chore(deps): add @deepnote/cloud-sync and align bundled @deepnote packages

[tkislan]

Summary

Adds @deepnote/cloud-sync 0.1.0 and @deepnote/cloud 0.2.1 as direct dependencies and moves @deepnote/blocks, convert, database-integrations and runtime-core to the versions cloud-sync pins, so the desktop bundle resolves one copy of each. Nothing in src/ imports the new packages yet.

• package.json and package-lock.json: the six dependency entries from the issue. The @deepnote/runtime-core ws override is removed instead of raised from 8.21.0 to 8.21.3 as the issue asks: runtime-core 0.7.0 requires ws ^8.21.3 itself, the lockfile is byte-identical without the override, and an exact pin would conflict with every runtime-core release that raises its ws floor. @deepnote/cli stays at 0.8.0 and keeps its own nested copies.
• src/test/mocks/deepnoteRuntimeCore.ts: the default startServer result is a complete runtime-core 0.7.0 ServerInfo (exited, stderrTail, childPids). Before this edit it was the only type error the bump produced.

Closes #560

Verification

Run on this branch after merging origin/main (7dfa54f, which adds #556 and #557 on top of v1.8.0):

• npm ls outside the @deepnote/cli, local-runner and reactivity subtrees shows one copy each of blocks 4.8.1, database-integrations 1.7.1, cloud 0.2.1, convert 4.0.3, runtime-core 0.7.0 and cloud-sync 0.1.0; runtime-core 0.7.0 uses ws@8.21.3.
• package.json and package-lock.json conflicted again (main converted the lockfile to lockfileVersion 3 in chore(deps): convert package-lock.json to lockfileVersion 3 #557 and bumped @deepnote/sql-language-server to 3.0.1 in chore(deps): bump @deepnote/sql-language-server to 3.0.1 #556). package.json keeps this branch's @deepnote/* bumps together with ^3.0.1. The lockfile is regenerated from main's lockfile and the merged package.json in a full checkout, not hand-merged: the 377 entries changed only by main equal main's, the 64 changed only by this branch equal this branch's, and the root entry is main's plus this branch's dependency changes. undici stays at 6.29.0 without the dev flag, because the CLI's runtime-core 0.5.0 reaches it from production code.
• CI's lockfile drift check, reproduced from a fresh checkout of the merged commit (CI=true npm install with scripts and an empty npm cache, then git diff --exit-code HEAD), leaves package-lock.json unchanged, and so does npm install in the working copy. better-npm-audit audit and audit --production (the CI audit jobs) exit 0 with only the existing .nsprc exceptions. qlty now scans the root lockfile; emulated with osv-scanner 2.7.0 and the repo's osv-scanner.toml, it reports the same three accepted advisories as on main and nothing new, and the lockfile is 1,421,354 bytes against qlty's 2,098,000-byte limit.
• npm run typecheck, lint, format and spell-check pass. Unit tests: 2879 passing, 0 failing, 239 pending.
• A VSIX was built from the merged tree and the installed bundle's sha256 matched the built dist/extension.node.js. On VS Code 1.111.0 the E2E workspace group (24 tests, includes main's new addExistingIntegration suite) and execution group (7 tests, includes helloWorld and sqlQueryChaining) pass.
• Before the merge, the execution and agent groups (the latter includes agentBlock) passed on VS Code 1.111.0 and on VS Code 1.95.3 (Electron 32.2.1, Node 20.18.0), with no module-load or syntax errors from @deepnote/runtime-core, ai or @ai-sdk/* in the extension host logs. The agent group and the 1.95.3 run were not repeated on the merged tree; the merges only brought in integrations code, the @deepnote/sql-language-server 3.0.1 bump, the lockfile format change and CI configuration.
• A rebuild of the desktop bundle config shows one path and version of each bundled @deepnote/* package. The runtime-core entry points load and run under Node 20.18.0.

