pr-shepherd 0.8.1 → 0.10.0

package/bin/commands/check.mjs

@@ -21,15 +21,17 @@ import { autoResolveOutdated } from "../comments/resolve.mjs";
 import { deriveMergeStatus } from "../merge-status/derive.mjs";
 import { loadConfig } from "../config/load.mjs";
 import { computeStatus } from "./check-status.mjs";
+import { loadSeenSet, markSeen } from "../state/seen-comments.mjs";
 export async function runCheck(opts) {
     const repo = await getRepoInfo();
     const prNumber = opts.prNumber ?? (await getCurrentPrNumber());
     if (prNumber === null) {
         throw new Error("No open PR found for current branch. Pass a PR number explicitly.");
     }
+    const config = loadConfig();
     // Only paginate APPROVED reviews when the caller will actually minimize them.
     // Otherwise the first-page cap of 50 (already in the batch) is plenty — no extra round-trip.
-    const paginateApprovedReviews = loadConfig().iterate.minimizeReviewSummaries.approvals;
+    const paginateApprovedReviews = config.iterate.minimizeApprovals;
     const result = await fetchPrBatch(prNumber, repo, { paginateApprovedReviews });
     let batchData = result.data;
     // GraphQL sometimes returns UNKNOWN for mergeable/mergeStateStatus while the
@@ -52,8 +54,10 @@ export async function runCheck(opts) {
     const inProgress = classifiedChecks.filter((c) => c.category === "in_progress");
     const skipped = classifiedChecks.filter((c) => c.category === "skipped");
     const filtered = classifiedChecks.filter((c) => c.category === "filtered");
-    // Triage failures (fetch logs) — skipped when caller will short-circuit before needing failureKind.
-    const triaged = failing.length > 0 && !opts.skipTriage ? await triageFailingChecks(failing, repo) : failing;
+    const triaged = failing.length > 0 && !opts.skipTriage
+        ? await triageFailingChecks(failing, repo, config.checks.logTailLines, config.checks.logTailChars)
+        : failing;
+    const stateKey = { owner: repo.owner, repo: repo.name, pr: prNumber };
     // Resolve threads and comments.
     const unresolvedThreads = batchData.reviewThreads.filter((t) => !t.isResolved && !t.isMinimized);
     const visibleComments = batchData.comments.filter((c) => !c.isMinimized);
@@ -67,6 +71,36 @@ export async function runCheck(opts) {
         autoResolveErrors = errors;
     }
     const activeThreads = unresolvedThreads.filter((t) => !t.isOutdated);
+    // First-look: collect previously-hidden items not yet seen by the agent.
+    const outdatedCandidates = batchData.reviewThreads.filter((t) => t.isOutdated);
+    const resolvedCandidates = batchData.reviewThreads.filter((t) => t.isResolved && !t.isOutdated);
+    const minimizedThreadCandidates = batchData.reviewThreads.filter((t) => t.isMinimized && !t.isResolved && !t.isOutdated);
+    const minimizedCommentCandidates = batchData.comments.filter((c) => c.isMinimized);
+    const seenSet = await loadSeenSet(stateKey);
+    const autoResolvedIds = new Set(autoResolved.map((t) => t.id));
+    const firstLookThreads = [
+        ...outdatedCandidates
+            .filter((t) => !seenSet.has(t.id))
+            .map((t) => ({
+            ...t,
+            firstLookStatus: "outdated",
+            autoResolved: autoResolvedIds.has(t.id),
+        })),
+        ...resolvedCandidates
+            .filter((t) => !seenSet.has(t.id))
+            .map((t) => ({ ...t, firstLookStatus: "resolved" })),
+        ...minimizedThreadCandidates
+            .filter((t) => !seenSet.has(t.id))
+            .map((t) => ({ ...t, firstLookStatus: "minimized" })),
+    ];
+    const firstLookComments = minimizedCommentCandidates
+        .filter((c) => !seenSet.has(c.id))
+        .map((c) => ({ ...c, firstLookStatus: "minimized" }));
+    // Mark first-look items as seen (best-effort — markSeen never throws).
+    await Promise.allSettled([
+        ...firstLookThreads.map((t) => markSeen(stateKey, t.id)),
+        ...firstLookComments.map((c) => markSeen(stateKey, c.id)),
+    ]);
     // Actionable: all active threads and all visible comments (no classification — LLM handles triage).
     const actionableThreads = activeThreads;
     const actionableComments = visibleComments;
@@ -99,9 +133,11 @@ export async function runCheck(opts) {
             actionable: actionableThreads,
             autoResolved,
             autoResolveErrors,
+            firstLook: firstLookThreads,
         },
         comments: {
             actionable: actionableComments,
+            firstLook: firstLookComments,
         },
         changesRequestedReviews: batchData.changesRequestedReviews,
         reviewSummaries: batchData.reviewSummaries,

