Migration/step 06

[surchs]

Title: chore(migration): step 06 annotation-tool
Branch: migration/step-06

Merge with a merge commit, not squash. This PR imports history.

Summary

• annotation-tool imported with full history into tools/annotation-tool (upstream 23767c4, rewritten head 4efb276). No submodules. .github/ deleted, including the dead build_docker_on_release.yml.
• test-node.yml gains a link-check input that runs the lychee job ported from upstream's checks.yaml, with the same arguments, from the tool folder so its lychee.toml applies.
• CI: annotation-tool job calling test-node.yml with unit, component and e2e enabled, no component-env, e2e-env: NB_DISABLE_CONFIG=false (as upstream's tests.yaml), and link-check: true. Filter: tools/annotation-tool/**, test-node.yml.
• just test annotation-tool (npm ci, lint, format, typecheck, unit, component).
• annotation-tool README: new "Development in the Neurobagel monorepo" section (setup, tests, no Docker image, releases); the old-repository Actions badges replaced by the monorepo CI badge. Root README: Step 6 row.

Checks run

Check	Result
scripts/check-unchanged.sh	OK: protected paths unchanged (all five tools)
git rev-list --count <rewritten-head> / annotation-tool-v* tags	362 / 32 (upstream 362 / 32)
npm ci	OK; husky prints install command is DEPRECATED / no .git, exits 0 (constraint 6, Step 8)
typecheck, lint:check, format:check, codespell	all pass
test:unit	240 passed (baseline 240)
Component tests (local, Cypress 15.21.1 image)	180 passed (baseline 180)
E2E tests (local, .env NB_DISABLE_CONFIG=false, against npm run preview)	20 passed (baseline 20)
lychee 0.24.2 (same version as lychee-action@v2's default), upstream args, from the tool folder	435 links, 0 errors, 59 excluded by lychee.toml
npm run build and grep -r "$(jq -r .version package.json)" dist/assets	finds "v","0.7.8", the version label injected by vite.config.ts
api / federation-api / bagel-cli tests	188 / 111 / 215 passed (baseline)
query-tool static checks / component tests	pass / 89 passed (baseline)
just lint	passes
CI on this PR	to be confirmed on GitHub

Documentation check: every command in the new README section was run verbatim from tools/annotation-tool/ in a fresh clone of this branch: npm ci, the four static/unit commands, npm run build, the e2e .env + npm run build, npm run preview (served 200; stopped by Ctrl+C equivalent, SIGINT to its process group). npm run test:component and npm run test:e2e cannot start natively in the local container (no libgtk-3); the same Cypress runs passed in the cypress/included image (180 and 20). just test annotation-tool ran npm ci, the static checks and unit tests (240 passed), then stopped at native Cypress for the same reason. The git clone URL was replaced by a local clone of this branch.

Deviations from the plan

• Ported annotation-tool's lychee link check, which the plan did not mention (plan updated).
• Not ported, as decided for Step 5/7d: handle_external_pr.yml, add_iss2project.yml, stale.yml, scorecard.yml. deploy.yaml and release.yaml are replaced in Steps 12–14.
• Coverage uploads and the merge-coverage job (Codecov) are not ported (approved in Step 0).

🤖 Generated with Claude Code