pr-shepherd 0.46.1 → 0.46.2

package/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "pr-shepherd",
   "description": "Autonomous PR CI monitor and review-comment resolver for agentic coding tools",
-  "version": "0.46.1",
+  "version": "0.46.2",
   "author": {
     "name": "Jonathan Ong",
     "email": "jonathanrichardong@gmail.com"

package/README.md

@@ -84,7 +84,7 @@ See [docs/actions.md](docs/actions.md) for the complete output contract and [doc
 This system is opinionated and works best with PRs that use required status checks and conversation resolution.
 
 - A human inline thread whose original comment has `viewerDidAuthor: true` is replied to and resolved when its latest comment is unmarked. An unmarked other-human inline thread remains reply-only; a marker-ended other-human thread is already acknowledged and receives no further mutation. Human items are never minimized.
-- Detected bots and configured `botUsernames` review threads are returned until resolved when the required mutation is authorized and the thread has a source location. Unauthorized or unlocated items are surfaced once and then marker-gated until edited. Bot/non-human threads, PR comments, and review summaries can be resolved or minimized when eligible. Review summaries are not minimized while known inline child threads from that review remain unresolved.
+- Detected bots and configured `botUsernames` review threads are returned until resolved when the required mutation is authorized and the thread has a source location. Authorized outdated bot threads remain resolution-only work even when GitHub clears their source line, because resolving by thread ID does not require that location. Unauthorized or other unlocated items are surfaced once and then marker-gated until edited. Bot/non-human threads, PR comments, and review summaries can be resolved or minimized when eligible. Review summaries are not minimized while known inline child threads from that review remain unresolved.
 - Shepherd identifies its own latest reply only when that comment begins `<!-- pr-shepherd -->`, not from author equality. A marked viewer-authored thread can be resolved without another reply as a retry.
 - Every review thread/comment/review summary is surfaced at least once, even if already outdated, resolved, or minimized; edited items re-surface through seen markers.
 - Draft PRs can be marked ready automatically when clean; disable with `actions.autoMarkReady: false` or `--no-auto-mark-ready`.

package/bin/commands/check.mjs

@@ -17,7 +17,7 @@ import { classifyReviewsForDisplay, classifyChangesRequestedReviewsForDisplay, }
 import { autoMinimizeComments, autoResolveThreads } from "../comments/resolve.mjs";
 import { markReviewInlineThreadMarkers } from "../comments/review-thread-markers.mjs";
 import { isConfiguredBotAuthor, isHumanAuthor, normalizeBotUsernames, } from "../comments/authors.mjs";
-import { buildThreadMutationRouting } from "./iterate/thread-mutation-routing.mjs";
+import { buildThreadMutationRouting, canResolveOutdatedBotWithoutLocation, } from "./iterate/thread-mutation-routing.mjs";
 import { discoverRuleFiles, loadRules } from "../classify/loader.mjs";
 import { buildClassifyIndex, partitionBatch } from "../classify/apply.mjs";
 import { EXIT, ShepherdError } from "../exit-codes.mjs";
@@ -86,10 +86,11 @@ export async function runCheck(opts) {
     const replyThreadIds = new Set(threadMutationRouting.replyThreadIds);
     const resolveThreadIds = new Set(threadMutationRouting.resolveThreadIds);
     const repeatableThreadIds = new Set(visibleThreadCandidates
-        .filter((thread) => thread.path !== null &&
+        .filter((thread) => (thread.path !== null &&
         thread.line !== null &&
         (!replyThreadIds.has(thread.id) || thread.viewerCanReply === true) &&
-        (!resolveThreadIds.has(thread.id) || thread.viewerCanResolve === true))
+        (!resolveThreadIds.has(thread.id) || thread.viewerCanResolve === true)) ||
+        canResolveOutdatedBotWithoutLocation(thread, botUsernames))
         .map((thread) => thread.id));
     const threadVisibility = classifyThreadVisibility(visibleThreadCandidates, seenMap, botUsernames, repeatableThreadIds);
     const firstLookComments = minimizedCommentCandidates.flatMap((c) => {