package/bin/commands/commit-suggestion.mjs

@@ -3,7 +3,7 @@ import { readFile, writeFile, unlink } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { promisify } from "node:util";
-import { getRepoInfo, getCurrentPrNumber, getPrHead, getCurrentBranch } from "../github/client.mjs";
+import { getRepoInfo, getCurrentPrNumber, getCurrentBranch } from "../github/client.mjs";
 import { fetchPrBatch } from "../github/batch.mjs";
 import { applyResolveOptions } from "../comments/resolve.mjs";
 import { parseSuggestion, isCommittableSuggestion } from "../suggestions/parse.mjs";
@@ -25,19 +25,21 @@ export async function runCommitSuggestion(opts) {
     if (prNumber === null) {
         throw new Error("No open PR found for current branch. Pass a PR number explicitly.");
     }
-    const head = await getPrHead(prNumber, repo.owner, repo.name);
     const currentBranch = await getCurrentBranch();
-    if (currentBranch !== head.ref) {
-        throw new Error(`Current branch "${currentBranch}" does not match PR head branch "${head.ref}". ` +
-            `Check out "${head.ref}" before applying suggestions.`);
-    }
     const { stdout: localHeadOut } = await execFile("git", ["rev-parse", "HEAD"]);
     const localHeadSha = localHeadOut.trim();
-    if (localHeadSha !== head.sha) {
-        throw new Error(`Local HEAD ${localHeadSha} does not match PR head ${head.sha}. ` +
-            `Pull/rebase "${head.ref}" to the latest PR head and try again.`);
-    }
     const { data } = await fetchPrBatch(prNumber, repo);
+    if (!data.headRepoWithOwner) {
+        throw new Error(`PR #${prNumber} head repository is unavailable (fork may have been deleted).`);
+    }
+    if (currentBranch !== data.headRefName) {
+        throw new Error(`Current branch "${currentBranch}" does not match PR head branch "${data.headRefName}". ` +
+            `Check out "${data.headRefName}" before applying suggestions.`);
+    }
+    if (localHeadSha !== data.headRefOid) {
+        throw new Error(`Local HEAD ${localHeadSha} does not match PR head ${data.headRefOid}. ` +
+            `Pull/rebase "${data.headRefName}" to the latest PR head and try again.`);
+    }
     const thread = data.reviewThreads.find((t) => t.id === opts.threadId);
     if (!thread) {
         throw new Error(`Thread ${opts.threadId} not found on PR #${prNumber}.`);

