automata-cli 0.1.0-feature-030-do-work.198 → 0.1.0-feature-030-do-work.202

package/dist/{ConfigWizard-NTK7NLAE.js → ConfigWizard-26Y5YBF7.js}

@@ -252,7 +252,8 @@ function ConfigWizard() {
     "do-work-max-runs": {
       setValue: setDoWorkMaxRuns,
       onSubmit: () => {
-        const parsedMaxRuns = Number.parseInt(doWorkMaxRuns, 10);
+        const trimmedMaxRuns = doWorkMaxRuns.trim();
+        const parsedMaxRuns = /^\d+$/.test(trimmedMaxRuns) ? Number(trimmedMaxRuns) : Number.NaN;
         const current = readRawConfig();
         writeConfig({
           ...current,
@@ -264,7 +265,7 @@ function ConfigWizard() {
               claude: doWorkClaudeModel.trim() || void 0,
               codex: doWorkCodexModel.trim() || void 0
             },
-            maxRunsPerTick: Number.isNaN(parsedMaxRuns) || parsedMaxRuns < 0 ? void 0 : parsedMaxRuns
+            maxRunsPerTick: Number.isSafeInteger(parsedMaxRuns) && parsedMaxRuns >= 0 ? parsedMaxRuns : void 0
           }
         });
         exit();

package/dist/index.js

@@ -183,7 +183,7 @@ var configCommand = new Command("config").description("Configure automata settin
   const [{ render }, React, { ConfigWizard }] = await Promise.all([
     import("ink"),
     import("react"),
-    import("./ConfigWizard-NTK7NLAE.js")
+    import("./ConfigWizard-26Y5YBF7.js")
   ]);
   const { waitUntilExit } = render(React.createElement(ConfigWizard));
   await waitUntilExit();
@@ -693,8 +693,12 @@ function isUpstreamGone(branch) {
   const { status } = run2("git", ["ls-remote", "--exit-code", "--heads", "origin", branch]);
   return status !== 0;
 }
-function hasUncommittedChanges() {
-  const { stdout } = run2("git", ["status", "--porcelain"]);
+function hasUncommittedChanges(excludePaths = []) {
+  const args = ["status", "--porcelain"];
+  if (excludePaths.length > 0) {
+    args.push("--", ".", ...excludePaths.map((path) => `:(exclude)${path}`));
+  }
+  const { stdout } = run2("git", args);
   return stdout.trim().length > 0;
 }
 function checkoutAndPull(targetBranch) {
@@ -1517,26 +1521,16 @@ function handleExitCode(status, toolName) {
   }
 }
 
-// src/claude/claudeService.ts
-function resolveCommand(name) {
-  const pathDirs = (process.env["PATH"] ?? "").split(delimiter);
-  for (const dir of pathDirs) {
-    const candidate = join(dir, name);
-    if (existsSync(candidate)) return candidate;
-  }
-  return name;
+// src/cli/childRegistry.ts
+var active = /* @__PURE__ */ new Set();
+function trackChild(child) {
+  active.add(child);
 }
-function buildClaudeArgs(prompt, options = {}) {
-  const args = [];
-  if (options.yolo) args.push("--dangerously-skip-permissions");
-  if (options.model) args.push("--model", options.model);
-  if (options.verbose) args.push("--verbose", "--output-format", "stream-json");
-  args.push("-p", prompt);
-  return args;
+function untrackChild(child) {
+  active.delete(child);
 }
-var activeChildren = /* @__PURE__ */ new Set();
-function terminateActiveClaudeProcesses(timeoutMs = 1e4) {
-  const children = [...activeChildren];
+function terminateTrackedChildren(timeoutMs = 1e4) {
+  const children = [...active];
   if (children.length === 0) return Promise.resolve();
   const exits = children.map(
     (child) => new Promise((resolve2) => {
@@ -1559,6 +1553,62 @@ function terminateActiveClaudeProcesses(timeoutMs = 1e4) {
     })
   ]);
 }
+
+// src/claude/claudeService.ts
+function resolveCommand(name) {
+  const pathDirs = (process.env["PATH"] ?? "").split(delimiter);
+  for (const dir of pathDirs) {
+    const candidate = join(dir, name);
+    if (existsSync(candidate)) return candidate;
+  }
+  return name;
+}
+function buildClaudeArgs(prompt, options = {}) {
+  const args = [];
+  if (options.yolo) args.push("--dangerously-skip-permissions");
