Add collaborative markdown document tools

[samwillis]

Summary

Stacked on #4555. Adds collaborative markdown documents for Electric Agents. This PR consumes the streaming tool-call hook from #4555, but keeps the markdown document implementation in a separate layer.

What this adds:

• A document manifest entry for markdown docs with:
  • content MIME: text/markdown
  • transport MIME: application/vnd.electric-agents.markdown-yjs
  • provider: y-durable-streams
  • Y.Text name: markdown
• Horton/worker markdown tools for creating, reading, replacing, editing, and streaming inserts into markdown docs.
• Runtime-side document sessions that materialize a wake-local Y.Doc, keep it synced through @durable-streams/y-durable-streams, and append binary Yjs updates to durable streams.
• Raw Yjs update and awareness stream support on the server; the server creates streams and serves metadata but does not semantically edit document content.
• CodeMirror/Yjs markdown editor UI with open and split-right actions from timeline and manifest surfaces.
• Agent and user presence plumbing based on Yjs awareness, with agent cursor placement during streamed insert/replace operations.
• Worker sharing of markdown document refs so spawned workers can collaborate on the same document.

Architecture notes:

• The agent runtime owns semantic document edits. Tools mutate the local wake-scoped Y.Doc; the Yjs provider writes updates to the durable stream.
• The agents server stays deliberately dumb for document contents: it creates/locates streams, proxies durable stream access, and stores the manifest row.
• Presence follows the same split: clients and agents publish raw Yjs awareness updates; the server does not interpret cursor positions.
• Basic replace/edit tools remain available for non-streaming edits; streamed insert/replace builds on feat(agents): Add streaming tool call argument support #4555's onArgsDelta hook.

Validation

• pnpm --filter @electric-ax/agents-runtime typecheck
• pnpm --filter @electric-ax/agents-server-ui typecheck
• pnpm --filter @electric-ax/agents typecheck
• pnpm --filter @electric-ax/agents-server typecheck
• pnpm --filter @electric-ax/agents-runtime exec vitest run test/markdown-docs-tools.test.ts test/outbound-bridge.test.ts test/pi-adapter.test.ts
• pnpm --filter @electric-ax/agents-runtime exec vitest run test/runtime-dsl.test.ts
• pnpm --filter @electric-ax/agents exec vitest run test/spawn-worker-tool.test.ts test/horton-tool-composition.test.ts test/horton-system-prompt.test.ts
• pnpm --filter @electric-ax/agents-server exec vitest run test/electric-agents-routes.test.ts test/electric-agents-status.test.ts test/electric-agents-manager-write-validation.test.ts
• pnpm --filter @electric-ax/agents-server-ui exec vitest run src/components/views/MarkdownDocumentView.test.ts src/lib/workspace/workspaceReducer.test.ts
• pnpm --filter @electric-examples/yjs run typecheck
• pnpm --filter @electric-ax/agents-mobile run ci:check
• git diff --check

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[codecov]

Codecov Report

❌ Patch coverage is 53.46633% with 933 lines in your changes missing coverage. Please review.
✅ Project coverage is 56.60%. Comparing base (636d716) to head (28be27c).
✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
packages/agents-runtime/src/tools/markdown-docs.ts	76.32%	224 Missing ⚠️
...r-ui/src/components/views/MarkdownDocumentView.tsx	8.77%	156 Missing ⚠️
packages/agents-runtime/src/markdown-yjs.ts	43.41%	116 Missing ⚠️
...es/agents-runtime/src/markdown-document-session.ts	0.86%	115 Missing ⚠️
...ckages/agents-runtime/src/runtime-server-client.ts	8.19%	112 Missing ⚠️
packages/agents-server/src/markdown-documents.ts	44.15%	43 Missing ⚠️
...agents-server-ui/src/components/EntityTimeline.tsx	0.00%	24 Missing ⚠️
packages/agents-runtime/src/process-wake.ts	8.00%	23 Missing ⚠️
packages/agents-runtime/src/manifest-helpers.ts	12.00%	22 Missing ⚠️
packages/agents-server/src/entity-manager.ts	77.27%	20 Missing ⚠️
... and 8 more

