@agentproto/runtime 2.7.0 → 2.8.0

package/dist/index.mjs

@@ -1,6 +1,6 @@
+import { join, resolve, dirname, basename, isAbsolute, normalize, relative, extname, delimiter, sep } from 'path';
 import { createReadStream, promises, readdirSync, readFileSync, mkdirSync, writeFileSync, existsSync, renameSync, chmodSync, openSync, closeSync, realpathSync, statSync, createWriteStream } from 'fs';
 import { homedir, hostname, tmpdir } from 'os';
-import { join, dirname, resolve, basename, isAbsolute, normalize, relative, extname, delimiter, sep } from 'path';
 import { createInterface } from 'readline';
 import { timingSafeEqual, createHmac, randomBytes, randomUUID, createHash } from 'crypto';
 import { mkdir, writeFile, unlink, readdir, readFile, stat, chmod, rename, rm, appendFile, mkdtemp, realpath, access } from 'fs/promises';
@@ -198,6 +198,127 @@ var init_tool_call_record = __esm({
   "src/tool-call-record.ts"() {
   }
 });
+function cwdLabel(cwd, workspaceSlug) {
+  const leaf = basename(cwd);
+  if (!workspaceSlug || workspaceSlug === leaf) return workspaceSlug ?? leaf;
+  return `${workspaceSlug}/${leaf}`;
+}
+function sessionFooterProvenance(session, options = {}) {
+  const prov = {
+    sessionId: session.id,
+    label: session.label,
+    adapter: session.harness ?? session.adapterSlug,
+    model: session.model,
+    authProfile: session.accessProfile?.label ?? session.accessProfile?.profileRef,
+    parentSessionId: options.supervisor?.id,
+    costUsd: session.costUsd,
+    tokensIn: session.tokensIn,
+    tokensOut: session.tokensOut,
+    source: options.source ?? "daemon",
+    host: options.host,
+    cwd: session.cwd,
+    workspaceSlug: session.workspaceSlug
+  };
+  return { prov, authMode: session.auth?.mode };
+}
+function buildSessionPrFooter(session, options = {}) {
+  const { prov, authMode } = sessionFooterProvenance(session, options);
+  return buildFooter({ prov, authMode, sha: options.sha, kind: "PR" });
+}
+function appendFooterOnce(body, footer) {
+  if (hasProvenanceFooter(body)) return body;
+  return `${body}${footer}`;
+}
+function hasProvenanceFooter(body) {
+  return new RegExp(`<sub>[^\\n]*${MARKER}`).test(body);
+}
+function parseGhPrCreate(command, args, stdout) {
+  if (basename(command) !== "gh") return null;
+  const positionals = args.filter((a) => !a.startsWith("-"));
+  if (positionals[0] !== "pr" || positionals[1] !== "create") return null;
+  const re = /https?:\/\/\S+?\/pull\/(\d+)/g;
+  let match;
+  let last = null;
+  while ((match = re.exec(stdout)) !== null) {
+    last = { url: match[0], number: Number(match[1]) };
+  }
+  return last;
+}
+function detectShellPrCreate(command, resultText) {
+  if (!command || !resultText) return null;
+  const unquoted = command.replace(/'[^']*'/g, " ").replace(/"(?:[^"\\]|\\.)*"/g, " ");
+  if (!/(^|[\s;&|({])gh\s+pr\s+create(\s|$)/.test(unquoted)) return null;
+  const re = /https?:\/\/\S+?\/pull\/(\d+)/g;
+  let match;
+  let last = null;
+  while ((match = re.exec(resultText)) !== null) {
+    last = { url: match[0], number: Number(match[1]) };
+  }
+  return last;
+}
+function cwdRelated(sessionCwd, cwd) {
+  if (sessionCwd === cwd) return true;
+  const sep2 = "/";
+  return cwd.startsWith(sessionCwd + sep2) || sessionCwd.startsWith(cwd + sep2);
+}
+function pickExecutorSession(sessions, cwd) {
+  const candidates = sessions.filter(
+    (s) => s.kind === "agent-cli" && typeof s.cwd === "string" && cwdRelated(s.cwd, cwd)
+  );
+  if (candidates.length === 0) return void 0;
+  const alive = (s) => s.status === "running" || s.status === "starting";
+  const byRecency = (a, b) => (b.startedAt ?? "").localeCompare(a.startedAt ?? "");
+  const live = candidates.filter(alive).sort(byRecency);
+  if (live.length > 0) return live[0];
+  return [...candidates].sort(byRecency)[0];
+}
+var MARKER, fmtTokens, buildFooter;