+  if (options.model) args.push("--model", options.model);
+  if (options.verbose) args.push("--verbose", "--output-format", "stream-json");
+  args.push("-p", prompt);
+  return args;
+}
+function runClaude(prompt, options = {}) {
+  return new Promise((resolve2, reject) => {
+    const claudeBin = resolveCommand("claude");
+    const args = buildClaudeArgs(prompt, { yolo: true, model: options.model, verbose: true });
+    const child = spawn(claudeBin, args, { stdio: ["inherit", "pipe", "inherit"] });
+    trackChild(child);
+    const rl = createInterface({ input: child.stdout });
+    let turnCount = 0;
+    rl.on("line", (line) => {
+      if (options.printSteps !== true) return;
+      try {
+        const event = JSON.parse(line);
+        formatEvent(event, turnCount);
+        if (event["type"] === "assistant") turnCount++;
+      } catch {
+      }
+    });
+    child.on("error", (err) => {
+      untrackChild(child);
+      const nodeErr = err;
+      reject(
+        nodeErr.code === "ENOENT" ? new Error("`claude` CLI is not installed or not on PATH.") : new Error(nodeErr.message)
+      );
+    });
+    child.on("close", (code, signal) => {
+      untrackChild(child);
+      if (code === 0) {
+        resolve2();
+        return;
+      }
+      reject(
+        new Error(
+          signal === null ? `Claude Code exited with code ${String(code)}.` : `Claude Code terminated on ${signal}.`
+        )
+      );
+    });
+  });
+}
 function invokeClaudeCode(prompt, options = {}) {
   if (options.verbose) {
     return invokeClaudeCodeVerbose(prompt, options.yolo ?? false, options.model);
@@ -1577,7 +1627,6 @@ function invokeClaudeCodeVerbose(prompt, yolo, model) {
     const claudeBin = resolveCommand("claude");
     const args = buildClaudeArgs(prompt, { yolo, model, verbose: true });
     const child = spawn(claudeBin, args, { stdio: ["inherit", "pipe", "inherit"] });
-    activeChildren.add(child);
     const rl = createInterface({ input: child.stdout });
     let turnCount = 0;
     child.on("error", (err) => {
@@ -1592,7 +1641,6 @@ function invokeClaudeCodeVerbose(prompt, yolo, model) {
       }
     });
     child.on("close", (code) => {
-      activeChildren.delete(child);
       handleExitCode(code, "Claude Code");
       resolve2();
     });
@@ -1663,7 +1711,7 @@ function summarizeTool(name, input) {
 }
 
 // src/codex/codexService.ts
-import { spawnSync as spawnSync5 } from "child_process";
+import { spawn as spawn2, spawnSync as spawnSync5 } from "child_process";
 function buildCodexArgs(prompt, options = {}) {
   const args = ["exec"];
   if (options.yolo) args.push("--dangerously-bypass-approvals-and-sandbox");
@@ -1684,6 +1732,33 @@ function invokeCodexCodeSync(prompt, yolo, model) {
   handleSpawnError(result.error, "codex");
   handleExitCode(result.status, "Codex");
 }
+function runCodex(prompt, options = {}) {
+  return new Promise((resolve2, reject) => {
+    const codexBin = resolveCommand("codex");
+    const args = buildCodexArgs(prompt, { yolo: true, model: options.model });
+    const child = spawn2(codexBin, args, { stdio: "inherit" });
+    trackChild(child);
+    child.on("error", (err) => {
+      untrackChild(child);
+      const nodeErr = err;
+      reject(
+        nodeErr.code === "ENOENT" ? new Error("`codex` CLI is not installed or not on PATH.") : new Error(nodeErr.message)
+      );
+    });
+    child.on("close", (code, signal) => {
+      untrackChild(child);
+      if (code === 0) {
+        resolve2();
+        return;
+      }
+      reject(
+        new Error(
+          signal === null ? `Codex exited with code ${String(code)}.` : `Codex terminated on ${signal}.`
+        )
+      );
+    });
+  });
+}
 
 // src/commands/getReady.ts
 function writeOverflowHint(output, issues, limit) {