package/bin/commands/iterate/classify.mjs

@@ -1,58 +1,13 @@
-// Logins treated as bot authors regardless of the GitHub Bot/User user type.
-// Mirrors plugin/skills/resolve/SKILL.md §3 — kept in sync with the resolve triage guidance.
-const KNOWN_BOT_LOGINS = new Set([
-    "copilot-pull-request-reviewer",
-    "gemini-code-assist",
-    "coderabbitai",
-]);
-function isBotAuthor(login) {
-    const bare = login.replace(/\[bot\]$/, "");
-    if (bare !== login)
-        return true;
-    return KNOWN_BOT_LOGINS.has(bare);
-}
-export function classifyReviewSummaries(summaries, approvals, cfg) {
-    const minimizeIds = [];
-    const surfacedSummaries = [];
-    for (const r of summaries) {
-        const enabled = isBotAuthor(r.author) ? cfg.bots : cfg.humans;
-        if (enabled)
-            minimizeIds.push(r.id);
-        else
-            surfacedSummaries.push(r);
-    }
-    if (cfg.approvals) {
+export function classifyReviewSummaries(summaries, approvals, minimizeApprovals) {
+    const minimizeIds = summaries.map((r) => r.id);
+    if (minimizeApprovals) {
         for (const r of approvals)
             minimizeIds.push(r.id);
+        return { minimizeIds, surfacedApprovals: [] };
     }
-    return { minimizeIds, surfacedSummaries };
-}
-// Patterns that indicate a comment is bot-generated noise rather than actionable feedback.
-// Conservative: only match explicit known patterns to avoid accidentally suppressing real reviews.
-const NOISE_PATTERNS = [
-    /you have reached your daily quota/i,
-    /please wait up to \d+ hours?/i,
-    /rate[\s-]?limit(?:ed)?\s*[-—:]\s*try again/i,
-    /resuming (monitoring|watch|checking)/i,
-    /restarting (monitoring|watch)/i,
-];
-function isNoiseComment(comment) {
-    return NOISE_PATTERNS.some((p) => p.test(comment.body));
-}
-export function classifyComments(comments) {
-    const actionable = [];
-    const noiseIds = [];
-    for (const c of comments) {
-        if (isNoiseComment(c)) {
-            noiseIds.push(c.id);
-        }
-        else {
-            actionable.push(c);
-        }
-    }
-    return { actionable, noiseIds };
+    return { minimizeIds, surfacedApprovals: approvals };
 }
-export function buildResolveCommand(threads, actionableComments, allCommentIds, reviews, checks, prNumber) {
+export function buildResolveCommand(threads, allCommentIds, reviews, checks, prNumber) {
     const argv = ["npx", "pr-shepherd", "resolve", String(prNumber)];
     if (threads.length > 0) {
         argv.push("--resolve-thread-ids", threads.map((t) => t.id).join(","));
@@ -65,9 +20,10 @@ export function buildResolveCommand(threads, actionableComments, allCommentIds,
         argv.push("--dismiss-review-ids", reviews.map((r) => r.id).join(","));
         argv.push("--message", "$DISMISS_MESSAGE");
     }
-    // A push happens when there is code to change — threads, actionable comments, CI checks, or reviews.
-    // Noise-only comment minimization skips commit/push, so requiresHeadSha must be false.
-    const requiresHeadSha = threads.length > 0 || actionableComments.length > 0 || checks.length > 0 || reviews.length > 0;
+    // A push is required when threads, CI failures, or changes-requested reviews are present — the
+    // CLI knows those imply code edits. Comments are surfaced for the agent to evaluate; the CLI
+    // cannot know whether a given comment will require a push, so comments are excluded here.
+    const requiresHeadSha = threads.length > 0 || checks.length > 0 || reviews.length > 0;
     // hasMutations = we appended at least one of --resolve-thread-ids,
     // --minimize-comment-ids, or --dismiss-review-ids. Returned explicitly
     // (rather than derived from argv.length) so callers don't couple to the

package/bin/commands/iterate/escalate.mjs

@@ -1,5 +1,5 @@
 import { loadConfig } from "../../config/load.mjs";
-export function checkEscalateTriggers(actionableThreads, actionableComments, changesRequestedReviews, actionableChecks, threadAttempts, hasConflicts) {
+export function checkEscalateTriggers(actionableThreads, actionableComments, changesRequestedReviews, failingChecks, threadAttempts, hasConflicts) {
     const triggers = [];
     const maxAttempts = loadConfig().iterate.fixAttemptsPerThread;
     // Trigger 1: fix thrash — same thread dispatched too many times without resolving.
@@ -12,7 +12,7 @@ export function checkEscalateTriggers(actionableThreads, actionableComments, cha
     if (changesRequestedReviews.length > 0 &&
         actionableThreads.length === 0 &&
         actionableComments.length === 0 &&
-        actionableChecks.length === 0 &&
+        failingChecks.length === 0 &&
         !hasConflicts) {
         triggers.push("pr-level-changes-requested");
     }
@@ -31,8 +31,8 @@ export function checkEscalateTriggers(actionableThreads, actionableComments, cha
 /**
  * Validate the base branch name from the GraphQL batch (`report.baseBranch`)
  * and fall back safely if it's missing/unsafe. The branch is interpolated into
- * shell commands by `buildRebaseShellScript` and `buildFixInstructions`, so we
- * reject anything outside `[A-Za-z0-9._/-]` to prevent shell injection.
+ * shell commands by `buildFixInstructions`, so we reject anything outside
+ * `[A-Za-z0-9._/-]` to prevent shell injection.
  */
 export function validateBaseBranch(raw) {
     const trimmed = raw.trim();
@@ -52,18 +52,9 @@ export function validateBaseBranch(raw) {
     }
     return { branch: trimmed, isFallback: false };
 }
-export function buildRebaseShellScript(baseBranch) {
-    return [
-        `if ! git diff --quiet || ! git diff --cached --quiet; then`,
-        `  echo "SKIP rebase: dirty worktree (uncommitted changes present)"`,
-        `  exit 1`,
-        `fi`,
-        `git fetch origin && git rebase origin/${baseBranch} && git push --force-with-lease`,
-    ].join("\n");
-}
 export function buildEscalateHumanMessage(escalate, pr) {
     const lines = [];
-    lines.push("⚠️  /pr-shepherd:monitor paused — needs human direction");
+    lines.push("⚠️ /pr-shepherd:monitor paused — needs human direction");
     lines.push("");
     lines.push(`**Triggers:** ${escalate.triggers.map((t) => `\`${t}\``).join(", ")}`);
     lines.push("");

