Keep the Planner while its workflows run, with Stop/Resume and a run card

[lavaman131]

Stacked on #215. Partly implements #221.

An atomic Planner session that starts an Atomic workflow now outlives its turn. Until now, Chopin destroyed the session when the turn ended, which left the run orphaned seconds after launch.

What changes

• The session stays while it owns runs. An atomic Planner session is kept, with its owner binding and the loaded document, as long as it has live or paused workflow runs. Chopin tracks those runs through Atomic's workflow activity stream. The next turn reuses the session, so the Planner can still steer its runs over Intercom. The session is released when its runs end, when the owner binding ends, or when the document closes.
• Stop and Resume. Stop Planner pauses the session's live runs through the session's own workflow tool, which returns a structured result instead of a dropped UI notice. Atomic can't pause a run whose only live stage is waiting on a question, so that run is quit instead. It stays resumable and its open question is withdrawn from Decisions. The new chat:resume message and the Resume Planner button resume paused runs.
• Run card in Chat. Each run gets a card showing its name, status (running, waiting on Decisions, paused, finished, blocked, failed, or stopped), elapsed time, and each stage with its status and duration. A pulsing dot marks live work and stays still under reduced motion. Ended runs collapse to one line with the stages behind a toggle, and the transcript records how each run ended. A design-audit specimen covers the running, waiting, paused, blocked and finished states.
• create_document outcomes. It now reports title-taken, and declares its idempotency-conflict, document-unavailable and validation-issue outcomes in its output schema. Before, strict MCP clients rejected those responses as schema violations.
• Working directory. Without a checkout, the Planner's working directory moves from the shared tmp directory to a per-channel directory under Chopin's per-user state directory.

Verification

• bun test: 1755 pass, 2 PostgreSQL skips, 0 fail.
• bun run types and bun run ci pass, with no new Impeccable findings.
• Manual agent-browser run against a local server, with the full atomic Planner running a planning workflow on a private demo repository:
  • the run card tracked the stages;
  • Stop paused the run and Resume continued it;
  • two Decisions questions were answered in the browser;
  • the workflow wrote its formal specification and plan, and the document reached revision 12.

Known gaps

• The card's "Waiting on N Decisions" link doesn't appear, because the waiting count stays 0 for questions that come from HostInput.
• The Planner isn't prompted to report a run's outcome when the run ends.
• Pause and resume should move to typed SDK primitives once Add workflow run management primitives to the SDK (list, pause, quit, resume) bastani-inc/atomic#3377 lands.

Assistant-workflow: inline
Assistant-verification: bun test passed: 1755 pass, 2 skip, 0 fail
Assistant-verification: bun run types and bun run ci passed
Assistant-verification: agent-browser E2E passed: run card, Stop/Resume, Decisions answered, workflow wrote its spec and plan
Co-authored-by: Alex Lavaee lavaman131@github.com