+var init_pr_provenance = __esm({
+  "src/pr-provenance.ts"() {
+    MARKER = "@agentproto-bot";
+    fmtTokens = (n) => {
+      if (typeof n !== "number" || !Number.isFinite(n)) return null;
+      return n >= 1e3 ? `${(n / 1e3).toFixed(1)}k` : String(n);
+    };
+    buildFooter = ({
+      prov,
+      authMode,
+      runId,
+      runUrl,
+      sha,
+      kind = "review"
+    }) => {
+      const parts = [`\u{1F916} **${MARKER}** \u2014 ${kind}`];
+      if (prov?.sessionId) {
+        parts.push(`session \`${prov.sessionId}\`${prov.label ? ` (\`${prov.label}\`)` : ""}`);
+      }
+      if (prov?.adapter) parts.push([prov.adapter, authMode].filter(Boolean).join(" / "));
+      else if (!prov?.sessionId) parts.push(`legacy fallback${authMode ? ` (${authMode})` : ""}`);
+      else if (authMode) parts.push(authMode);
+      if (prov?.authProfile) parts.push(`auth-profile \`${prov.authProfile}\``);
+      if (prov?.model) parts.push(`model \`${prov.model}\``);
+      if (prov?.sandboxId) parts.push(`e2b \`${prov.sandboxId}\``);
+      if (prov?.parentSessionId) parts.push(`supervisor \`${prov.parentSessionId}\``);
+      const tin = fmtTokens(prov?.tokensIn);
+      const tout = fmtTokens(prov?.tokensOut);
+      if (tin || tout) parts.push(`${tin ?? "?"} in / ${tout ?? "?"} out`);
+      if (typeof prov?.costUsd === "number") {
+        parts.push(`$${prov.costUsd.toFixed(4)}${prov.source && prov.source !== "adapter" ? ` (${prov.source})` : ""}`);
+      }
+      const showLocalHostCwd = prov?.source === "local" || prov?.source === "daemon" || !runId;
+      if (runId && !showLocalHostCwd) parts.push(`run [${runId}](${runUrl})`);
+      if (showLocalHostCwd) {
+        if (prov?.host) parts.push(`host \`${prov.host}\``);
+        if (prov?.cwd) parts.push(`cwd \`${cwdLabel(prov.cwd, prov.workspaceSlug)}\``);
+      }
+      if (sha) parts.push(`sha \`${sha.slice(0, 7)}\``);
+      return `
+
+---
+<sub>${parts.join(" \xB7 ")}</sub>`;
+    };
+  }
+});
 function sessionTranscriptDir(sessionId, baseDir) {
   return join(baseDir ?? join(homedir(), ".agentproto", "sessions"), sessionId);
 }
@@ -390,6 +511,10 @@ function createTranscriptWriter(opts) {
           const meta = evt.toolCallId ? state.toolCallMeta.get(evt.toolCallId) : void 0;
           if (evt.toolCallId) state.toolCallMeta.delete(evt.toolCallId);
           const { command, args } = extractCommandArgs(meta?.arguments);
+          const createdPr = evt.isError ?? false ? null : detectShellPrCreate(
+            command ?? meta?.toolName,
+            typeof evt.result === "string" ? evt.result : void 0
+          );
           writeRecord(sessionId, state, {
             kind: "tool-call-record",
             sessionId,
@@ -397,7 +522,8 @@ function createTranscriptWriter(opts) {
             ...command !== void 0 ? { command } : {},
             ...args !== void 0 ? { args } : {},
             isError: evt.isError ?? false,
-            ...meta ? { durationMs: Date.now() - meta.startedAt } : {}
+            ...meta ? { durationMs: Date.now() - meta.startedAt } : {},
+            ...createdPr ? { createdPrUrl: createdPr.url, createdPrNumber: createdPr.number } : {}
           });
           break;
         }
@@ -522,6 +648,7 @@ var DEBOUNCE_MS;
 var init_transcript_writer = __esm({
   "src/transcript-writer.ts"() {
     init_tool_call_record();
+    init_pr_provenance();
     DEBOUNCE_MS = 250;
   }
 });
@@ -634,14 +761,13 @@ function renderMarkdown(session, opts = {}) {
 function renderJson(session) {
   return JSON.stringify(session, null, 2);
 }
-async function exportClaudeCodeSession(adapterSessionId, cwd) {
+async function exportClaudeCodeSession(adapterSessionId, cwd, configDir) {
   if (!cwd) {
     throw new Error(
       "claude-code exporter: cwd is required to locate the JSONL file.\nPass cwd explicitly or use a session id that is in the registry."