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

@@ -5,7 +5,7 @@ import { toAgentThread, toAgentComment, toAgentChecks } from "../../reporters/ag
 import { hashBody, markSeen } from "../../state/seen-comments.mjs";
 import { checkEscalateTriggers, validateBaseBranch, buildEscalateSuggestion, buildEscalateHumanMessage, } from "./escalate.mjs";
 import { buildResolveCommand } from "./classify.mjs";
-import { buildThreadMutationRouting } from "./thread-mutation-routing.mjs";
+import { buildThreadMutationRouting, canResolveOutdatedBotWithoutLocation, } from "./thread-mutation-routing.mjs";
 import { buildFixInstructions } from "./render.mjs";
 import { applyStallGuard } from "./stall.mjs";
 import { annotationMarkerBody, checksWithActionableAnnotations } from "../check-annotations.mjs";
@@ -157,7 +157,9 @@ export async function handleFixCode(ctx) {
         isConfiguredBotAuthor(review, botUsernames));
     const skippedDismissalIds = new Set(unauthorizedDismissals.map((review) => review.id));
     const changesRequestedReviewsForWork = actionableChangesRequestedReviews.filter((review) => !skippedDismissalIds.has(review.id));
-    const resolutionOnlyThreadsForWork = resolutionOnlyThreads.filter((thread) => !skippedThreadIds.has(thread.id) && thread.path !== null && thread.line !== null);
+    const resolutionOnlyThreadsForWork = resolutionOnlyThreads.filter((thread) => !skippedThreadIds.has(thread.id) &&
+        ((thread.path !== null && thread.line !== null) ||
+            canResolveOutdatedBotWithoutLocation(thread, botUsernames)));
     const hasConflicts = report.mergeStatus.status === "CONFLICTS";
     const isBehind = report.mergeStatus.status === "BEHIND";
     const { behindBaseHint } = loadConfig().iterate;
@@ -209,15 +211,16 @@ export async function handleFixCode(ctx) {
     const { resolveCommand, resolveOnlyCommand } = buildResolveCommand(retryableAgentThreads, resolutionOnlyThreadsForWork, allCommentIds, changesRequestedReviewsForWork, failingAgentChecks, prReference, botUsernames, ruleAutoResolveThreadIds, report.viewerAuthorization, allThreads);
     // Safety: if the base branch is unknown, escalate when a push is plausible — the agent
     // would need the correct base to rebase safely. This is a conservative guard, not a
-    // prediction that the agent *will* push. Intentionally broader than `pushLikely` above:
-    // resolution-only threads also need a known base in case the agent does push.
+    // prediction that the agent *will* push. Located resolution-only threads retain that guard;
+    // an outdated bot thread resolved only by ID has no code or push path.
+    const locatedResolutionOnlyThreadsForWork = resolutionOnlyThreadsForWork.filter((thread) => thread.path !== null && thread.line !== null);
     const pushIsPlausible = retryableActionableThreads.length > 0 ||
         failingAgentChecks.length > 0 ||
         annotatedExtra.length > 0 ||
         hasConflicts ||
         changesRequestedReviewsForWork.length > 0 ||
         actionableComments.length > 0 ||
-        resolutionOnlyThreadsForWork.length > 0;
+        locatedResolutionOnlyThreadsForWork.length > 0;
     if (baseLookup.isFallback && pushIsPlausible) {
         const fallbackEscalateBase = {
             triggers: ["base-branch-unknown"],

package/bin/commands/iterate/thread-mutation-routing.d.mts

@@ -6,4 +6,5 @@ export interface ThreadMutationRouting {
     standaloneResolveThreadIds: string[];
     resolveThreadIds: string[];
 }
+export declare function canResolveOutdatedBotWithoutLocation(thread: ReviewThread, botUsernames: NormalizedBotUsernames): boolean;
 export declare function buildThreadMutationRouting(threads: Array<AgentThread | ReviewThread>, botUsernames: NormalizedBotUsernames, ruleAutoResolveThreadIds: string[]): ThreadMutationRouting;

