Document C1 codemod recipe + C6 wave boundaries + N-scan TODO deadlines (T2 iteration)

Address T2 review asks from Karpathy (request_changes) + Jobs
(approve with minor asks) without touching published commits:

- scripts/codemod/README.md (new): records remove-appdatabase-passthrough.mjs
  usage, the completeness proof for METHOD_TO_MODULE (typecheck-clean +
  524 tests green at 118e3d8 = no orphaned call sites), and the sequential
  revert recipe for C1 (3 -> 2 -> 1, not independent because 118e3d8
  bundled vault simplification).

- CONTRIBUTING.md (new): pass-through ban + codemod usage + sequential
  revert recipe + file-size ceiling + C6 wave cap. Whitelisted in
  .gitignore alongside the existing doc exceptions.

- docs/proposals/C6.2-error-taxonomy-phase2.md: wave 2 scope boundary
  names renderer-adjacent / api-server / browser / automation / skills
  explicitly and excludes src/main/database/** + src/main/worker/runtime/**
  (B2 / M10 high-churn zones). Wave 2 and wave 3 each capped at 30
  catch sites so C6 cannot expand without bound.

- src/main/agent-runtime/artifact-projector.ts, runtime-bridge.ts:
  N-scan TODOs now carry a death date ("TODO(M-followup by 2026-05-20)").
  If the date passes without decomposition, a follow-up session MUST
  revisit or justify the exception.

Karpathy T2 asks #1 and #2 (split part 3 / "independent revert" language)
are addressed in CONTRIBUTING + codemod README as documentation, not
history rewrites, because 118e3d8 is already published.

Typecheck clean. No structural code changes; pure docs + comment edits.

.gitignore

@@ -60,6 +60,8 @@ oldreference/
 !/.planning/**/*.md
 !/src/main/prompt-builder/**/*.md
 !/scripts/README.md
+!/scripts/codemod/README.md
+!/CONTRIBUTING.md
 # Bundled Agent Skills ship their SKILL.md / README.md as source of truth.
 # The Pi skills loader rejects entries whose frontmatter `name` diverges from
 # the parent directory; losing SKILL.md to the blanket *.md ignore meant a