package/bin/commands/iterate/fix-code.mjs

@@ -1,13 +1,13 @@
 import { readFixAttempts, writeFixAttempts } from "../../state/fix-attempts.mjs";
 import { toAgentThread, toAgentComment, toAgentChecks } from "../../reporters/agent.mjs";
 import { checkEscalateTriggers, validateBaseBranch, buildEscalateSuggestion, buildEscalateHumanMessage, } from "./escalate.mjs";
-import { classifyComments, buildResolveCommand } from "./classify.mjs";
+import { buildResolveCommand } from "./classify.mjs";
 import { buildFixInstructions } from "./render.mjs";
 import { applyStallGuard } from "./stall.mjs";
 import { tryCancelRun } from "./helpers.mjs";
 export async function handleFixCode(ctx) {
-    const { base, report, opts, headSha, stallKey, prNumber, stallTimeoutSeconds, repoOwner, repoName, reviewSummaryIds, surfacedSummaries, } = ctx;
-    const actionableChecks = report.checks.failing.filter((f) => f.failureKind === "actionable");
+    const { base, report, opts, headSha, stallKey, prNumber, stallTimeoutSeconds, repoOwner, repoName, reviewSummaryIds, surfacedApprovals, } = ctx;
+    const failingChecks = report.checks.failing;
     const stored = await readFixAttempts({ owner: repoOwner, repo: repoName, pr: prNumber });
     const isNewSha = stored?.headSha !== headSha;
     // Accumulate across shas — only increment when a push is detected (sha changed)
@@ -17,7 +17,7 @@ export async function handleFixCode(ctx) {
             currentAttempts[t.id] = (currentAttempts[t.id] ?? 0) + 1;
         }
     }
-    const escalateTriggers = checkEscalateTriggers(report.threads.actionable, report.comments.actionable, report.changesRequestedReviews, actionableChecks, currentAttempts, report.mergeStatus.status === "CONFLICTS");
+    const escalateTriggers = checkEscalateTriggers(report.threads.actionable, report.comments.actionable, report.changesRequestedReviews, failingChecks, currentAttempts, report.mergeStatus.status === "CONFLICTS");
     if (escalateTriggers.triggers.length > 0) {
         const escalateBase = {
             triggers: escalateTriggers.triggers,
@@ -41,23 +41,19 @@ export async function handleFixCode(ctx) {
     let cancelled = [];
     if (!opts.noAutoCancelActionable) {
         const uniqueRunIds = [
-            ...new Set(actionableChecks.map((c) => c.runId).filter((id) => id !== null)),
+            ...new Set(failingChecks.map((c) => c.runId).filter((id) => id !== null)),
         ];
         const results = await Promise.all(uniqueRunIds.map((id) => tryCancelRun(id, repoOwner, repoName)));
         cancelled = results.filter((id) => id !== null);
     }
     const baseLookup = validateBaseBranch(report.baseBranch);
     const threads = report.threads.actionable.map(toAgentThread);
-    const { actionable: actionableComments, noiseIds: noiseCommentIds } = classifyComments(report.comments.actionable.map(toAgentComment));
-    const checks = toAgentChecks(actionableChecks);
+    const actionableComments = report.comments.actionable.map(toAgentComment);
+    const checks = toAgentChecks(failingChecks);
     const { changesRequestedReviews } = report;
     const hasConflicts = report.mergeStatus.status === "CONFLICTS";
-    const allCommentIds = [
-        ...actionableComments.map((c) => c.id),
-        ...noiseCommentIds,
-        ...reviewSummaryIds,
-    ];
-    const resolveCommand = buildResolveCommand(threads, actionableComments, allCommentIds, changesRequestedReviews, checks, prNumber);
+    const allCommentIds = [...actionableComments.map((c) => c.id), ...reviewSummaryIds];
+    const resolveCommand = buildResolveCommand(threads, allCommentIds, changesRequestedReviews, checks, prNumber);
     if (baseLookup.isFallback && (resolveCommand.requiresHeadSha || hasConflicts)) {
         const fallbackEscalateBase = {
             triggers: ["base-branch-unknown"],
@@ -75,7 +71,9 @@ export async function handleFixCode(ctx) {
             },
         };
     }
-    const instructions = buildFixInstructions(threads, actionableComments, checks, changesRequestedReviews, baseLookup.branch, resolveCommand, hasConflicts, prNumber, cancelled.length);
+    const firstLookThreads = report.threads.firstLook;
+    const firstLookComments = report.comments.firstLook;
+    const instructions = buildFixInstructions(threads, actionableComments, checks, changesRequestedReviews, baseLookup.branch, resolveCommand, hasConflicts, prNumber, cancelled.length, firstLookThreads, firstLookComments);
     return applyStallGuard(stallKey, stallTimeoutSeconds, headSha, base, prNumber, {
         ...base,
         baseBranch: baseLookup.branch,
@@ -84,13 +82,14 @@ export async function handleFixCode(ctx) {
             mode: "rebase-and-push",
             threads,
             actionableComments,
-            noiseCommentIds,
             reviewSummaryIds,
-            surfacedSummaries,
+            surfacedApprovals,
             checks,
             changesRequestedReviews,
             resolveCommand,
             instructions,
+            firstLookThreads,
+            firstLookComments,
         },
         cancelled,
     }, report, reviewSummaryIds);