     );
   }
-  const encoded = claudeProjectSlug(cwd);
-  const filePath = join(homedir(), ".claude", "projects", encoded, `${adapterSessionId}.jsonl`);
+  const filePath = join(claudeCodeProjectDir(cwd, configDir), `${adapterSessionId}.jsonl`);
   let stream;
   try {
     stream = createReadStream(filePath, { encoding: "utf8" });
@@ -1735,6 +1861,7 @@ async function exportAgentSession(input) {
   let adapterSlug = input.adapter;
   let cwd = input.cwd;
   let adapterSessionId = sessionId;
+  let configDir;
   const err = (msg) => ({
     sessionId,
     adapter: adapterSlug ?? "unknown",
@@ -1747,6 +1874,7 @@ async function exportAgentSession(input) {
   if (desc) {
     adapterSlug = adapterSlug ?? desc.adapterSlug;
     cwd = cwd ?? desc.cwd;
+    configDir = desc.adapterConfigDir;
     if (desc.adapterSessionId) adapterSessionId = desc.adapterSessionId;
   }
   const tryNative = async () => {
@@ -1764,7 +1892,7 @@ Pass adapter explicitly or use a known session id (sess_xxx or name).`
 Only sessions spawned via claude-code or hermes can be exported.`
       );
     }
-    return exporter.exportSession(adapterSessionId, cwd);
+    return exporter.exportSession(adapterSessionId, cwd, configDir);
   };
   const tryDaemon = () => exportDaemonEventsSession(daemonSessionId, desc);
   let session;
@@ -1844,8 +1972,9 @@ var init_transcript_export = __esm({
 function claudeProjectSlug(cwd) {
   return cwd.replace(/[^a-zA-Z0-9]/g, "-");
 }
-function claudeCodeProjectDir(cwd) {
-  return resolve(homedir(), ".claude", "projects", claudeProjectSlug(cwd));
+function claudeCodeProjectDir(cwd, configDir) {
+  const base = configDir ?? resolve(homedir(), ".claude");
+  return resolve(base, "projects", claudeProjectSlug(cwd));
 }
 function extractFirstText(content) {
   if (typeof content === "string") {
@@ -1906,8 +2035,8 @@ function claudeEntrypointFor(mode) {
   return mode === "native" ? "cli" : "sdk-ts";
 }
 async function discoverClaudeCode(input) {
-  const { cwd, since, until, attachmentMode, expectedId } = input;
-  const dir = claudeCodeProjectDir(cwd);
+  const { cwd, since, until, attachmentMode, configDir, expectedId } = input;
+  const dir = claudeCodeProjectDir(cwd, configDir);
   if (expectedId) {
     const filePath = join(dir, `${expectedId}.jsonl`);
     try {
@@ -1952,9 +2081,9 @@ async function discoverClaudeCode(input) {
   scored.sort((a, b) => b.mtimeMs - a.mtimeMs);
   return scored.map((s) => s.candidate);
 }
-async function readClaudeCode(conversationId, cwd) {
+async function readClaudeCode(conversationId, cwd, configDir) {
   const { exportClaudeCodeSession: exportClaudeCodeSession2 } = await Promise.resolve().then(() => (init_transcript_export(), transcript_export_exports));
-  return exportClaudeCodeSession2(conversationId, cwd);
+  return exportClaudeCodeSession2(conversationId, cwd, configDir);
 }
 async function discoverHermes(input) {
   const { discoverHermesSessions: discoverHermesSessions2 } = await Promise.resolve().then(() => (init_transcript_export(), transcript_export_exports));
@@ -2274,11 +2403,12 @@ var RESUME_STRATEGIES = Object.fromEntries(
       {
         outputHint: store.outputHint,
         storeAs: store.storeAs,
-        fsProbe: async (cwd, prevStartedAt, expectedId) => {
+        fsProbe: async (cwd, prevStartedAt, expectedId, configDir) => {
           const candidates = await s.discover({
             cwd,
             since: prevStartedAt,
-            expectedId
+            expectedId,
+            configDir
           });
           return candidates[0]?.conversationId ?? null;
         },
@@ -2322,7 +2452,10 @@ async function augmentWithFsResume(prev) {
   const id = await strategy.fsProbe(
     prev.cwd,
     prev.startedAt,
-    prev.adapterSessionId
+    prev.adapterSessionId,
+    // A config-dir-isolated session (#824) persisted its transcript under
+    // its own CLAUDE_CONFIG_DIR — probe there, not the global ~/.claude.
+    prev.adapterConfigDir
   );
   if (!id) return prev;
   return {
@@ -4890,109 +5023,9 @@ async function loadSpawnDedupe(loadCfg = loadConfig) {
   }
   return DEFAULT_SPAWN_DEDUPE;
 }
-var MARKER = "@agentproto-bot";
-var fmtTokens = (n) => {
-  if (typeof n !== "number" || !Number.isFinite(n)) return null;
-  return n >= 1e3 ? `${(n / 1e3).toFixed(1)}k` : String(n);
-};
-function cwdLabel(cwd, workspaceSlug) {
-  const leaf = basename(cwd);
-  if (!workspaceSlug || workspaceSlug === leaf) return workspaceSlug ?? leaf;
