Control Planner workflows through Atomic's session run control

Atomic's SDK now exposes
session.workflows (bastani-inc/atomic#3377). Stop and Resume now call
session.workflows.pause({ all: true }) and resume each paused run, and a
partial pause reports the runs still active, replacing the workflow tool
called with a hand-built tool context and the quit fallback.

Atomic now counts a run whose stage waits on a question as paused and
leaves the question open, so Stop no longer withdraws it from Decisions.
An answer given while the run is paused is recorded but returned to the
run only after Resume, so the paused run never advances. A run with a
stage waiting on a question now shows as waiting on Decisions even when
no prompt lifecycle event arrives.

Assistant-model: Claude Opus 5.5
Assistant-workflow: inline
Assistant-verification: bun test passed: 1757 pass, 2 PostgreSQL skips, 0 fail, including run control, held answers for paused and child runs, and the waiting count
Assistant-verification: bun run types passed: all workspaces
Assistant-verification: bun run ci passed: dprint, oxlint, tokens, type scale, Impeccable (no new findings)
User-preference: Use Atomic's SDK run-control primitives instead of slash commands or tool workarounds
Co-authored-by: Alex Lavaee <lavaman131@github.com>