package/bin/commands/iterate/helpers.mjs

@@ -13,7 +13,8 @@ export function buildSummary(report) {
 /**
  * Build the full list of CI checks relevant to PR readiness: triggered by a PR
  * event (or StatusContext with null event), completed, and not skipped/neutral.
- * Includes both passing and failing. Failing entries carry failureKind + errorExcerpt.
+ * Includes both passing and failing. Failing entries carry workflowName, jobName,
+ * failedStep, and summary.
  */
 export function buildRelevantChecks(report) {
     const excluded = new Set([null, "SKIPPED", "NEUTRAL"]);
@@ -41,10 +42,10 @@ export function buildRelevantChecks(report) {
                 conclusion,
                 runId: c.runId,
                 detailsUrl: c.detailsUrl || null,
-                failureKind: c.failureKind,
-                workflowName: c.workflowName,
-                failedStep: c.failedStep,
-                summary: c.summary,
+                ...(c.workflowName !== undefined && { workflowName: c.workflowName }),
+                ...(c.jobName !== undefined && { jobName: c.jobName }),
+                ...(c.failedStep !== undefined && { failedStep: c.failedStep }),
+                ...(c.summary !== undefined && { summary: c.summary }),
             },
         ];
     });
@@ -91,6 +92,8 @@ export function buildCooldownResult(prNumber, readyDelaySeconds) {
         status: "UNKNOWN",
         state: "UNKNOWN",
         mergeStateStatus: "UNKNOWN",
+        mergeStatus: "UNKNOWN",
+        reviewDecision: null,
         copilotReviewInProgress: false,
         isDraft: false,
         shouldCancel: false,