-  return `${workspaceSlug}/${leaf}`;
-}
-var buildFooter = ({
-  prov,
-  authMode,
-  runId,
-  runUrl,
-  sha,
-  kind = "review"
-}) => {
-  const parts = [`\u{1F916} **${MARKER}** \u2014 ${kind}`];
-  if (prov?.sessionId) {
-    parts.push(`session \`${prov.sessionId}\`${prov.label ? ` (\`${prov.label}\`)` : ""}`);
-  }
-  if (prov?.adapter) parts.push([prov.adapter, authMode].filter(Boolean).join(" / "));
-  else if (!prov?.sessionId) parts.push(`legacy fallback${authMode ? ` (${authMode})` : ""}`);
-  else if (authMode) parts.push(authMode);
-  if (prov?.authProfile) parts.push(`auth-profile \`${prov.authProfile}\``);
-  if (prov?.model) parts.push(`model \`${prov.model}\``);
-  if (prov?.sandboxId) parts.push(`e2b \`${prov.sandboxId}\``);
-  if (prov?.parentSessionId) parts.push(`supervisor \`${prov.parentSessionId}\``);
-  const tin = fmtTokens(prov?.tokensIn);
-  const tout = fmtTokens(prov?.tokensOut);
-  if (tin || tout) parts.push(`${tin ?? "?"} in / ${tout ?? "?"} out`);
-  if (typeof prov?.costUsd === "number") {
-    parts.push(`$${prov.costUsd.toFixed(4)}${prov.source && prov.source !== "adapter" ? ` (${prov.source})` : ""}`);
-  }
-  const showLocalHostCwd = prov?.source === "local" || prov?.source === "daemon" || !runId;
-  if (runId && !showLocalHostCwd) parts.push(`run [${runId}](${runUrl})`);
-  if (showLocalHostCwd) {
-    if (prov?.host) parts.push(`host \`${prov.host}\``);
-    if (prov?.cwd) parts.push(`cwd \`${cwdLabel(prov.cwd, prov.workspaceSlug)}\``);
-  }
-  if (sha) parts.push(`sha \`${sha.slice(0, 7)}\``);
-  return `
-
----
-<sub>${parts.join(" \xB7 ")}</sub>`;
-};
-function sessionFooterProvenance(session, options = {}) {
-  const prov = {
-    sessionId: session.id,
-    label: session.label,
-    adapter: session.harness ?? session.adapterSlug,
-    model: session.model,
-    authProfile: session.accessProfile?.label ?? session.accessProfile?.profileRef,
-    parentSessionId: options.supervisor?.id,
-    costUsd: session.costUsd,
-    tokensIn: session.tokensIn,
-    tokensOut: session.tokensOut,
-    source: options.source ?? "daemon",
-    host: options.host,
-    cwd: session.cwd,
-    workspaceSlug: session.workspaceSlug
-  };
-  return { prov, authMode: session.auth?.mode };
-}
-function buildSessionPrFooter(session, options = {}) {
-  const { prov, authMode } = sessionFooterProvenance(session, options);
-  return buildFooter({ prov, authMode, sha: options.sha, kind: "PR" });
-}
-function appendFooterOnce(body, footer) {
-  if (body.includes(MARKER)) return body;
-  return `${body}${footer}`;
-}
-function parseGhPrCreate(command, args, stdout) {
-  if (basename(command) !== "gh") return null;
-  const positionals = args.filter((a) => !a.startsWith("-"));
-  if (positionals[0] !== "pr" || positionals[1] !== "create") return null;
-  const re = /https?:\/\/\S+?\/pull\/(\d+)/g;
-  let match;
-  let last = null;
-  while ((match = re.exec(stdout)) !== null) {
-    last = { url: match[0], number: Number(match[1]) };
-  }
-  return last;
-}
-function cwdRelated(sessionCwd, cwd) {
-  if (sessionCwd === cwd) return true;
-  const sep2 = "/";
-  return cwd.startsWith(sessionCwd + sep2) || sessionCwd.startsWith(cwd + sep2);
-}
-function pickExecutorSession(sessions, cwd) {
-  const candidates = sessions.filter(
-    (s) => s.kind === "agent-cli" && typeof s.cwd === "string" && cwdRelated(s.cwd, cwd)
-  );
-  if (candidates.length === 0) return void 0;
-  const alive = (s) => s.status === "running" || s.status === "starting";
-  const byRecency = (a, b) => (b.startedAt ?? "").localeCompare(a.startedAt ?? "");
-  const live = candidates.filter(alive).sort(byRecency);
-  if (live.length > 0) return live[0];
-  return [...candidates].sort(byRecency)[0];
-}
 
 // src/gh-provenance-shim.ts
+init_pr_provenance();
 var PROVENANCE_WRAP_GH_ENV = "AGENTPROTO_PROVENANCE_WRAP_GH";
 var DEFAULT_WRAP_GH = false;
 var GH_PROVENANCE_ENABLE_ENV = "AGENTPROTO_GH_PROVENANCE";
@@ -5364,6 +5397,11 @@ async function resolveAccessProfileAuth(input) {
     }
   };
 }
+function shouldInjectDaemonSelfMount(adapter, sandbox) {
+  if (adapter === "hermes") return true;
+  if (adapter === "claude-code") return sandbox === void 0;
+  return false;
+}
 function cleanAgentLines(lines) {
   return lines.map((l) => l.replace(/\x1b\[[0-9;]*m/g, "")).filter((l) => {
     const t = l.trim();
@@ -5634,7 +5672,7 @@ async function spawnAgentSession(deps2, input) {
   const delegationDenied = role.toolPolicy.delegation === "deny";
