Fix conference room chat crashes: duplicate message IDs, empty bubbles, and untrusted directory

Three bugs fixed:
1. Deduplicate run messages when same run appears in both linkedRuns and liveRuns
   during transition, preventing assistant-ui MessageRepository crash.
2. Render waitingText as content in live run messages so empty transcript
   doesn't produce an empty chat bubble.
3. Auto-initialize git repo in agent home directories so Claude Code doesn't
   reject the workspace as untrusted.

Co-Authored-By: Paperclip <noreply@paperclip.ing>

packages/adapters/claude-local/src/server/execute.ts

@@ -1,3 +1,4 @@
+import { execFile } from "node:child_process";
 import fs from "node:fs/promises";
 import path from "node:path";
 import { fileURLToPath } from "node:url";
@@ -56,6 +57,16 @@ import { prepareClaudePromptBundle } from "./prompt-cache.js";
 
 const __moduleDir = path.dirname(fileURLToPath(import.meta.url));
 
+async function ensureGitRepo(dir: string): Promise<void> {
+  try {
+    await fs.access(path.join(dir, ".git"));
+  } catch {
+    await new Promise<void>((resolve, reject) => {
+      execFile("git", ["init"], { cwd: dir }, (err) => (err ? reject(err) : resolve()));
+    });
+  }
+}
+
 interface ClaudeExecutionInput {
   runId: string;
   agent: AdapterExecutionContext["agent"];
@@ -146,6 +157,9 @@ async function buildClaudeRuntimeConfig(input: ClaudeExecutionInput): Promise<Cl
   const effectiveWorkspaceCwd = useConfiguredInsteadOfAgentHome ? "" : workspaceCwd;
   const cwd = effectiveWorkspaceCwd || configuredCwd || process.cwd();
   await ensureAbsoluteDirectory(cwd, { createIfMissing: true });
+  if (workspaceSource === "agent_home" || (!effectiveWorkspaceCwd && !configuredCwd)) {
+    await ensureGitRepo(cwd);
+  }
 
   const envConfig = parseObject(config.env);
   const hasExplicitApiKey =

ui/src/lib/issue-chat-messages.ts

@@ -747,7 +747,11 @@ function createLiveRunMessage(args: {
         ? ""
         : "Working...";
 
-  const content = parts;
+  const content: typeof parts = parts.length > 0
+    ? parts
+    : waitingText
+      ? [{ type: "text", text: waitingText }]
+      : [];
 
   const message: ThreadAssistantMessage = {
     id: `run-assistant:${run.id}`,
@@ -859,7 +863,9 @@ export function buildIssueChatMessages(args: {
     });
   }
 
+  const linkedRunIds = new Set(linkedRuns.map((r) => r.runId));
   for (const run of normalizeLiveRuns(liveRuns, activeRun, issueId)) {
+    if (linkedRunIds.has(run.id)) continue;
     orderedMessages.push({
       createdAtMs: toTimestamp(run.startedAt ?? run.createdAt),
       order: 3,