation

Deduplicate reference.md (remove directory tree, molecule diagram/commands).
Delete issues/ directory (belongs in beads tracker).
Inline AT spike report findings into witness doc, delete spike report.
Move formula-resolution and mol-mall-design to design/ directory.
Merge operational-state into property-layers.
Rename work-queue.md to scheduler.md.
Trim stale/aspirational sections from why-these-features and federation.

Net reduction: ~1,100 lines, 5 files eliminated/moved.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: steveyegge