[emaarco]

Summary

src/ had 27 loose files at its root, and several folders held modules that belonged elsewhere: format ops and the renderer lived in diagram/, the clean engine's types in layout/, and C7/C8 defaults in ops/. The folder names did not say where code lives or where new code should go.

This PR gives each pipeline stage its own folder: shared/, model/, ids/, xml/, platform/profiles/, ops/, diagram/, layout/ (clean/, incremental.ts), format/, render/, validate/, query/, pipeline/, report/. Only the three entries index.ts, api.ts and cli.ts stay at the root.

• It moves 43 files and changes no logic. Git detects every move as a rename (96–100 % similar), so blame and log --follow keep working.
• Imports and path references follow the moves: code comments, tests, the iso check, the fuzzer, docs/, CONTRIBUTING.md and the PR template. HANDOVER.md, CHANGELOG.md and the October audit are history and keep their old paths.
• The public API is unchanged: src/index.ts and src/node/index.ts export the same names.
• CONTRIBUTING.md now has a table of the folders and a rule for where new code goes.

Import-direction violations remain (e.g. ops/set.ts → layout/index.ts). This PR doesn't add the architecture test that would fix and enforce them.

Checklist

• npm run typecheck passes
• npm run gate passes (from an empty dist/: 2317 tests, iso check, regress budget, fuzz 0 errors)
• src/report/guide.ts and the matching page in docs/ are updated (only if a command, option or output changed)
• PR title is a changelog-worthy Conventional-Commit summary

Linked issue

None.