package/bin/commands/iterate/index.mjs

@@ -9,7 +9,6 @@ import { classifyReviewSummaries } from "./classify.mjs";
 import { applyStallGuard } from "./stall.mjs";
 import { buildWaitLog } from "./render.mjs";
 import { handleFixCode } from "./fix-code.mjs";
-import { buildRerunCiResult } from "./steps.mjs";
 export async function runIterate(opts) {
     const config = loadConfig();
     const cooldownSeconds = opts.cooldownSeconds ?? config.iterate.cooldownSeconds;
@@ -36,6 +35,8 @@ export async function runIterate(opts) {
             repo: report.repo,
             status: report.status,
             mergeStateStatus: report.mergeStatus.mergeStateStatus,
+            mergeStatus: report.mergeStatus.status,
+            reviewDecision: report.mergeStatus.reviewDecision,
             copilotReviewInProgress: report.mergeStatus.copilotReviewInProgress,
             isDraft: report.mergeStatus.isDraft,
             shouldCancel: true,
@@ -61,6 +62,8 @@ export async function runIterate(opts) {
         status: report.status,
         state: report.mergeStatus.state,
         mergeStateStatus: report.mergeStatus.mergeStateStatus,
+        mergeStatus: report.mergeStatus.status,
+        reviewDecision: report.mergeStatus.reviewDecision,
         copilotReviewInProgress: report.mergeStatus.copilotReviewInProgress,
         isDraft: report.mergeStatus.isDraft,
         shouldCancel: readyState.shouldCancel,
@@ -70,24 +73,31 @@ export async function runIterate(opts) {
         checks: buildRelevantChecks(report),
     };
     if (readyState.shouldCancel) {
+        let cancelNote;
+        if (base.mergeStatus !== "BLOCKED")
+            cancelNote = "has been ready for review";
+        else if (base.reviewDecision === "REVIEW_REQUIRED")
+            cancelNote = "is awaiting human review";
+        else if (base.reviewDecision === "APPROVED")
+            cancelNote = "is awaiting additional approvals";
+        else
+            cancelNote = "is awaiting human review or branch protection resolution";
         return {
             ...base,
             action: "cancel",
             reason: "ready-delay-elapsed",
-            log: `CANCEL: PR #${base.pr} has been ready for review — ready-delay elapsed, stopping monitor`,
+            log: `CANCEL: PR #${base.pr} ${cancelNote} — ready-delay elapsed, stopping monitor`,
         };
     }
     const headSha = (await getCurrentHeadSha()) ?? "unknown";
     const stallKey = { owner: repoOwner, repo: repoName, pr: prNumber };
-    const { minimizeIds: reviewSummaryIds, surfacedSummaries } = classifyReviewSummaries(report.reviewSummaries, report.approvedReviews, config.iterate.minimizeReviewSummaries);
-    const actionableChecks = report.checks.failing.filter((f) => f.failureKind === "actionable");
+    const { minimizeIds: reviewSummaryIds, surfacedApprovals } = classifyReviewSummaries(report.reviewSummaries, report.approvedReviews, config.iterate.minimizeApprovals);
     const hasActionableWork = report.threads.actionable.length > 0 ||
         report.comments.actionable.length > 0 ||
         report.changesRequestedReviews.length > 0 ||
-        actionableChecks.length > 0 ||
+        report.checks.failing.length > 0 ||
         report.mergeStatus.status === "CONFLICTS" ||
-        reviewSummaryIds.length > 0 ||
-        surfacedSummaries.length > 0;
+        reviewSummaryIds.length > 0;
     if (hasActionableWork) {
         return handleFixCode({
             base,
@@ -100,13 +110,9 @@ export async function runIterate(opts) {
             repoOwner,
             repoName,
             reviewSummaryIds,
-            surfacedSummaries,
+            surfacedApprovals,
         });
     }
-    const transientChecks = report.checks.failing.filter((f) => (f.failureKind === "timeout" || f.failureKind === "cancelled") && f.runId !== null);
-    if (transientChecks.length > 0) {
-        return buildRerunCiResult(transientChecks, base, prNumber, stallKey, stallTimeoutSeconds, headSha, report, reviewSummaryIds);
-    }
     const canMarkReady = report.status === "READY" &&
         report.mergeStatus.isDraft &&
         !report.mergeStatus.copilotReviewInProgress &&

