paperclip-github-plugin 0.8.11 → 0.9.0

package/README.md

@@ -44,7 +44,7 @@ The plugin adds a full in-host workflow instead of a one-off import script:
 2. Connect one or more GitHub repositories to Paperclip projects.
 3. Run a sync manually or let the scheduled job keep things up to date.
 
-During sync, the plugin imports one top-level Paperclip issue per GitHub issue, stamps it with a namespaced GitHub Sync plugin origin, updates already imported issues instead of recreating them, maps GitHub labels into Paperclip labels, and keeps GitHub-specific metadata in dedicated Paperclip surfaces rather than stuffing everything into the issue description. On Paperclip `2026.428.0` and newer, the detail surfaces can also recover GitHub issue and pull request links from Paperclip's own `originKind` / `originId` fields when the plugin registry or legacy hidden marker is missing.
+During sync, the plugin imports one top-level Paperclip issue per GitHub issue, stamps it with a namespaced GitHub Sync plugin origin, updates already imported issues instead of recreating them, maps GitHub labels into Paperclip labels, and keeps GitHub-specific metadata in dedicated Paperclip surfaces rather than stuffing everything into the issue description. On Paperclip `2026.512.0` and newer, the plugin passes the intended initial import status explicitly so Paperclip's assigned-issue creation defaults cannot override GitHub Sync's routing, and the detail surfaces can recover GitHub issue and pull request links from Paperclip's own `originKind` / `originId` fields when the plugin registry or legacy hidden marker is missing.
 
 When the host exposes plugin issue creation, imported GitHub issues are created through the Paperclip plugin SDK path so they are not attributed to the connected board user. The worker still uses direct local Paperclip REST calls for label sync and for description, assignee, or status repair paths when those routes are available.
 
@@ -94,7 +94,7 @@ If a Paperclip issue was created locally or by an agent workflow before GitHub S
 
 Manual GitHub issue links are added to the same import registry and issue-link entity used by normal sync, so future syncs update the Paperclip issue from the GitHub issue. Manual pull request links are added to the PR-link entity used by the project Pull Requests page, so future syncs monitor PR status even when there is no closing GitHub issue.
 
-Linked Paperclip issues can also be unlinked from the GitHub detail surface. Unlinking removes the active GitHub Sync link metadata and import-registry tracking for that Paperclip issue without deleting either side, so the issue stays local until it is linked again.
+Operators can unlink a linked Paperclip issue from the GitHub detail surface when they intentionally want GitHub Sync to stop updating it. Agent-facing tools and native agent API routes can create durable issue and pull request links, but they do not expose an unlink operation; internal sync repair may still tombstone a link when GitHub transfers an issue to an unmapped repository.
 
 ### Agent workflows built in
 
@@ -104,7 +104,7 @@ They can also link a Paperclip issue to a GitHub issue or pull request in any ac
 ## Requirements
 
 - Node.js 20+
-- a Paperclip host with plugin installation enabled. GitHub Sync is built and tested against Paperclip `2026.428.0`; the manifest relies on explicit capabilities instead of a strict host-version gate because current latest/development hosts can report `0.0.0` during plugin upgrade.
+- a Paperclip host with plugin installation enabled. GitHub Sync is built and tested against Paperclip `2026.512.0`; the manifest relies on explicit capabilities instead of a strict host-version gate because current latest/development hosts can report `0.0.0` during plugin upgrade.
 - a GitHub token with API access to the repositories you want to sync
 
 ## Install from npm
@@ -219,7 +219,7 @@ Notes:
 
 GitHub Sync uses direct worker-side Paperclip REST calls for host paths that are not fully covered by the plugin SDK, such as label reconciliation and some issue repair paths. By default, manual setup and sync actions use the current browser origin. If that origin is not reachable from the plugin worker, set **Worker Paperclip API URL** in GitHub Sync settings; the value is saved internally as plugin config `paperclipApiBaseUrl`.
 
-For private LAN, Docker, Kubernetes, custom DNS, or self-signed-certificate deployments, set that field to a local route the plugin worker can reach, such as `http://localhost:3100`, and port-forward or route that address to the Paperclip API when needed. Do not rely on exporting a process environment variable named `PAPERCLIP_API_URL` to Paperclip; Paperclip `2026.428.0` does not pass that value through to plugin worker runtime.
+For private LAN, Docker, Kubernetes, custom DNS, or self-signed-certificate deployments, set that field to a local route the plugin worker can reach, such as `http://localhost:3100`, and port-forward or route that address to the Paperclip API when needed. Do not rely on exporting a process environment variable named `PAPERCLIP_API_URL` to Paperclip; release-target verification keeps this as explicit plugin configuration because worker runtime environments do not guarantee that process variable.
 
