Keep docs/SPEC.md Project Structure tree in sync with actual internal/ layout

[JeremiahChurch]

Summary

The "Project Structure" tree in docs/SPEC.md has drifted from the actual repository layout as new packages have been added under internal/. Contributors reading the spec get a misleading picture of the code.

Fix

1. Walk the current internal/ tree and reconcile it with the tree shown in docs/SPEC.md.
2. Add missing packages, remove deleted ones, and fix any renamed directories.
3. Consider trimming the tree to only the top one or two levels so future churn doesn't immediately invalidate it again.

Acceptance criteria

• Tree in docs/SPEC.md matches internal/ at the level of detail shown.
• Short note near the tree (or a CONTRIBUTING line) reminding editors to update it when adding/removing a package.