fix: allow research runs to restart after stop; improve FTS search, agent limits, and timeouts

- AgentTree.restart() revives a stopped run in the same session: resets the
  root, archives old branches, and restores spawnability (stop no longer
  cancels the root).
- ResearchLoop.start() restarts from stopped/completed and resets iteration
  counters; setGoal is allowed in terminal states; supervisor 'start' revives
  the tree when the root is not spawnable.
- Cancelled/failed/archived children no longer count toward the per-agent
  child limit and archived agents are ignored by the duplicate-task guard.
- cancel() no longer overwrites an already recorded agent result.
- Add agent_timeout_seconds (default 1800) so hung agent sessions fail
  instead of blocking wait() forever.
- FTS search now prefix-matches tokens (tolerates inflections) and safely
  handles punctuation/FTS5 metacharacters instead of returning false
  negatives or throwing.
- Add tests for restart semantics, child limits, result preservation,
  agent timeouts, and FTS morphology/special characters (38/38 passing).

src/supervisor.ts

@@ -49,7 +49,7 @@ export class SupervisorIntegration {
       name: "research_control", label: "Research loop control", description: "Start, record, inspect, pause, resume, or stop the explicit research state machine. Record one report per completed iteration; coded stop conditions prevent infinite prompt loops.",
       promptSnippet: "Control the bounded autonomous research loop",
       parameters: Type.Object({ action: StringEnum(["start", "status", "record_iteration", "pause", "resume", "stop"] as const), goal: Type.Optional(Type.String()), report: Type.Optional(Type.Object({ goal: Type.String(), tasks: Type.Array(Type.String()), activeAgents: Type.Array(Type.String()), expectedOutput: Type.String(), state: Type.String(), newFindings: Type.Integer({ minimum: 0 }), closedQuestions: Type.Integer({ minimum: 0 }), contradictions: Type.Integer({ minimum: 0 }), reason: Type.String(), goalAchieved: Type.Optional(Type.Boolean()), criticalMethodError: Type.Optional(Type.Boolean()), onlyExternalQuestions: Type.Optional(Type.Boolean()), userDecisionRequired: Type.Optional(Type.Boolean()) })) }),
-      execute: async (_id, params) => { const { tree, loop } = this.required(); if (params.action === "start") { if (!params.goal?.trim()) throw new Error("goal is required"); tree.setGoal(params.goal); loop.setGoal(params.goal); loop.start(); return toolText(loop.snapshot()); } if (params.action === "status") return toolText(loop.snapshot()); if (params.action === "pause") { loop.pause(); tree.pause(); } else if (params.action === "resume") { loop.resume(); tree.resume(); } else if (params.action === "stop") { loop.stop(); await tree.stop(); } else { if (!params.report) throw new Error("report is required"); return toolText(loop.record(params.report)); } return toolText(loop.snapshot()); },
+      execute: async (_id, params) => { const { tree, loop } = this.required(); if (params.action === "start") { if (!params.goal?.trim()) throw new Error("goal is required"); const loopState = loop.snapshot(); const loopTerminal = ["stopped", "completed"].includes(loopState.status); const root = tree.inspect(tree.rootId); const rootSpawnable = !["cancelled", "failed", "archived"].includes(root.status); if (loopTerminal || tree.status !== "active" || !rootSpawnable) tree.restart(params.goal); loop.setGoal(params.goal); loop.start(); return toolText(loop.snapshot()); } if (params.action === "status") return toolText(loop.snapshot()); if (params.action === "pause") { loop.pause(); tree.pause(); } else if (params.action === "resume") { loop.resume(); tree.resume(); } else if (params.action === "stop") { loop.stop(); await tree.stop(); } else { if (!params.report) throw new Error("report is required"); return toolText(loop.record(params.report)); } return toolText(loop.snapshot()); },
     });
   }