   let mcpServers = input.mcpServers;
   const mintedSessionId = mintSessionId();
-  if (!mcpServers && input.adapter === "hermes" && daemonMcpUrl) {
+  if (!mcpServers && shouldInjectDaemonSelfMount(input.adapter, input.sandbox) && daemonMcpUrl) {
     let ref = delegationDenied ? `${daemonMcpUrl}${daemonMcpUrl.includes("?") ? "&" : "?"}denyTools=${DELEGATION_TOOL_NAMES.join(",")}` : daemonMcpUrl;
     ref += `${ref.includes("?") ? "&" : "?"}callerSessionId=${encodeURIComponent(mintedSessionId)}`;
     mcpServers = [{ name: "agentproto", transport: "http", ref }];
@@ -7468,11 +7506,13 @@ function listBuckets(root) {
   }
 }
 var serialize = (snapshot) => JSON.stringify(snapshot, null, 2) + "\n";
+var tmpSeq = 0;
+var tmpPathFor = (target) => `${target}.tmp.${process.pid}.${++tmpSeq}`;
 async function writeBucketSnapshot(root, slug, snapshot) {
   const dir = bucketDir(root, slug);
   await promises.mkdir(dir, { recursive: true });
   const target = bucketSessionsFile(root, slug);
-  const tmp = `${target}.tmp.${process.pid}`;
+  const tmp = tmpPathFor(target);
   await promises.writeFile(tmp, serialize(snapshot), "utf8");
   await promises.rename(tmp, target);
 }
@@ -7480,7 +7520,7 @@ function writeBucketSnapshotSync(root, slug, snapshot) {
   const dir = bucketDir(root, slug);
   mkdirSync(dir, { recursive: true });
   const target = bucketSessionsFile(root, slug);
-  const tmp = `${target}.tmp.${process.pid}`;
+  const tmp = tmpPathFor(target);
   writeFileSync(tmp, serialize(snapshot), "utf8");
   renameSync(tmp, target);
 }
@@ -7585,9 +7625,9 @@ async function listClaudeSubagents(projectDir, adapterSessionId) {
   return entries.filter((e) => e.startsWith("agent-") && e.endsWith(".jsonl")).map((e) => join(dir, e)).sort();
 }
 async function resolveNativeLink(input) {
-  const { cwd, adapterSlug, adapterSessionId } = input;
+  const { cwd, adapterSlug, adapterSessionId, adapterConfigDir } = input;
   if (adapterSlug === "claude-code") {
-    const dir = claudeCodeProjectDir(cwd);
+    const dir = claudeCodeProjectDir(cwd, adapterConfigDir);
     const path = join(dir, `${adapterSessionId}.jsonl`);
     const subagents = await listClaudeSubagents(dir, adapterSessionId);
     return { kind: "claude-jsonl", path, subagents };
@@ -7937,6 +7977,21 @@ function formatAccessForSpawn(desc) {
   if (!desc.accessProfile?.profileRef) return void 0;
   return { profileRef: desc.accessProfile.profileRef };
 }
+function stripOwnCallerStamp(servers, prevId) {
+  if (!servers) return servers;
+  return servers.map((entry) => {
+    if (entry.transport !== "http" || typeof entry.ref !== "string") return entry;
+    let url;
+    try {
+      url = new URL(entry.ref);
+    } catch {
+      return entry;
+    }
+    if (url.searchParams.get("callerSessionId") !== prevId) return entry;
+    url.searchParams.delete("callerSessionId");
+    return { ...entry, ref: url.toString() };
+  });
+}
 function formatPostureForSpawn(desc) {
   return desc.posture;
 }
@@ -7966,7 +8021,7 @@ async function continueAgentSessionFresh(deps2, prev, opts = {}) {
     access: formatAccessForSpawn(prev),
     posture: formatPostureForSpawn(prev),
     contextProfile: prev.contextProfile,
-    mcpServers: prev.mcpServers,
+    mcpServers: stripOwnCallerStamp(prev.mcpServers, prev.id),
     label: prev.label ? `${prev.label} (continued)` : void 0,
     title: prev.title ? `${prev.title} (continued)` : void 0,
     contextContinuity: opts.contextContinuity ?? prev.contextContinuity,
@@ -8175,6 +8230,14 @@ function stampProcessAlive(desc) {
     desc.processAlive = false;
   }
 }
+function killChildIfSpawned(child, signal) {
+  if (!child) return;
+  if (typeof child.pid !== "number" || child.pid <= 0) return;
+  try {
+    child.kill(signal);
+  } catch {
+  }
+}
 function stampInterrupted(desc) {
   if (desc.killedMidTurn === true && desc.endedReason === "daemon-restart") {
     desc.interrupted = true;
@@ -8544,7 +8607,14 @@ function createSessionsRegistry(opts) {
     if (!adapterSlug || !adapterSessionId || !cwd) return;
     void (async () => {
       try {
-        const native = await resolveNativeLink({ cwd, adapterSlug, adapterSessionId });
+        const native = await resolveNativeLink({
+          cwd,
+          adapterSlug,
+          adapterSessionId,
+          // Config-dir-isolated session (#824): the native transcript lives
+          // under the session's own CLAUDE_CONFIG_DIR, not ~/.claude.