package/bin/commands/iterate/render.mjs

@@ -28,22 +28,26 @@ export function renderResolveCommand(rc) {
     }
     return parts.join(" ");
 }
-export function buildFixInstructions(threads, actionableComments, checks, reviews, baseBranch, resolveCommand, hasConflicts, prNumber, cancelledCount) {
+export function buildFixInstructions(threads, actionableComments, checks, reviews, baseBranch, resolveCommand, hasConflicts, prNumber, cancelledCount, firstLookThreads = [], firstLookComments = []) {
     const instructions = [];
+    const hasSuggestions = threads.some((t) => t.suggestion);
+    if (hasSuggestions) {
+        instructions.push(`For each thread marked \`[suggestion]\` under \`## Review threads\`: run \`npx pr-shepherd commit-suggestion ${prNumber} --thread-id <id> --message "<one-sentence headline>" --format=json\`, one thread at a time. On \`applied: true\` the CLI already resolved the thread — remove its ID from \`--resolve-thread-ids\` in the \`resolve:\` command below. On \`applied: false\` read \`reason\` and \`patch\`, fall through to the manual-edit step, and do not retry the same command. Optionally pass \`--dry-run\` (omitting \`--message\`) to preview the patch without mutating the working tree.`);
+    }
     if (threads.length > 0 || actionableComments.length > 0) {
-        instructions.push(`Apply code fixes: read and edit each file referenced under \`## Review threads\` and \`## Actionable comments\` above.`);
+        const suggestionFallback = hasSuggestions
+            ? ` When applying a \`[suggestion]\` thread manually (e.g. after a failed \`commit-suggestion\` run), replace the exact line range shown in the heading (\`path:startLine-endLine\`) with the replacement shown in its \`Replaces lines …\` block verbatim — an empty replacement deletes those lines, a single blank line replaces the range with one blank line.`
+            : "";
+        instructions.push(`Apply code fixes: read and edit each file referenced under \`## Review threads\` and \`## Actionable comments\` above.${suggestionFallback}`);
     }
-    // Mirror the truthiness checks in `formatIterateResult` (cli/iterate-formatter.mts) so each
-    // AgentCheck maps to the same bullet shape here as there: runId → runId
-    // bullet, else detailsUrl → external bullet, else `(no runId)` bullet.
     const checksWithRunId = checks.filter((c) => c.runId);
     const externalChecks = checks.filter((c) => !c.runId && c.detailsUrl);
     const bareChecks = checks.filter((c) => !c.runId && !c.detailsUrl);
     if (checksWithRunId.length > 0) {
-        instructions.push(`For each bullet in \`## Failing checks\` whose backticked locator is a numeric runId (GitHub Actions): run \`gh run view <runId> --log-failed\`, identify the failure, and apply the fix.`);
+        instructions.push(`For each failing check under \`## Failing checks\` with a run ID, examine the log tail in the fenced block to decide what to do:\n   - If the log tail shows a transient runner or infrastructure failure (network timeout, runner setup crash, OOM kill), run \`gh run rerun <runId> --failed\` and stop this iteration — CI will re-run automatically.\n   - If the log tail shows a real test or build failure, apply a code fix.\n   - If the fenced log block is absent, run \`gh run view <runId> --log-failed\` first to fetch it, then choose between rerun and fix above.`);
     }
     if (externalChecks.length > 0) {
-        instructions.push(`For each bullet in \`## Failing checks\` starting with \`external\` (external status check): open the linked URL in a browser to inspect the failure — \`gh run view\` cannot fetch logs for external checks.`);
+        instructions.push(`For each bullet in \`## Failing checks\` starting with \`external\` (external status check): open the linked URL in a browser to inspect the failure — log tails are not available for external checks.`);
     }
     if (bareChecks.length > 0) {
         instructions.push(`For each bullet in \`## Failing checks\` starting with \`(no runId)\`: there is no run or details URL to inspect. Escalate these to a human — they require manual investigation outside the pr-shepherd flow.`);
@@ -84,6 +88,13 @@ export function buildFixInstructions(threads, actionableComments, checks, review
     if (needsPush && cancelledCount > 0) {
         instructions.push(`Do not re-run \`gh run cancel\` on the IDs listed under \`## Cancelled runs\` — the CLI cancelled those runs before your push, and your push has already triggered new runs with different IDs.`);
     }
+    const firstLookTotal = firstLookThreads.length + firstLookComments.length;
+    if (firstLookTotal > 0) {
+        instructions.push(`Items in \`## First-look items\` are for acknowledgement only — do not pass their IDs to \`--resolve-thread-ids\`, \`--minimize-comment-ids\`, or \`--dismiss-review-ids\`. Acknowledge each one with a one-line classification (e.g. "outdated — addressed by commit abc1234", "resolved — already fixed", "minimized — noise").`);
+    }
+    if (resolveCommand.hasMutations) {
+        instructions.push(`For any large decisions or rejections you made this iteration, add or update a \`## Shepherd Journal\` section in the PR description (\`gh pr edit ${prNumber} --body …\`) summarizing each decision. For threads and comments, use the markdown link shown in its heading above; for reviews, reference the review ID.`);
+    }
     if (needsPush) {
         instructions.push(`Stop this iteration — CI needs time to run on the new push before the next tick.`);
     }
@@ -96,15 +107,20 @@ export function buildFixInstructions(threads, actionableComments, checks, review
     return instructions;
 }
 export function buildWaitLog(base) {
-    const { summary, mergeStateStatus, remainingSeconds } = base;
+    const { summary, remainingSeconds } = base;
     const parts = [`WAIT: ${summary.passing} passing, ${summary.inProgress} in-progress`];
-    switch (mergeStateStatus) {
+    switch (base.mergeStatus) {
+        case "BLOCKED":
+            if (base.reviewDecision === "REVIEW_REQUIRED")
+                parts.push("awaiting human review");
+            else if (base.reviewDecision === "APPROVED")
+                parts.push("awaiting additional approvals");
+            else
+                parts.push("awaiting human review or branch protection");
+            break;
         case "BEHIND":
             parts.push("branch is behind base");
             break;
-        case "BLOCKED":
-            parts.push("blocked by pending reviews or required status checks");
-            break;
         case "DRAFT":
             parts.push("PR is a draft");
             break;