@@ -2314,7 +2389,7 @@ function getIssueSurface(issueNumber) {
       "view",
       String(issueNumber),
       "--json",
-      "number,title,body,url,state,author,createdAt,assignees,comments"
+      "number,title,body,url,state,author,createdAt,assignees,labels,comments"
     ],
     `read issue #${String(issueNumber)}`
   );
@@ -2336,6 +2411,7 @@ function getIssueSurface(issueNumber) {
     issue: { number: raw.number, title: raw.title, body: raw.body, url: raw.url },
     state: raw.state === "CLOSED" ? "CLOSED" : "OPEN",
     assignees: (raw.assignees ?? []).map(login).filter((name) => name.length > 0),
+    labels: (raw.labels ?? []).map((label) => label.name ?? "").filter((name) => name.length > 0),
     messages
   };
 }
@@ -2366,9 +2442,8 @@ function indexPullRequest(map, node) {
     updatedAt: node.updatedAt
   };
   if (node.closingIssuesReferences.pageInfo?.hasNextPage) {
-    process.stderr.write(
-      `Warning: pull request #${String(node.number)} closes more than 50 issues; some links were not read.
-`
+    throw new Error(
+      `Pull request #${String(node.number)} closes more than 50 issues, so the issue-to-pull-request map cannot be read completely. Refusing the tick rather than risk starting work on an issue that already has a pull request.`
     );
   }
   for (const issue of node.closingIssuesReferences.nodes) {
@@ -2397,17 +2472,16 @@ function getOpenPrLinkMap() {
     }
     cursor = connection.pageInfo.endCursor;
   }
-  process.stderr.write(
-    `Warning: stopped paginating open pull requests after ${String(MAX_LINK_MAP_PAGES)} pages; the issue-to-pull-request map may be incomplete.
-`
+  throw new Error(
+    `Stopped paginating open pull requests after ${String(MAX_LINK_MAP_PAGES)} pages, so the issue-to-pull-request map cannot be trusted. Refusing the tick rather than risk starting work on an issue that already has a pull request.`
   );
-  return map;
 }
 var REVIEW_THREADS_QUERY2 = `
-query($owner:String!,$repo:String!,$prNumber:Int!){
+query($owner:String!,$repo:String!,$prNumber:Int!,$cursor:String){
   repository(owner:$owner,name:$repo){
     pullRequest(number:$prNumber){
-      reviewThreads(first:100){
+      reviewThreads(first:100, after:$cursor){
+        pageInfo{ hasNextPage endCursor }
         nodes{
           isResolved isOutdated path line
           comments(last:100){
@@ -2418,11 +2492,57 @@ query($owner:String!,$repo:String!,$prNumber:Int!){
     }
   }
 }`.trim();
+var MAX_THREAD_PAGES = 50;
 function normalizePrState(state) {
   if (state === "MERGED") return "MERGED";
   if (state === "CLOSED") return "CLOSED";
   return "OPEN";
 }
+function getReviewThreads(prNumber) {
+  const { owner, repo } = getRepoSlug();
+  const threads = [];
+  let cursor = null;
+  for (let page = 0; page < MAX_THREAD_PAGES; page++) {
+    const args = [
+      "api",
+      "graphql",
+      "-f",
+      `query=${REVIEW_THREADS_QUERY2}`,
+      "-f",
+      `owner=${owner}`,
+      "-f",
+      `repo=${repo}`,
+      "-F",
+      `prNumber=${String(prNumber)}`
+    ];
+    if (cursor !== null) args.push("-f", `cursor=${cursor}`);
+    const response = ghJson(
+      args,
+      `query review threads for pull request #${String(prNumber)}`
+    );
+    const connection = response.data.repository.pullRequest.reviewThreads;
+    for (const node of connection.nodes) {
+      threads.push({
+        path: node.path,
+        line: node.line ?? null,
+        isResolved: node.isResolved,
+        comments: node.comments.nodes.map((comment) => ({
+          kind: "thread-comment",
+          author: login(comment.author),
+          body: comment.body,
+          createdAt: comment.createdAt
+        })).sort(byCreatedAt2)
+      });
+    }
+    if (!connection.pageInfo?.hasNextPage || connection.pageInfo.endCursor === null) {