+          ...desc.adapterConfigDir ? { adapterConfigDir: desc.adapterConfigDir } : {}
+        });
         const registered = readRegisteredSlugs(workspacesConfigPath);
         const slug = resolveBucketSlug(desc.workspaceSlug, registered);
         const record2 = {
@@ -8553,6 +8623,7 @@ function createSessionsRegistry(opts) {
           cwd,
           adapterSlug,
           adapterSessionId,
+          ...desc.adapterConfigDir ? { adapterConfigDir: desc.adapterConfigDir } : {},
           ...native ? { native } : {},
           agentprotoTranscript: sessionEventsPath(desc.id, transcriptBaseDir),
           ...desc.title ? { title: desc.title } : {},
@@ -8568,7 +8639,7 @@ function createSessionsRegistry(opts) {
     })();
   };
   const schedulePersist = () => {
-    if (!persist) return;
+    if (!persist || shutdownDone) return;
     if (persistTimer) clearTimeout(persistTimer);
     persistTimer = setTimeout(() => {
       void persistSnapshot();
@@ -8604,11 +8675,13 @@ function createSessionsRegistry(opts) {
     rows,
     heldIdsByBucket.get(slug) ?? EMPTY_ID_SET
   );
-  const persistSnapshot = async () => {
+  const persistOnce = async () => {
     try {
+      if (shutdownDone) return;
       const savedAt = (/* @__PURE__ */ new Date()).toISOString();
       if (partitioned) {
         for (const [slug, rows] of groupRowsByBucket()) {
+          if (shutdownDone) return;
           await writeBucketSnapshot(bucketsRoot, slug, {
             savedAt,
             sessions: rowsToWrite(slug, rows)
@@ -8625,6 +8698,24 @@ function createSessionsRegistry(opts) {
       );
     }
   };
+  let persistRunning = false;
+  let persistRerun = false;
+  const persistSnapshot = async () => {
+    if (shutdownDone) return;
+    if (persistRunning) {
+      persistRerun = true;
+      return;
+    }
+    persistRunning = true;
+    try {
+      do {
+        persistRerun = false;
+        await persistOnce();
+      } while (persistRerun && !shutdownDone);
+    } finally {
+      persistRunning = false;
+    }
+  };
   const appendLine = (rt, line, stream) => {
     rt.recentLines.push(line);
     if (rt.recentLines.length > RECENT_LINES_CAP) {
@@ -10524,7 +10615,7 @@ ${message}`;
         }
         void terminalTranscriptWriter.close(rt.desc.id);
       }
-      rt.child?.kill(signal);
+      killChildIfSpawned(rt.child, signal);
       if (rt.browserStop) {
         void rt.browserStop().catch(() => void 0);
       }
@@ -10549,7 +10640,7 @@ ${message}`;
         tracedSessions.delete(rt.desc.id);
         rt.agentSession = void 0;
       }
-      rt.child?.kill("SIGTERM");
+      killChildIfSpawned(rt.child, "SIGTERM");
       schedulePersist();
       const banner = "\u2500\u2500 reaped after being idle past the threshold; the adapter process was freed. Re-prompt to resume this session in place. \u2500\u2500";
       appendLine(rt, banner, "stdout");
@@ -10830,7 +10921,7 @@ ${message}`;
           } catch {
           }
         }
-        rt.child?.kill("SIGTERM");
+        killChildIfSpawned(rt.child, "SIGTERM");
         emitExited(rt);
       }
     }
@@ -10876,9 +10967,17 @@ function loadHistorySnapshot(persistPath, sessions, sessionEvents, bucketSlug, s
   try {
     parsed = JSON.parse(raw);
   } catch {
-    console.warn(
-      `[sessions] history file ${persistPath} is malformed \u2014 ignoring`
-    );
+    const quarantine = `${persistPath}.corrupt-${Date.now()}`;
+    try {
+      renameSync(persistPath, quarantine);
+      console.warn(
+        `[sessions] history file ${persistPath} is malformed \u2014 quarantined to ${quarantine} and starting this bucket empty`
+      );
+    } catch {
+      console.warn(
+        `[sessions] history file ${persistPath} is malformed and could not be quarantined \u2014 ignoring`
+      );
+    }
     return;
   }
   if (!Array.isArray(parsed.sessions)) return;
@@ -10939,6 +11038,9 @@ function quoteArg(arg) {
   if (/^[a-zA-Z0-9._/=:@,+-]+$/.test(arg)) return arg;
   return `"${arg.replace(/(["\\$`])/g, "\\$1")}"`;
 }
+
+// src/pr-provenance-stamp.ts
+init_pr_provenance();
 async function stampPrProvenance(input) {
   try {
     if (input.exitCode !== 0) return { stamped: false, reason: "command failed" };
@@ -10972,19 +11074,19 @@ async function stampFooterOnPr(input) {
     const view = await run(["pr", "view", input.prUrl, "--json", "body", "--jq", ".body"], input.cwd);
     if (view.exitCode !== 0) return { stamped: false, reason: `gh pr view exit ${view.exitCode}` };
     const body = view.stdout.replace(/\n+$/, "");
-    const alreadyStamped = body.includes(MARKER);
+    const alreadyStamped = hasProvenanceFooter(body);
     if (!alreadyStamped) {
       const newBody = appendFooterOnce(body, footer);
       const edit = await run(["pr", "edit", input.prUrl, "--body", newBody], input.cwd);
       if (edit.exitCode !== 0) {
         return { stamped: false, reason: `gh pr edit exit ${edit.exitCode}` };
       }
+      input.registry.recordOpenedPr(input.session.id, {
+        adapter: input.session.harness ?? input.session.adapterSlug ?? "gh",
+        number: input.prNumber,
+        url: input.prUrl
+      });
     }
-    input.registry.recordOpenedPr(input.session.id, {
-      adapter: input.session.harness ?? input.session.adapterSlug ?? "gh",
-      number: input.prNumber,
-      url: input.prUrl
-    });
     return {
       stamped: true,
       url: input.prUrl,
@@ -13719,7 +13821,10 @@ async function resolveConversationId(desc) {
     // A live/ongoing session has no endedAt yet and must keep matching
     // with no upper bound — only a dead session's endedAt narrows.
