Add app-console runme helpers for run-all and clear-outputs

[hamelsmu]

Summary

• add a new runme namespace in the App Console with:
  • runme.getCurrentNotebook()
  • runme.runAll([notebookOrUri])
  • runme.clearOutputs([notebookOrUri])
  • runme.help()
• preserve custom global help() in JSKernel so App Console namespace help remains visible
• add unit tests for runme console helper behavior
• add quick-start hint snippets for the new commands in the empty notebook view

Testing

• cd web/app && npx vitest run src/lib/runtime/runmeConsole.test.ts
• cd web && pnpm run build
• cd web/app && bash test/browser/test-smoke.sh 5173
• browser verification with agent-browser:
  • loaded a notebook and ran runme.help()
  • ran runme.runAll("local://...") and confirmed console summary output
  • ran runme.clearOutputs("local://...") and confirmed console summary output

Notes

• runme.getCurrentNotebook() can return null when no active doc is resolved; runme.runAll/clearOutputs accept an explicit notebook URI for this case.
• Existing unrelated test/typecheck failures remain on this branch (not introduced by this change).

Closes #46

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Return null when specialized store is unavailable

resolveStore falls back to localStore for fs:///contents:// URIs whenever the dedicated store is not initialized yet, which makes callers (for example NotebookContext loaders) invoke LocalNotebooks methods with non-local:// URIs and fail at runtime; this can surface as failed notebook loads and current-doc reset during startup races. For non-local schemes, the resolver should return null until the matching store is ready instead of silently routing to the local store.

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[chatgpt-codex-connector]

Print help text to the console output

This help implementation only returns a string, but JSKernel.run does not print expression return values, so entering help() (the prompt’s suggested command) shows no help text to the user. The new top-level help path should write through sendStdout (like runme.help) so command discovery actually works in the app console.

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[Copilot]

Pull request overview

This PR expands the app’s developer-facing console and notebook UX by introducing a new runme helper namespace in the App Console (run all cells / clear outputs), plus supporting changes to notebook storage routing (fs:// vs contents://), markdown cell rendering, and test/fixture coverage for UI + large payload scenarios.

Changes:

• Add runme.* App Console helpers (getCurrentNotebook, runAll, clearOutputs, help) and preserve a global help() in JSKernel.
• Improve notebook handling: store resolution by URI scheme, conflict-result type plumbing, cell refId normalization for JSON fixtures, debounced auto-save, and base64 chunking helper.
• Add UI/testing support: empty-state quick-start snippets, global toast, browser smoke/integration scripts, and several fixture notebooks (including large-payload).

Reviewed changes

Copilot reviewed 39 out of 41 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
pnpm-lock.yaml	Adds lock entries for new markdown-related dependencies (e.g., remark-gfm).
packages/react-components/src/components/index.tsx	Re-exports MarkdownCell.
packages/react-components/src/components/Actions/tests/MarkdownCell.test.tsx	Adds unit tests for the react-components MarkdownCell.
packages/react-components/src/components/Actions/MarkdownCell.tsx	Introduces Jupyter-style in-place markdown rendering for react-components.
packages/react-components/package.json	Adds remark-gfm dependency.
app/vite.config.mts	Ignores notebook fixture writes to avoid dev full-page reload loops.
app/test/fixtures/notebooks/ui-test.runme.md	Adds UI/UX test notebook fixture.
app/test/fixtures/notebooks/subdirectory/nested-notebook.json	Adds nested fixture to test explorer folder navigation.
app/test/fixtures/notebooks/large-payload-test.runme.md	Adds >100KB payload fixture for large payload/base64 testing.
app/test/fixtures/notebooks/hello-world.json	Adds simple JSON notebook fixture.
app/test/fixtures/notebooks/cell-types.json	Adds multi-language + markdown features JSON fixture.
app/test/fixtures/notebooks/cell-types-test.runme.md	Adds multi-language .runme.md fixture.
app/test/fixtures/notebooks/basic-test.runme.md	Adds basic .runme.md fixture.
app/test/browser/test-smoke.sh	Adds startup/blank-screen smoke test using agent-browser.
app/test/browser/test-notebook-ui.sh	Adds notebook UI integration test using fixtures + screenshots.
app/test/browser/test-app-console-commands.sh	Adds App Console integration test for explorer commands.
app/test/browser/README.md	Documents browser integration test setup and fixtures.
app/src/storage/storeResolver.ts	Adds URI-scheme routing to pick the correct NotebookStore.
app/src/storage/notebook.ts	Changes NotebookStore.save() to return ConflictResult.
app/src/storage/fs.ts	Ensures loaded JSON notebooks have stable refIds for cells.
app/src/storage/drive.ts	Updates Drive store save() to return ConflictResult.
app/src/storage/contents.ts	Adds chunked UTF-8→base64 helper and uses it for create-write path.
app/src/lib/toast.ts	Adds lightweight global toast event bus.
app/src/lib/runtime/runmeConsole.ts	Implements runme.* console helper API (run-all / clear-outputs).
app/src/lib/runtime/runmeConsole.test.ts	Adds unit tests for runmeConsole behavior.
app/src/lib/runtime/jsKernel.ts	Preserves a custom global help() if provided; otherwise uses default.
app/src/lib/runtime/AppState.ts	Reorders localNotebooks field and setter placement.
app/src/lib/notebookData.ts	Adds store abstraction, debounced persistence, and backend-error toasts.
app/src/lib/aisreClient.ts	Adds parser-service deserialize helper.
app/src/index.css	Adds selection styling for quick-start code snippet.
app/src/contexts/NotebookContext.tsx	Uses resolveStore and avoids persisting on initial loads.
app/src/contexts/CurrentDocContext.tsx	Allows direct contents:// and fs:// doc resolution from URL.
app/src/components/Workspace/WorkspaceExplorer.tsx	Improves tree row layout/wrapping; avoids store mirroring for fs/contents docs.
app/src/components/Toast.tsx	Adds global toast UI component.
app/src/components/AppConsole/AppConsole.tsx	Adds runme + expanded explorer helpers; captures output for tests; updates console banner/help.
app/src/components/Actions/MarkdownCell.tsx	Updates app markdown cell for accessibility + edit/render switching.
app/src/components/Actions/Editor.tsx	Switches Monaco theme to vs-dark; avoids bad width fallbacks; adjusts wrapper styling.
app/src/components/Actions/Actions.tsx	Updates markdown/code cell chrome, adds empty-state quick-start console snippets.
app/src/App.tsx	Wires global toast; passes agent endpoint to initializer for Contents store.
app/package.json	Adds typecheck script.
app/.env.development	Updates default agent/runner endpoint ports to 9977.