 ## GitHub agent tools
 
@@ -354,8 +354,8 @@ Useful scripts:
 
 - `pnpm dev` watches the manifest, worker, and UI bundles and rebuilds them into `dist/`
 - `pnpm dev:ui` starts a local Paperclip plugin UI dev server from `dist/ui` on port `4177`
-- `pnpm test:e2e` builds the plugin, boots an isolated Paperclip `2026.428.0` instance, installs the plugin, and verifies the hosted settings page renders
-- `pnpm verify:manual` builds the plugin, boots a local-trusted Paperclip `2026.428.0` instance for manual inspection, seeds a `Dummy Company` with a mapped review project and a `CEO` agent on the Codex local adapter using model `gpt-5.4`, installs the plugin, and opens the company dashboard without seeding KPI history.
+- `pnpm test:e2e` builds the plugin, boots an isolated Paperclip `2026.512.0` instance, installs the plugin, and verifies the hosted settings page renders
+- `pnpm verify:manual` builds the plugin, boots a local-trusted Paperclip `2026.512.0` instance for manual inspection, seeds a `Dummy Company` with a mapped review project and a `CEO` agent on the Codex local adapter using model `gpt-5.4`, installs the plugin, and opens the company dashboard without seeding KPI history.
 
 For fast hosted UI iteration, run `pnpm dev` in one terminal and `pnpm dev:ui` in another.
 

package/dist/manifest.js

@@ -642,7 +642,7 @@ var PULL_REQUEST_ASSET_API_ROUTE_URL_PATH = `/api/plugins/${GITHUB_SYNC_PLUGIN_I
 var require2 = createRequire(import.meta.url);
 var packageJson = require2("../package.json");
 var SCHEDULE_TICK_CRON = "* * * * *";
-var MANIFEST_VERSION = "0.8.11"?.trim() || typeof packageJson.version === "string" && packageJson.version.trim() || process.env.npm_package_version?.trim() || "0.0.0-dev";
+var MANIFEST_VERSION = "0.9.0"?.trim() || typeof packageJson.version === "string" && packageJson.version.trim() || process.env.npm_package_version?.trim() || "0.0.0-dev";
 var manifest = {
   id: GITHUB_SYNC_PLUGIN_ID,
   apiVersion: 1,