     ...desc.endedAt ? { until: desc.endedAt } : {},
-    ...attachmentMode ? { attachmentMode } : {}
+    ...attachmentMode ? { attachmentMode } : {},
+    // A config-dir-isolated session's store lives under its own
+    // CLAUDE_CONFIG_DIR (#824), not the provider's global dir.
+    ...desc.adapterConfigDir ? { configDir: desc.adapterConfigDir } : {}
   });
   if (candidates.length === 0) {
     return {
@@ -13778,7 +13883,7 @@ async function readConversation(registry, input) {
     });
   }
   try {
-    const session = await store.read(resolved.conversationId, desc.cwd);
+    const session = await store.read(resolved.conversationId, desc.cwd, desc.adapterConfigDir);
     const content = format === "json" ? renderJson(session) : renderMarkdown(session);
     return {
       conversation: session,
@@ -16006,7 +16111,7 @@ function registerBrainTools(server, opts) {
   );
   server.tool(
     "workspace_brain_status",
-    "Report how current a workspace's brain is: how many sessions are indexed, how many known-but-pending remain, total bytes, and whether the index is query-ready. Resolves the workspace as the explicit `workspace` argument, else the calling session's own workspace.",
+    "Report how current a workspace's brain is: how many sessions are indexed, how many known-but-pending remain, how many were skipped as permanently unavailable (no transcript ever reachable \u2014 bash PTYs, GC'd transcripts; retry one explicitly with `workspace_brain_ingest`'s `sessionId`), total bytes, and whether the index is query-ready. Resolves the workspace as the explicit `workspace` argument, else the calling session's own workspace.",
     {
       workspace: z.string().optional().describe("Workspace slug. Omit to use the calling session's workspace.")
     },
@@ -16088,7 +16193,7 @@ async function readSessionForBrain(sessionId) {
     const store = CONVERSATION_STORES[record2.adapterSlug];
     if (store) {
       try {
-        const exported = await store.read(record2.adapterSessionId, record2.cwd);
+        const exported = await store.read(record2.adapterSessionId, record2.cwd, record2.adapterConfigDir);
         if (exported?.messages?.length) return exported;
       } catch {
       }
@@ -19411,9 +19516,11 @@ ${panelBridgeScript("agentproto-live-session")}
 // ============================================================
 // INLINED REDUCER COPY \u2014 hand-kept mirror of live-session-app.logic.ts.
 // Plain JS, same semantics: coalesce consecutive text-delta of the same
-// session, pair tool-call/tool-result by toolCallId, pass through
-// turn-end/usage_update, ignore unknown kinds. Keep in sync with the
-// TS module; the TS module is the one the test suite imports.
+// session (and rejoin an unterminated mid-line fragment split by an
+// interleaved record \u2014 see the TS module's text-delta arm), pair
+// tool-call/tool-result by toolCallId, pass through turn-end/usage_update,
+// ignore unknown kinds. Keep in sync with the TS module; the TS module is
+// the one the test suite imports.
 // ============================================================
 
 function initialTimelineState() {
@@ -19424,22 +19531,50 @@ function rowId(record, rows) {
   return record.seq != null ? (record.kind + '-' + record.seq) : (record.kind + '-' + rows.length);
 }
 
+// Fold a text-delta record into an existing row (fresh object), keeping the
+// row's "partial" hint in step with the latest record \u2014 see mergeTextDelta in
+// the TS module.
+function mergeTextDelta(row, record) {
+  var merged = Object.assign({}, row, {
+    text: row.text + (record.text || ''),
+    seq: record.seq,
+    ts: record.ts,
+  });
+  if (record.partial === true) merged.partial = true;
+  else delete merged.partial;
+  return merged;
+}
+
 function reduceEvent(state, record) {
   switch (record.kind) {
     case 'text-delta': {
       var last = state.rows[state.rows.length - 1];
       if (last && last.kind === 'text' && last.sessionId === record.sessionId) {
-        var merged = Object.assign({}, last, {
-          text: last.text + (record.text || ''),
-          seq: record.seq,
-          ts: record.ts,
-        });
-        return { rows: state.rows.slice(0, -1).concat([merged]) };
+        return { rows: state.rows.slice(0, -1).concat([mergeTextDelta(last, record)]) };
+      }
+      // Debounce can flush an unterminated mid-word fragment, let a tool-call
+      // land, then flush the continuation. Terminated lines carry their
+      // trailing newline (transcript-writer contract) \u2014 look back within the
+      // same turn (bounded by this session's last turn-end) for that
+      // session's most recent text row; if unterminated (or flagged
+      // partial), continue it in place instead of splitting the sentence.