Files not reviewed (1)

• pnpm-lock.yaml: Language not supported

Comments suppressed due to low confidence (1)

app/src/storage/fs.ts:387

• FilesystemNotebookStore implements NotebookStore, but its save() method still returns Promise<void> and throws on conflict. With the updated NotebookStore.save(): Promise<ConflictResult>, this store should return a ConflictResult (and ideally not throw for the conflict case) so callers can handle conflicts consistently across stores.

    const notebook = fromJsonString(parser_pb.NotebookSchema, text, {
      ignoreUnknownFields: true,
    });
    ensureCellRefIds(notebook);
    return notebook;
  }

  async save(uri: string, notebook: parser_pb.Notebook): Promise<void> {
    const parsed = parseFsUri(uri);

---

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[Copilot]

NotebookStore.save() now returns Promise<ConflictResult>, but there are still implementations (e.g. FilesystemNotebookStore and ContentsNotebookStore) returning Promise<void>, which will cause TypeScript errors and/or inconsistent conflict handling. Update all NotebookStore implementers so their save() signature matches and they return { conflicted: false } on success and { conflicted: true, ... } (instead of throwing) when a conflict is detected.

[Copilot]

The new utf8ToBase64() helper is added to avoid stack/size issues, but ContentsNotebookStore.save() still uses btoa(json) (see below in the file), so saving large notebooks can still hit the same failure mode. Consider switching save() to use utf8ToBase64() as well, and update save() to return ConflictResult to match the updated NotebookStore interface.

Suggested change

	binary += String.fromCharCode(...chunk);
	for (let j = 0; j < chunk.length; j++) {
	binary += String.fromCharCode(chunk[j]);
	}

[Copilot]

ensureNotebook uses fsStore when calling resolveStore(...), but fsStore is missing from the hook dependency array. This can leave NotebookData instances bound to a stale store if the filesystem store initializes after the callback is memoized. Add fsStore to the dependency list (and any other referenced store values).

Suggested change

	[emit, notebookStore, contentsStore],
	[emit, notebookStore, fsStore, contentsStore],

[Copilot]

This effect calls resolveStore(item.uri, notebookStore, fsStore, contentsStore) but fsStore is not included in the dependency array. If fsStore becomes available after the effect has run, open fs:// notebooks may never load (or may load via the wrong store). Include fsStore (and any other referenced store values) in the deps.

[Copilot]

sequenceLabel returns a single space when no sequence is set, but the UI now always renders it inside brackets ([{sequenceLabel}]), which produces a visible "[ ]" placeholder for most cells. Either only render the label when a real sequence exists, or have sequenceLabel return an empty string and skip the brackets when blank.

[hamelsmu]

Superseded by #82, which replays only the issue #46 changes on top of current main.