package/dist/worker.js

@@ -2857,21 +2857,10 @@ async function buildToolbarSyncState(ctx, input) {
   if (entityType === "issue" && entityId && companyId) {
     const link = await resolvePaperclipIssueGitHubLink(ctx, entityId, companyId);
     if (link) {
-      const mappings2 = getSyncableMappingsForTarget(settings.mappings, {
-        kind: "issue",
-        companyId,
-        projectId: link.paperclipProjectId,
-        issueId: entityId,
-        repositoryUrl: link.repositoryUrl,
-        githubIssueId: link.githubIssueId,
-        githubIssueNumber: link.githubIssueNumber,
-        githubIssueUrl: link.githubIssueUrl,
-        displayLabel: `issue #${link.githubIssueNumber}`
-      });
       return {
         kind: "issue",
         visible: false,
-        canRun: githubTokenConfigured && mappings2.length > 0,
+        canRun: githubTokenConfigured,
         label: `Sync #${link.githubIssueNumber}`,
         message: `Sync ${link.repositoryUrl.replace(/^https:\/\/github\.com\//, "")} issue #${link.githubIssueNumber}.`,
         syncState: settings.syncState,
@@ -2880,20 +2869,10 @@ async function buildToolbarSyncState(ctx, input) {
       };
     }
     const pullRequestLink = await resolvePaperclipIssueGitHubPullRequestLink(ctx, entityId, companyId);
-    const mappings = pullRequestLink ? getSyncableMappingsForTarget(settings.mappings, {
-      kind: "issue",
-      companyId,
-      projectId: pullRequestLink.data.paperclipProjectId,
-      issueId: entityId,
-      repositoryUrl: pullRequestLink.data.repositoryUrl,
-      githubPullRequestNumber: pullRequestLink.data.githubPullRequestNumber,
-      githubPullRequestUrl: pullRequestLink.data.githubPullRequestUrl,
-      displayLabel: `pull request #${pullRequestLink.data.githubPullRequestNumber}`
-    }) : [];
     return {
       kind: "issue",
       visible: false,
-      canRun: githubTokenConfigured && mappings.length > 0,
+      canRun: githubTokenConfigured && Boolean(pullRequestLink),
       label: pullRequestLink?.data.githubPullRequestNumber ? `Sync PR #${pullRequestLink.data.githubPullRequestNumber}` : "Sync issue",
       message: pullRequestLink ? `Sync ${pullRequestLink.data.repositoryUrl.replace(/^https:\/\/github\.com\//, "")} pull request #${pullRequestLink.data.githubPullRequestNumber}.` : "This Paperclip issue is not linked to GitHub yet.",
       syncState: settings.syncState,
@@ -5702,9 +5681,19 @@ function buildPaperclipIssueStatusTransitionComment(params) {
   };
 }
 function buildPaperclipPullRequestIssueStatusTransitionComment(params) {
-  const reason = describeGitHubLinkedPullRequestsStatusReason([params.pullRequest]);
+  const reason = describeGitHubDirectPullRequestIssueStatusReason(params.pullRequests);
   return `GitHub Sync updated the status from \`${formatPaperclipIssueStatus(params.previousStatus)}\` to \`${formatPaperclipIssueStatus(params.nextStatus)}\` because ${reason}.`;
 }
+function describeGitHubDirectPullRequestIssueStatusReason(pullRequests) {
+  const openPullRequests = pullRequests.map((entry) => entry.pullRequest).filter((pullRequest) => Boolean(pullRequest));
+  if (openPullRequests.length > 0) {
+    return describeGitHubLinkedPullRequestsStatusReason(openPullRequests);
+  }
+  if (pullRequests.some((entry) => entry.lifecycleState === "merged")) {
+    return pullRequests.length === 1 ? "the linked pull request was merged" : "at least one linked pull request was merged";
+  }
+  return pullRequests.length === 1 ? "the linked pull request was closed without merge" : "all linked pull requests were closed without merge";
+}
 function resolvePaperclipIssueStatus(params) {
   const {
     currentStatus,
@@ -5757,6 +5746,23 @@ function resolvePaperclipPullRequestIssueStatus(params) {
     preserveTransientUnknownMergeabilityWait: currentStatus === "done" || currentStatus === "in_review"
   });
 }
+function resolvePaperclipDirectPullRequestIssueStatus(params) {
+  const { currentStatus, pullRequests, hasExecutorHandoffTarget } = params;
+  const openPullRequests = pullRequests.map((entry) => entry.pullRequest).filter((pullRequest) => Boolean(pullRequest));
+  if (openPullRequests.length > 0) {
+    if (shouldPreserveBlockedExternalPullRequestWait({
+      currentStatus,
+      linkedPullRequests: openPullRequests
+    })) {
+      return "blocked";
+    }
+    return resolvePaperclipStatusFromLinkedPullRequests(openPullRequests, {
+      preferInProgress: hasExecutorHandoffTarget,
+      preserveTransientUnknownMergeabilityWait: currentStatus === "done" || currentStatus === "in_review"
+    });
+  }
+  return pullRequests.some((entry) => entry.lifecycleState === "merged") ? "done" : "cancelled";
+}
 async function listLinkedPullRequestsForIssue(octokit, repository, issueNumber) {
   const linkedPullRequests = [];
   const seenPullRequestKeys = /* @__PURE__ */ new Set();
@@ -8996,6 +9002,16 @@ async function assignImportedPaperclipIssueToUser(ctx, params) {
     });
   }
 }
+async function ensurePaperclipIssueStandardWorkMode(ctx, issue, companyId) {
+  if (!("workMode" in issue) || issue.workMode === "standard") {
+    return issue;
+  }
+  return ctx.issues.update(
+    issue.id,
+    { workMode: "standard" },
+    companyId
+  );
+}