+      for (var i = state.rows.length - 1; i >= 0; i--) {
+        var prior = state.rows[i];
+        if (prior.sessionId !== record.sessionId) continue;
+        if (prior.kind === 'turn-end') break;
+        if (prior.kind !== 'text') continue;
+        if (prior.partial === true || !prior.text.endsWith('\\n')) {
+          var patched = state.rows.slice();
+          patched[i] = mergeTextDelta(prior, record);
+          return { rows: patched };
+        }
+        break;
       }
       var row = {
         kind: 'text', id: rowId(record, state.rows), seq: record.seq, ts: record.ts,
         sessionId: record.sessionId, text: record.text || '',
       };
+      if (record.partial === true) row.partial = true;
       return { rows: state.rows.concat([row]) };
     }
     case 'tool-call': {
@@ -24384,6 +24519,7 @@ async function startHttpServer(opts) {
         // node+entry pair launchd (or the shell) exec'd. Lifecycle tooling
         // (`agentproto daemon start/stop/status`) reports these.
         version: opts.meta.version ?? null,
+        build: opts.meta.build ?? null,
         pid: process.pid,
         node: process.execPath,
         entry: process.argv[1] ?? null,
@@ -30148,25 +30284,38 @@ function createPrProvenanceReconciler(opts) {
       if (last !== void 0 && Date.now() - last < POLL_THROTTLE_MS) return;
       lastPollAt.set(sessionId, Date.now());
     }
+    const shouldStamp = (url) => {
+      if (stampedPrUrls.has(url)) return false;
+      if (desc.openedPrs && desc.openedPrs.some((recorded) => recorded.url === url)) {
+        stampedPrUrls.add(url);
+        return false;
+      }
+      return true;
+    };
+    const supervisor = desc.parentSessionId != null ? opts.registry.get(desc.parentSessionId) ?? { id: desc.parentSessionId } : null;
+    const stamp = async (pr2) => {
+      const outcome = await stampFooterOnPr({
+        registry: opts.registry,
+        session: desc,
+        supervisor,
+        prNumber: pr2.number,
+        prUrl: pr2.url,
+        cwd,
+        ...opts.run ? { run: opts.run } : {},
+        ...opts.host ? { host: opts.host } : {}
+      });
+      if (outcome.stamped) stampedPrUrls.add(pr2.url);
+    };
+    const records = await (opts.listToolCalls ?? readToolCallRecords)(sessionId);
+    for (const record2 of records) {
+      if (!record2.createdPrUrl || record2.createdPrNumber === void 0) continue;
+      if (!shouldStamp(record2.createdPrUrl)) continue;
+      await stamp({ number: record2.createdPrNumber, url: record2.createdPrUrl });
+    }
     const pr = await opts.resolveOpenPr(cwd);
     if (!pr) return;
-    if (stampedPrUrls.has(pr.url)) return;
-    if (desc.openedPrs && desc.openedPrs.some((recorded) => recorded.url === pr.url)) {
-      stampedPrUrls.add(pr.url);
-      return;
-    }
-    const supervisor = desc.parentSessionId != null ? opts.registry.get(desc.parentSessionId) ?? { id: desc.parentSessionId } : null;
-    const outcome = await stampFooterOnPr({
-      registry: opts.registry,
-      session: desc,
-      supervisor,
-      prNumber: pr.number,
-      prUrl: pr.url,
-      cwd,
-      ...opts.run ? { run: opts.run } : {},
-      ...opts.host ? { host: opts.host } : {}
-    });
-    if (outcome.stamped) stampedPrUrls.add(pr.url);
+    if (!shouldStamp(pr.url)) return;
+    await stamp(pr);
   };
   const safeReconcile = (sessionId, terminal) => {
     void reconcile(sessionId, terminal).catch(() => {
@@ -32424,7 +32573,9 @@ function registerDaemonHealthTools(server, opts) {
         idleReapAfterMs: opts.idleReapAfterMs,
         crashDetectIntervalMs: opts.crashDetectIntervalMs ?? 0,
         restartSweepIntervalMs: opts.restartSweepIntervalMs ?? 0,
-        turnStallAfterMs: opts.turnStallAfterMs ?? 0
+        turnStallAfterMs: opts.turnStallAfterMs ?? 0,
+        version: opts.version ?? null,
+        build: opts.build ?? null
       });
     }
   );
@@ -34930,7 +35081,9 @@ async function createGateway(opts) {
       idleReapAfterMs,
       crashDetectIntervalMs,
       restartSweepIntervalMs,
-      turnStallAfterMs
+      turnStallAfterMs,
+      ...opts.version ? { version: opts.version } : {},
+      ...opts.build ? { build: opts.build } : {}
     });
     registerCommandTools(server, {
       workspace,
@@ -35234,6 +35387,7 @@ async function createGateway(opts) {
       registered,
       startedAt,
       ...opts.version ? { version: opts.version } : {},
+      ...opts.build ? { build: opts.build } : {},
       resumeSessionsOnBoot: opts.resumeSessionsOnBoot === true,
       idleReapAfterMs,
       crashDetectIntervalMs,