+      return threads;
+    }
+    cursor = connection.pageInfo.endCursor;
+  }
+  throw new Error(
+    `Stopped paginating review threads for pull request #${String(prNumber)} after ${String(MAX_THREAD_PAGES)} pages; refusing rather than answering only part of the feedback.`
+  );
+}
 function getPrSurface(prNumber) {
   const raw = ghJson(
     [
@@ -2450,35 +2570,7 @@ function getPrSurface(prNumber) {
       createdAt: review.submittedAt ?? review.createdAt ?? ""
     }))
   ].sort(byCreatedAt2);
-  const { owner, repo } = getRepoSlug();
-  const threadsResponse = ghJson(
-    [
-      "api",
-      "graphql",
-      "-f",
-      `query=${REVIEW_THREADS_QUERY2}`,
-      "-f",
-      `owner=${owner}`,
-      "-f",
-      `repo=${repo}`,
-      "-F",
-      `prNumber=${String(prNumber)}`
-    ],
-    `query review threads for pull request #${String(prNumber)}`
-  );
-  const threads = threadsResponse.data.repository.pullRequest.reviewThreads.nodes.map(
-    (node) => ({
-      path: node.path,
-      line: node.line ?? null,
-      isResolved: node.isResolved,
-      comments: node.comments.nodes.map((comment) => ({
-        kind: "thread-comment",
-        author: login(comment.author),
-        body: comment.body,
-        createdAt: comment.createdAt
-      })).sort(byCreatedAt2)
-    })
-  );
+  const threads = getReviewThreads(prNumber);
   const state = normalizePrState(raw.state);
   return {
     pr: {
@@ -2731,54 +2823,14 @@ function composePrompt(input) {
   return lines.join("\n");
 }
 
-// src/git/workspaceService.ts
-function dirtyTree() {
-  return {
-    ok: false,
-    reason: "dirty-tree",
-    detail: "the working tree has uncommitted changes; commit or stash them yourself and re-run"
-  };
-}
-function prepareBaseBranch(baseBranch) {
-  if (hasUncommittedChanges()) return dirtyTree();
-  const checkout = checkoutBranch(baseBranch);
-  if (!checkout.ok) {
-    return { ok: false, reason: "checkout-failed", detail: checkout.stderr };
-  }
-  const pull = pullFastForwardOnly();
-  if (!pull.ok) {
-    return { ok: false, reason: "pull-failed", detail: pull.stderr };
-  }
-  return { ok: true, branch: baseBranch };
-}
-function preparePrBranch(headRefName) {
-  if (hasUncommittedChanges()) return dirtyTree();
-  const fetched = fetchBranch(headRefName);
-  if (!fetched.ok) {
-    return { ok: false, reason: "checkout-failed", detail: fetched.stderr };
-  }
-  const checkout = checkoutBranch(headRefName);
-  if (!checkout.ok) {
-    const created = createTrackingBranch(headRefName);
-    if (!created.ok) {
-      return { ok: false, reason: "checkout-failed", detail: created.stderr };
-    }
-    return { ok: true, branch: headRefName };
-  }
-  const pull = pullFastForwardOnly(headRefName);
-  if (!pull.ok) {
-    return { ok: false, reason: "pull-failed", detail: pull.stderr };
-  }
-  return { ok: true, branch: headRefName };
-}
-
 // src/run/runLock.ts
-import { writeFileSync, readFileSync as readFileSync3, unlinkSync, mkdirSync } from "fs";
+import { writeFileSync, readFileSync as readFileSync3, unlinkSync, mkdirSync, renameSync } from "fs";
 import { randomUUID } from "crypto";
 import { hostname } from "os";
 import { join as join2 } from "path";
 var LOCK_DIR = ".automata";
 var LOCK_FILE = "automata.lock";
+var RUN_LOCK_RELATIVE_PATH = `${LOCK_DIR}/${LOCK_FILE}`;
 function lockPath() {
   return join2(process.cwd(), LOCK_DIR, LOCK_FILE);
 }
@@ -2831,7 +2883,7 @@ function makeHandle(path, token) {
     }
   };
 }
-function write(path, command, token) {
+function write(path, command, token, flag = "wx") {
   const owner = {
     pid: process.pid,
     startedAt: (/* @__PURE__ */ new Date()).toISOString(),
@@ -2839,7 +2891,7 @@ function write(path, command, token) {
     command,
     token
   };