Additional details and impacted files

@@                            Coverage Diff                            @@
##           samwillis/agents-streaming-tool-calls    #4530      +/-   ##
=========================================================================
+ Coverage                                  55.05%   56.60%   +1.55%     
=========================================================================
  Files                                        318      360      +42     
  Lines                                      37016    40834    +3818     
  Branches                                   10547    11241     +694     
=========================================================================
+ Hits                                       20379    23116    +2737     
- Misses                                     16604    17661    +1057     
- Partials                                      33       57      +24     

Flag	Coverage Δ
packages/agents	72.03% <82.45%> (+1.50%)	⬆️
packages/agents-mcp	77.54% <ø> (?)
packages/agents-mobile	84.09% <ø> (+12.66%)	⬆️
packages/agents-runtime	79.23% <58.11%> (-1.18%)	⬇️
packages/agents-server	72.87% <61.92%> (-1.12%)	⬇️
packages/agents-server-ui	6.12% <6.60%> (+0.45%)	⬆️
packages/electric-ax	46.42% <ø> (ø)
packages/experimental	87.73% <ø> (?)
packages/react-hooks	86.48% <ø> (?)
packages/start	82.83% <ø> (?)
packages/typescript-client	91.83% <ø> (?)
packages/y-electric	56.05% <ø> (?)
typescript	56.60% <53.46%> (+1.55%)	⬆️
unit-tests	56.60% <53.46%> (+1.55%)	⬆️

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[github-actions]

Electric Agents Desktop Builds

Build artifacts for commit 28be27c.

Platform	Status	Artifact
macOS Apple Silicon	Passed	DMG
macOS Intel	Passed	DMG
Windows x64	Passed	Installer
Linux x64	Passed	AppImage / deb

Workflow run

[github-actions]

Electric Agents Mobile Build

Local mobile checks ran for commit 28be27c.

The EAS Android preview build was skipped because the mobile-eas-build label is not present.
Add the mobile-eas-build label to this PR to produce an installable preview build.

Workflow run

[kevin-dp]

I checked out this branch to give it a spin. I asked Horton to create a markdown document which it did. Then i opened it in the pane on the right and i added some text to the document. Then i asked Horton to tell me what i added to the document. However, it told me that the document is unchanged. And if i open the document again the changes are indeed missing. So it seems that my changes aren't automatically saving.

I asked Claude about it and it told me this is a bug:

Found it — this is a real bug in the PR, not a missing save step. Your edits are being silently rejected by the server. Here's the full chain, verified empirically against your running stack:

What's happening

1. There is no save button by design — the editor streams every keystroke to a server-side "updates stream" for the doc.
2. But when Horton's turn (wake) that created the document finished, the agent runtime closed its document session. YjsProvider.disconnect() ends by calling producer.close(), which sends a final append with a stream-closed: true header — and that permanently closes the document's update stream on the server.
3. From that moment, every write from anyone — your editor, future agent edits — gets HTTP 409 "Stream is closed". The client library swallows the error (its flush() even resolves successfully), so the UI keeps showing "Connected" and your text stays in local memory only.
4. When Horton re-read the doc, it correctly saw only the original server-side content — your sentence never made it there.

How I verified it

• Fetched your doc's raw stream from the server: it contains Horton's original markdown but no "SYNCINGG" — your edit never landed.
• Replayed the editor's exact write path with a script: appends to your doc return 409 Stream is closed.
• Controlled experiment on a fresh doc: session A writes fine (200), disconnects (final append carries stream-closed: true, server answers 204), then session B's writes all fail with 409. Reproduces every time.

Where the fix belongs

The closing call is in @durable-streams/y-durable-streams (v0.2.7, latest): disconnect() → closeUpdatesProducer() → producer.close(), and in @durable-streams/client a producer's close() means "close the stream", not "leave the session". For a multi-writer collaborative doc, no single participant's disconnect should close the shared stream. Either the provider needs a flush-without-close disconnect, the PR's wake-scoped session close() (packages/agents-runtime/src/markdown-document-session.ts:100) shouldn't disconnect this way, or the agents-server needs to implement the stream-rollover the protocol seems to expect. A second, smaller issue: the UI shows "Connected" while writes 409 — sync failures should surface in that status indicator.

There's no workaround for testing user→agent edits right now — every doc's stream gets closed as soon as the creating wake ends.