package/bin/commands/iterate/stall.mjs

@@ -3,7 +3,7 @@ import { toAgentThread, toAgentComment } from "../../reporters/agent.mjs";
 import { buildEscalateSuggestion, buildEscalateHumanMessage } from "./escalate.mjs";
 export function computeStallFingerprint(action, headSha, base, report, reviewSummaryIds) {
     const checks = [
-        ...report.checks.failing.map((f) => `failing:${f.name}:${f.failureKind ?? ""}`),
+        ...report.checks.failing.map((f) => `failing:${f.name}:${f.conclusion}`),
         ...report.checks.inProgress.map((p) => `inProgress:${p.name}`),
     ].sort();
     const threads = report.threads.actionable.map((t) => t.id).sort();

package/bin/commands/log-file.mjs

@@ -0,0 +1,7 @@
+import { getRepoInfo } from "../github/client.mjs";
+import { resolveLogPath } from "../log/log-file.mjs";
+export async function runLogFile() {
+    const { owner, name } = await getRepoInfo();
+    const path = await resolveLogPath({ owner, repo: name });
+    return { path };
+}

package/bin/commands/monitor.mjs

@@ -16,7 +16,12 @@ export async function runMonitor(opts) {
     if (!Number.isFinite(maxTurns) || maxTurns <= 0 || !Number.isInteger(maxTurns)) {
         throw new Error(`Invalid config: watch.maxTurns must be a positive integer, got ${JSON.stringify(maxTurns)}`);
     }
-    const loopTag = `# pr-shepherd-loop:pr=${prNumber}`;
+    // No space after `#` — `# text` is a CommonMark ATX heading; `#text` is not.
+    // Trailing `:` prevents substring false positives: without it, the dedup grep
+    // for pr=1 would match a cron prompt for pr=135. Both the CronList check in
+    // step 1 of formatMonitorResult's ## Instructions and the in-prompt Self-dedup
+    // block depend on this exact string — don't change the format.
+    const loopTag = `#pr-shepherd-loop:pr=${prNumber}:`;
     const loopPrompt = buildLoopPrompt(prNumber, loopTag, opts.readyDelaySuffix);
     const loopArgs = `${interval} --max-turns ${maxTurns} --expires ${expiresHours}h`;
     return { prNumber, loopTag, loopArgs, loopPrompt };
@@ -56,9 +61,7 @@ function validateReadyDelaySuffix(readyDelaySuffix) {
 }
 function buildLoopPrompt(prNumber, loopTag, readyDelaySuffix) {
     const validatedDelay = validateReadyDelaySuffix(readyDelaySuffix);
-    const iterateCmd = validatedDelay
-        ? `npx pr-shepherd iterate ${prNumber} --no-cache --ready-delay ${validatedDelay}`
-        : `npx pr-shepherd iterate ${prNumber} --no-cache`;
+    const iterateCmd = `npx pr-shepherd iterate ${prNumber}${validatedDelay ? ` --ready-delay ${validatedDelay}` : ""}`;
     return [
         loopTag,
         "",

package/bin/commands/ready-delay.mjs

@@ -7,8 +7,8 @@
  */
 import { readFile, writeFile, mkdir, unlink } from "node:fs/promises";
 import { join, dirname } from "node:path";
-import { tmpdir } from "node:os";
 import { SAFE_SEGMENT } from "../util/path-segment.mjs";
+import { resolveStateBase } from "../state/base.mjs";
 /**
  * Update the ready-delay state machine and return the current decision.
  *
@@ -64,7 +64,7 @@ function readySincePath(pr, owner, repo) {
             throw new Error(`Invalid path segment "${field}": ${value}`);
         }
     }
-    const base = process.env["PR_SHEPHERD_STATE_DIR"] ?? join(tmpdir(), "pr-shepherd-state");
+    const base = resolveStateBase();
     return join(base, `${owner}-${repo}`, String(pr), "ready-since.txt");
 }
 async function safeUnlink(path) {