-  writeFileSync(path, JSON.stringify(owner, null, 2) + "\n", { encoding: "utf8", flag: "wx" });
+  writeFileSync(path, JSON.stringify(owner, null, 2) + "\n", { encoding: "utf8", flag });
 }
 function acquireRunLock(command, staleMinutes) {
   const path = lockPath();
@@ -2855,27 +2907,73 @@ function acquireRunLock(command, staleMinutes) {
   if (!isStale(owner, staleMinutes)) {
     return { ok: false, heldBy: owner };
   }
+  return reclaim(path, command, token);
+}
+var UNKNOWN_OWNER = {
+  pid: 0,
+  startedAt: "unknown",
+  host: "unknown",
+  command: "unknown",
+  token: ""
+};
+function reclaim(path, command, token) {
+  const candidate = `${path}.${token}`;
   try {
-    unlinkSync(path);
-  } catch {
+    write(candidate, command, token, "w");
+    renameSync(candidate, path);
+  } catch (err) {
+    try {
+      unlinkSync(candidate);
+    } catch {
+    }
+    throw err;
   }
-  try {
-    write(path, command, token);
+  const winner = readOwner(path);
+  if (winner !== null && winner.token === token) {
     return { ok: true, handle: makeHandle(path, token) };
-  } catch (err) {
-    if (err.code !== "EEXIST") throw err;
-    const winner = readOwner(path);
-    return {
-      ok: false,
-      heldBy: winner ?? {
-        pid: 0,
-        startedAt: (/* @__PURE__ */ new Date()).toISOString(),
-        host: "unknown",
-        command: "unknown",
-        token: ""
-      }
-    };
   }
+  return { ok: false, heldBy: winner ?? UNKNOWN_OWNER };
+}
+
+// src/git/workspaceService.ts
+function dirtyTree() {
+  return {
+    ok: false,
+    reason: "dirty-tree",
+    detail: "the working tree has uncommitted changes; commit or stash them yourself and re-run"
+  };
+}
+function prepareBaseBranch(baseBranch) {
+  if (hasUncommittedChanges([RUN_LOCK_RELATIVE_PATH])) return dirtyTree();
+  const checkout = checkoutBranch(baseBranch);
+  if (!checkout.ok) {
+    return { ok: false, reason: "checkout-failed", detail: checkout.stderr };
+  }
+  const pull = pullFastForwardOnly();
+  if (!pull.ok) {
+    return { ok: false, reason: "pull-failed", detail: pull.stderr };
+  }
+  return { ok: true, branch: baseBranch };
+}
+function preparePrBranch(headRefName) {
+  if (hasUncommittedChanges([RUN_LOCK_RELATIVE_PATH])) return dirtyTree();
+  const fetched = fetchBranch(headRefName);
+  if (!fetched.ok) {
+    return { ok: false, reason: "checkout-failed", detail: fetched.stderr };
+  }
+  const checkout = checkoutBranch(headRefName);
+  if (!checkout.ok) {
+    const created = createTrackingBranch(headRefName);
+    if (!created.ok) {
+      return { ok: false, reason: "checkout-failed", detail: created.stderr };
+    }
+    return { ok: true, branch: headRefName };
+  }
+  const pull = pullFastForwardOnly(headRefName);
+  if (!pull.ok) {
+    return { ok: false, reason: "pull-failed", detail: pull.stderr };
+  }
+  return { ok: true, branch: headRefName };
 }
 
 // src/commands/doWork.ts
@@ -2891,10 +2989,14 @@ function fail(message) {
   process.exit(1);
 }
 function parsePositiveInt(value, label) {
-  const parsed = Number.parseInt(value, 10);
-  if (Number.isNaN(parsed) || parsed <= 0) {
+  const trimmed = value.trim();
+  if (!/^\d+$/.test(trimmed)) {
     fail(`${label} must be a positive integer (got "${value}").`);
   }
+  const parsed = Number(trimmed);
+  if (!Number.isSafeInteger(parsed) || parsed <= 0) {
+    fail(`${label} must be a positive integer within the safe range (got "${value}").`);
+  }
   return parsed;
 }
 function resolveSettings(options) {
@@ -2924,6 +3026,7 @@ function resolveSettings(options) {
     fail("No agent user configured. Run `automata config set agent-user <login>`.");
   }
   const doWork = config.doWork ?? {};
+  validateDoWorkConfig(doWork);
   let executor = doWork.executor ?? DEFAULT_DO_WORK.executor;