package/bin/commands/iterate/thread-mutation-routing.mjs

@@ -3,6 +3,13 @@ import { threadEndedByShepherd } from "../../comments/marker.mjs";
 function dedupeIds(ids) {
     return [...new Set(ids)];
 }
+export function canResolveOutdatedBotWithoutLocation(thread, botUsernames) {
+    return (!thread.isResolved &&
+        thread.isOutdated &&
+        (thread.path === null || thread.line === null) &&
+        isConfiguredBotAuthor(thread, botUsernames) &&
+        thread.viewerCanResolve === true);
+}
 export function buildThreadMutationRouting(threads, botUsernames, ruleAutoResolveThreadIds) {
     const isOrdinaryHuman = (thread) => isHumanAuthor(thread) && !isConfiguredBotAuthor(thread, botUsernames);
     const replyThreadIds = dedupeIds(threads

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pr-shepherd",
-  "version": "0.46.1",
+  "version": "0.46.2",
   "description": "Autonomous PR CI monitor and review-comment resolver for agentic coding tools",
   "keywords": [
     "automation",

package/plugins/pr-shepherd/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "pr-shepherd",
-  "version": "0.46.1",
+  "version": "0.46.2",
   "description": "Autonomous PR CI monitor and review-comment resolver for Codex.",
   "author": {
     "name": "Jonathan Ong",

package/plugins/pr-shepherd/.codex.mcp.json

@@ -2,7 +2,7 @@
   "mcpServers": {
     "pr-shepherd": {
       "command": "npx",
-      "args": ["--yes", "--package", "pr-shepherd@0.46.1", "pr-shepherd-mcp"]
+      "args": ["--yes", "--package", "pr-shepherd@0.46.2", "pr-shepherd-mcp"]
     }
   }
 }

package/plugins/pr-shepherd/.mcp.json

@@ -1,6 +1,6 @@
 {
   "pr-shepherd": {
     "command": "npx",
-    "args": ["--yes", "--package", "pr-shepherd@0.46.1", "pr-shepherd-mcp"]
+    "args": ["--yes", "--package", "pr-shepherd@0.46.2", "pr-shepherd-mcp"]
   }
 }

package/plugins/pr-shepherd/skills/pr-shepherd/SKILL.md

@@ -64,7 +64,7 @@ When several bullets share one runId (matrix jobs from the same run), the `rerun
 
 Applies to every `apply review:` / `resolve-only:` command the CLI prints. Covers only what stays safe if you run the printed command **unmodified** — `$HEAD_SHA`/`$DISMISS_MESSAGE` substitution remains a separate CLI-printed step because the command is unsafe by default without those placeholders.
 
-The CLI only includes IDs whose per-object GitHub viewer capability and semantic routing authorize the corresponding generated action. Direct `apply review` honors those emitted IDs without a second authorization preflight and surfaces GitHub's per-operation result. Do not reconstruct omitted review reply, thread resolution, or bot-review dismissal IDs and do not hand them off: denied or unverifiable generated mutations are one-look skips that Shepherd suppresses until the item is edited. Threads without a path or line follow the same skip rule.
+The CLI only includes IDs whose per-object GitHub viewer capability and semantic routing authorize the corresponding generated action. Direct `apply review` honors those emitted IDs without a second authorization preflight and surfaces GitHub's per-operation result. Do not reconstruct omitted review reply, thread resolution, or bot-review dismissal IDs and do not hand them off: denied or unverifiable generated mutations are one-look skips that Shepherd suppresses until the item is edited. Active threads without a path or line follow the same skip rule; authorized outdated bot threads are emitted for resolution by thread ID even when GitHub clears their source line.
 
 - Run every generated `apply review:` / `resolve-only:` command even when no code change is warranted. The command records the agent's disposition of the included review items; skipping it leaves bot threads active and can eventually trigger `fix-thrash`.
 - Never add first-look-only or check-annotation IDs to `--reply-thread-ids`, `--resolve-thread-ids`, `--dismiss-review-ids`, or `--minimize-comment-ids` — those flags are pre-populated by the CLI.