Behavior changes that come with the bump

The issue states there is no user-visible change. Review found the following; these are not addressed in this PR (out of scope for #560) and are worth follow-ups:

1. pivot-table blocks (@deepnote/blocks 4.8.x). 4.7.0 rejected a file containing a pivot-table block; 4.8.1 accepts it. The extension has no converter for it, so it takes the unknown-block fallback (src/notebooks/deepnote/deepnoteDataConverter.ts). Parsing was reproduced; the save path (the block coming back as an empty markdown block) was traced in code, not run end to end.
2. Agent blocks (@deepnote/runtime-core 0.7.0). auto now resolves to gpt-6.1-sol instead of gpt-5. With OPENAI_BASE_URL set, requests go to /responses instead of /chat/completions, and reasoning summaries are always requested. A gateway that only serves chat completions will fail. The E2E agent suite uses aimock, which serves both routes, so it cannot detect this.
3. stopServer. The default grace period grows from 2 s to 10 s, so an environment switch or shutdown with a busy server can take up to about 12 s longer. For a server killed by a signal, the wait is not skipped.

Smaller notes: re-resolving the @deepnote/cli subtree moved its nested ai and @ai-sdk/* packages to newer in-range versions and grew dist/deepnoteCli.cjs by roughly 100 KB.

Not verified

• Cursor (not covered by E2E, cannot be run in the agent environment).
• A real OpenAI API key (the agent suite uses a local stand-in server).
• The files and interpreter E2E groups were not run locally; CI runs them.

🤖 Generated with Claude Code

https://claude.ai/code/session_017pqrotDqxwXxXYVEG5Z7wh

Summary by CodeRabbit

• Chores
  • Updated supporting platform components and runtime compatibility.
  • No user-facing features or behavior changed in this update.

[linear-code]

BLU-6517

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📝 Walkthrough

The dependency declarations add @deepnote/cloud and @deepnote/cloud-sync, update selected @deepnote/* package ranges, and remove the runtime-core ws override. The runtime-core test mock imports ServerExit and adds exited, stderrTail, and childPids to the default server result.

Priority: ⬇️ Low

Estimated code review effort: 1 (Trivial) | ~5 minutes

Change: Other

Suggested reviewers: jamesbhobbs

Merge Risk: 🔵 Low · up to 7814e

The dependency upgrade may slightly change agent routing and server shutdown timing, although the issue asked for no behavior change. The risk is bounded and disclosed, so the owner should confirm it is acceptable before merging.

Pre-merge checks: 5 · 1

Failed checks: 1 warning

Check name	Status	Explanation	Resolution
Linked Issues check		[ #560 ] The requested dependency versions, direct dependencies, mock fields, CLI pin, and reported verification are present. The PR also reports user-visible behavior changes from the required upgrad…	Prevent the reported behavior changes while retaining the required dependency set, or update #560 to explicitly accept these dependency-induced behavior changes.

Passed checks: 5 passed

Check name	Status	Explanation
Out of Scope Changes check		The package declarations, lockfile regeneration, dependency-resolution checks, verification, and src/test/mocks/deepnoteRuntimeCore.ts update support [ #560 ]. The source change remains limited to t…
Docstring Coverage		No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 1…
Updates Docs		No feature is implemented in this pull request. The diff only updates dependencies, the lockfile, and a test mock; neither @deepnote/cloud nor @deepnote/cloud-sync is imported by source code. No d…
Description Check		Check skipped - CodeRabbit’s high-level summary is enabled.
Title check		The title clearly and concisely describes the main changes: adding @deepnote/cloud-sync and aligning bundled @deepnote packages.

Full details: Linked Issues check

Explanation

[ #560 ] The requested dependency versions, direct dependencies, mock fields, CLI pin, and reported verification are present. The PR also reports user-visible behavior changes from the required upgrades: pivot-table save behavior, agent model and API routing, and the stopServer grace period. The PR does not contain changes that preserve the issue's stated no-user-visible-behavior scope.

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 38%. Comparing base (c1c05a2) to head (a0ad007).
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@          Coverage Diff          @@
##            main    #561   +/-   ##
=====================================
  Coverage     38%     38%           
=====================================
  Files        822     822           
  Lines      41098   41098           
  Branches    9044    9044           
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  Hits       15620   15620           
  Misses     23405   23405           
  Partials    2073    2073           

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Actionable comments posted: 1

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Inline comments:
Review comments at @package.json:
- Line 2726: Preserve issue #560’s no-behavior-change contract for the
runtime-core dependency used by the extension: add compatibility around agent
provider routing and stopServer’s grace period, or explicitly update the issue
to accept those behavior changes and add coverage for both. The @deepnote/blocks
dependency change alone does not require a pivot-table fallback change.

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[dinohamzic]

@tkislan there are some conflicts to address

[tkislan]

@dinohamzic resolved now .. was because of lock file bump to V3