   if (options.with !== void 0) {
     const requested = options.with.toLowerCase();
@@ -2932,7 +3035,9 @@ function resolveSettings(options) {
     }
     executor = requested;
   }
-  checkAuthenticatedIdentity(agentUser, allowedUsers);
+  if (options.dryRun !== true) {
+    checkAuthenticatedIdentity(agentUser, allowedUsers);
+  }
   return {
     baseBranch: doWork.baseBranch ?? DEFAULT_DO_WORK.baseBranch,
     executor,
@@ -2970,7 +3075,7 @@ function checkAuthenticatedIdentity(agentUser, allowedUsers) {
     `\`gh\` is authenticated as "${login2}" but agentUser is "${agentUser}". Comments posted under that identity are neither the agent's nor an authorized user's, so they are filtered out of the conversation: the answer boundary would never advance and the same message would start a run on every tick. Authenticate \`gh\` as the agent account (${agentUser}) in this environment, or correct \`agentUser\`.`
   );
 }
-function planRun(item, settings, silent) {
+function planRun(item, settings) {
   const prompt = composePrompt({
     item,
     repo: getRepoSlug(),
@@ -2979,7 +3084,7 @@ function planRun(item, settings, silent) {
     frame: settings.prompts[item.turn]
   });
   const bin = resolveCommand(settings.executor === "codex" ? "codex" : "claude");
-  const args = settings.executor === "codex" ? buildCodexArgs(prompt, { yolo: true, model: settings.model }) : buildClaudeArgs(prompt, { yolo: true, verbose: !silent, model: settings.model });
+  const args = settings.executor === "codex" ? buildCodexArgs(prompt, { yolo: true, model: settings.model }) : buildClaudeArgs(prompt, { yolo: true, verbose: true, model: settings.model });
   return { prompt, bin, args, command: [bin, ...args].map(shellQuote).join(" ") };
 }
 function describePlannedRun(item, settings, run5) {
@@ -3013,6 +3118,36 @@ function describePlannedRun(item, settings, run5) {
   ];
   return lines.join("\n") + "\n";
 }
+function validateDoWorkConfig(doWork) {
+  if (doWork.executor !== void 0 && doWork.executor !== "claude" && doWork.executor !== "codex") {
+    fail(`doWork.executor must be 'claude' or 'codex', got '${String(doWork.executor)}'.`);
+  }
+  if (doWork.baseBranch !== void 0 && doWork.baseBranch.trim().length === 0) {
+    fail("doWork.baseBranch must not be empty.");
+  }
+  if (doWork.maxRunsPerTick !== void 0) {
+    if (!Number.isSafeInteger(doWork.maxRunsPerTick) || doWork.maxRunsPerTick < 0) {
+      fail(
+        `doWork.maxRunsPerTick must be a non-negative integer (0 = unlimited), got ${String(doWork.maxRunsPerTick)}.`
+      );
+    }
+  }
+  if (doWork.lockStaleMinutes !== void 0) {
+    if (!Number.isSafeInteger(doWork.lockStaleMinutes) || doWork.lockStaleMinutes <= 0) {
+      fail(`doWork.lockStaleMinutes must be a positive integer, got ${String(doWork.lockStaleMinutes)}.`);
+    }
+  }
+  for (const [key, value] of [
+    ["doWork.models.claude", doWork.models?.claude],
+    ["doWork.models.codex", doWork.models?.codex],
+    ["doWork.prompts.issueDiscuss", doWork.prompts?.issueDiscuss],
+    ["doWork.prompts.prWork", doWork.prompts?.prWork]
+  ]) {
+    if (value !== void 0 && (typeof value !== "string" || value.trim().length === 0)) {
+      fail(`${key} must be a non-empty string.`);
+    }
+  }
+}
 function discoverIssues(settings) {
   const candidates = listCandidateIssues(settings.technique, settings.discoveryValue, settings.limit);
   if (settings.onlyIssue === void 0) {
@@ -3026,11 +3161,25 @@ function discoverIssues(settings) {
   }
   const match = candidates.find((issue) => issue.number === settings.onlyIssue);
   if (match) return [match];
-  progress(
-    `Note: issue #${String(settings.onlyIssue)} does not match the configured discovery filter (${settings.technique} = ${settings.discoveryValue}); processing it anyway because --issue was given.
