01: integrate the enhancement branch stack into the run branch #342

Part of #341.

What to build: the run branch contains the complete outstanding enhancement stack — merge feat/zcode-wave3 (superset of the design-system waves and the token-alignment wave) into the run branch. Resolve the generated web bundle by regeneration (pnpm run build:web + restage), never by hand-editing bundle output. If the merge re-introduces .changeset/tower-ascii-titles-and-token-usage.md, delete it (shipped in #329, consumed by #330).

Blocked by: None (can start immediately).

Status: done

• Merge commit present on the run branch; git log shows the wave commits in history
• apps/pythinker-code/dist-web regenerated from the merged web source in the same change (fingerprint check passes)
• Stale changeset absent if it reappeared; no duplicate changelog entries
• Root gates green post-merge: typecheck, lint, sherif, build
• Web typecheck + build green

Demo path: git log --oneline on the run branch shows the wave history; root build passes with the fresh bundle.

Capability: standard/medium
Claims: exclusive: .agents/, apps/pythinker-web/, apps/pythinker-code/dist-web/**, .changeset/ ; shared-regenerate: pnpm-lock.yaml
Claims amended: +.agents/, +apps/pythinker-web/ (exclusive): integration ticket — the merge itself delivers the wave-stack content; later tickets own further edits there