+  const surface = getIssueSurface(settings.onlyIssue);
+  if (!issueMatchesFilter(surface, settings)) {
+    progress(
+      `Note: issue #${String(settings.onlyIssue)} does not match the configured discovery filter (${settings.technique} = ${settings.discoveryValue}); processing it anyway because --issue was given.
 `
-  );
-  return [getIssueSurface(settings.onlyIssue).issue];
+    );
+  }
+  return [surface.issue];
+}
+function issueMatchesFilter(surface, settings) {
+  const value = settings.discoveryValue.toLowerCase();
+  switch (settings.technique) {
+    case "label":
+      return surface.labels.some((label) => label.toLowerCase() === value);
+    case "assignee":
+      return surface.assignees.some((assignee) => assignee.toLowerCase() === value);
+    case "title-contains":
+      return surface.issue.title.toLowerCase().includes(value);
+  }
 }
 function buildIssueState(issue, linkMap) {
   const issueSurface = getIssueSurface(issue.number);
@@ -3053,6 +3202,13 @@ function describePlan(decisions) {
   });
   return lines.length === 0 ? "  (no issues matched the discovery filter)\n" : lines.join("\n") + "\n";
 }
+function refreshItem(item, settings, linkMap) {
+  return decideWork(
+    buildIssueState(item.issue, linkMap),
+    settings.participants,
+    settings.baseBranch
+  );
+}
 function readAnsweringSurface(item) {
   if (item.turn === "issue-discuss" || item.pr === null) {
     return getIssueSurface(item.issue.number).messages;
@@ -3060,6 +3216,9 @@ function readAnsweringSurface(item) {
   const surface = getPrSurface(item.pr.number);
   return [...surface.messages, ...surface.threads.flatMap((thread) => thread.comments)];
 }
+function markerSurfaceLabel(item) {
+  return item.turn === "pr-work" && item.pr ? `pull request #${String(item.pr.number)}` : `issue #${String(item.issue.number)}`;
+}
 function reconcileMarker(item, marker, agentUser, runError) {
   let answered;
   try {
@@ -3069,7 +3228,20 @@ function reconcileMarker(item, marker, agentUser, runError) {
       `  warning: could not re-read issue #${String(item.issue.number)} to check for an answer: ${err.message}
 `
     );
-    answered = false;
+    answered = "unknown";
+  }
+  if (answered === "unknown") {
+    const surface2 = markerSurfaceLabel(item);
+    try {
+      updateMarker(
+        marker,
+        `automata do-work: the agent run finished, but automata could not read ${surface2} afterwards to confirm whether an answer was posted. Check this thread and the branch before assuming either. Reply here to have another attempt made.`
+      );
+    } catch (updateErr) {
+      progress(`  warning: could not update the marker comment: ${updateErr.message}
+`);
+    }
+    return { outcome: "answered-no-reply", detail: "could not verify whether an answer was posted" };
   }
   if (answered) {
     try {
@@ -3080,7 +3252,8 @@ function reconcileMarker(item, marker, agentUser, runError) {
     }
     return runError === null ? { outcome: "answered", detail: "answered" } : { outcome: "answered", detail: `answered, but the run reported: ${runError.message}` };
   }
-  const explanation = runError === null ? "automata do-work: the agent run finished without posting an answer here. Nothing was changed on your behalf. Reply on this issue to have another attempt made." : `automata do-work: the agent run failed before posting an answer (${runError.message}). Reply on this issue to have another attempt made.`;
+  const surface = markerSurfaceLabel(item);
+  const explanation = runError === null ? `automata do-work: the agent run finished without posting an answer on ${surface}. It may still have changed the branch \`${item.branch}\` \u2014 check it before assuming otherwise. Reply on ${surface} to have another attempt made.` : `automata do-work: the agent run failed before posting an answer (${runError.message}). It may have left partial changes on the branch \`${item.branch}\`. Reply on ${surface} to have another attempt made.`;
   try {
     updateMarker(marker, explanation);
   } catch (err) {
@@ -3094,10 +3267,10 @@ function reconcileMarker(item, marker, agentUser, runError) {
 }
 async function invokeExecutor(prompt, settings, silent) {
   if (settings.executor === "codex") {
-    invokeCodexCode(prompt, { yolo: true, model: settings.model });
+    await runCodex(prompt, { model: settings.model });
     return;
   }
-  await invokeClaudeCode(prompt, { yolo: true, verbose: !silent, model: settings.model });
+  await runClaude(prompt, { model: settings.model, printSteps: !silent });
 }
 function repairIssueLink(item, baseBranch) {
   try {
@@ -3126,15 +3299,26 @@ function repairIssueLink(item, baseBranch) {
 `);
   }
 }
-async function processItem(item, settings, silent) {
+async function processItem(planned, settings, linkMap, silent) {
   const base = {
-    issue: item.issue.number,
-    title: item.issue.title,
-    turn: item.turn
+    issue: planned.issue.number,
+    title: planned.issue.title,
+    turn: planned.turn
   };
   progress(`
-#${String(item.issue.number)} ${item.turn}: ${item.reason}
+#${String(planned.issue.number)} ${planned.turn}: ${planned.reason}
+`);
+  const refreshed = refreshItem(planned, settings, linkMap);
+  if (refreshed.kind === "skip") {
+    progress(`  skipped: ${refreshed.detail}
 `);
+    return { ...base, outcome: "skipped", detail: `no longer actionable: ${refreshed.detail}` };
+  }
+  const item = refreshed.item;
+  if (item.turn !== planned.turn) {
+    progress(`  turn changed to ${item.turn} since the plan was built; using the current state.
+`);
+  }
   const prepared = item.turn === "issue-discuss" ? prepareBaseBranch(item.branch) : preparePrBranch(item.branch);
   if (!prepared.ok) {
     progress(`  skipped: ${prepared.reason} \u2014 ${prepared.detail}
@@ -3213,7 +3397,7 @@ var doWorkCommand = new Command6("do-work").description(
     if (shuttingDown) return;
     shuttingDown = true;
     progress("\nInterrupted: stopping the executor before releasing the run lock\u2026\n");
-    void terminateActiveClaudeProcesses().then(() => {
+    void terminateTrackedChildren().then(() => {
       handle.release();
       process.exit(130);
     });
@@ -3254,7 +3438,7 @@ ${describePlan(decisions)}`;
   const deferred = items.slice(runnable.length);
   const reports = [];
   for (const item of runnable) {
-    reports.push(await processItem(item, settings, options.silent === true));
+    reports.push(await processItem(item, settings, linkMap, options.silent === true));
   }
   for (const item of deferred) {
     progress(`
@@ -3279,7 +3463,7 @@ ${describePlan(decisions)}`;
 }
 function reportDryRun(items, decisions, settings, options) {
   const describable = settings.maxRuns > 0 ? items.slice(0, settings.maxRuns) : items;
-  const planned = describable.map((item) => planRun(item, settings, options.silent === true));
+  const planned = describable.map((item) => planRun(item, settings));
   if (options.json) {
     out(
       JSON.stringify(

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "automata-cli",
-  "version": "0.1.0-feature-030-do-work.198",
+  "version": "0.1.0-feature-030-do-work.202",
   "description": "Automata CLI tool",
   "type": "module",
   "bin": {