 async function createPaperclipIssue(ctx, mapping, advancedSettings, issue, availableLabels, paperclipApiBaseUrl, syncFailureContext) {
   if (!mapping.companyId || !mapping.paperclipProjectId) {
     throw new Error(`Mapping ${mapping.id} is missing resolved Paperclip project identifiers.`);
@@ -9003,15 +9019,20 @@ async function createPaperclipIssue(ctx, mapping, advancedSettings, issue, avail
   const title = issue.title;
   const description = buildPaperclipIssueDescription(issue);
   const defaultAssignee = getConfiguredAdvancedAssigneePrincipal(advancedSettings, "default");
-  const createdIssue = await ctx.issues.create({
-    companyId: mapping.companyId,
-    projectId: mapping.paperclipProjectId,
-    title,
-    ...description ? { description } : {},
-    originKind: GITHUB_ISSUE_ORIGIN_KIND,
-    originId: normalizeGitHubIssueHtmlUrl(issue.htmlUrl) ?? issue.htmlUrl,
-    ...defaultAssignee?.kind === "agent" ? { assigneeAgentId: defaultAssignee.id } : defaultAssignee?.kind === "user" ? { assigneeUserId: defaultAssignee.id } : {}
-  });
+  const createdIssue = await ensurePaperclipIssueStandardWorkMode(
+    ctx,
+    await ctx.issues.create({
+      companyId: mapping.companyId,
+      projectId: mapping.paperclipProjectId,
+      title,
+      ...description ? { description } : {},
+      status: advancedSettings.defaultStatus,
+      originKind: GITHUB_ISSUE_ORIGIN_KIND,
+      originId: normalizeGitHubIssueHtmlUrl(issue.htmlUrl) ?? issue.htmlUrl,
+      ...defaultAssignee?.kind === "agent" ? { assigneeAgentId: defaultAssignee.id } : defaultAssignee?.kind === "user" ? { assigneeUserId: defaultAssignee.id } : {}
+    }),
+    mapping.companyId
+  );
   const ensuredCreatedIssueId = createdIssue.id;
   const normalizedCreatedIssueDescription = createdIssue.description ?? void 0;
   const createPath = "sdk";
@@ -9729,6 +9750,18 @@ async function synchronizePaperclipIssueStatuses(ctx, octokit, repository, mappi
     updatedDescriptionsCount
   };
 }
+function groupGitHubPullRequestLinksByPaperclipIssue(pullRequestLinks) {
+  const groups = /* @__PURE__ */ new Map();
+  const sortedLinks = [...pullRequestLinks].sort(
+    (left, right) => left.paperclipIssueId.localeCompare(right.paperclipIssueId) || left.data.repositoryUrl.localeCompare(right.data.repositoryUrl) || left.data.githubPullRequestNumber - right.data.githubPullRequestNumber
+  );
+  for (const pullRequestLink of sortedLinks) {
+    const group = groups.get(pullRequestLink.paperclipIssueId) ?? [];
+    group.push(pullRequestLink);
+    groups.set(pullRequestLink.paperclipIssueId, group);
+  }
+  return groups;
+}
 async function synchronizePaperclipPullRequestIssueStatuses(ctx, octokit, mapping, advancedSettings, pullRequestLinks, paperclipApiBaseUrl, pullRequestStatusCache, syncFailureContext, failures, assertNotCancelled, onProgress) {
   if (!mapping.companyId || !ctx.issues || typeof ctx.issues.get !== "function" || typeof ctx.issues.update !== "function") {
     return {
@@ -9740,52 +9773,93 @@ async function synchronizePaperclipPullRequestIssueStatuses(ctx, octokit, mappin
   const mappingCompanyId = mapping.companyId;
   const mappingProjectId = mapping.paperclipProjectId;
   const totalIssueCount = pullRequestLinks.length;
+  const pullRequestLinkGroups = groupGitHubPullRequestLinksByPaperclipIssue(pullRequestLinks);
   const queuedIssueWakeups = [];
-  for (const pullRequestLink of pullRequestLinks) {
-    if (assertNotCancelled) {
-      await assertNotCancelled();
-    }
-    try {
-      const pullRequestRepository = requireRepositoryReference(pullRequestLink.data.repositoryUrl);
-      updateSyncFailureContext(syncFailureContext, {
-        phase: "evaluating_github_status",
-        repositoryUrl: pullRequestRepository.url,
-        githubIssueNumber: void 0
-      });
-      const pullRequestResponse = await octokit.rest.pulls.get({
-        owner: pullRequestRepository.owner,
-        repo: pullRequestRepository.repo,
-        pull_number: pullRequestLink.data.githubPullRequestNumber,
-        headers: {
-          "X-GitHub-Api-Version": GITHUB_API_VERSION
-        }
-      });
-      const livePullRequestState = getPullRequestApiState({
-        state: pullRequestResponse.data.state,
-        merged: pullRequestResponse.data.merged
-      }) === "open" ? "open" : "closed";
-      if (livePullRequestState !== pullRequestLink.data.githubPullRequestState || pullRequestResponse.data.html_url !== pullRequestLink.data.githubPullRequestUrl || pullRequestResponse.data.title !== pullRequestLink.data.title) {
-        await upsertGitHubPullRequestLinkRecord(ctx, {
-          companyId: pullRequestLink.data.companyId ?? mappingCompanyId,
-          projectId: pullRequestLink.data.paperclipProjectId ?? mappingProjectId,
-          issueId: pullRequestLink.paperclipIssueId,
+  for (const [paperclipIssueId, issuePullRequestLinks] of pullRequestLinkGroups.entries()) {
+    const pullRequestSnapshots = [];
+    let groupHadFailure = false;
+    for (const pullRequestLink of issuePullRequestLinks) {
+      if (assertNotCancelled) {
+        await assertNotCancelled();
+      }
+      try {
+        const pullRequestRepository = requireRepositoryReference(pullRequestLink.data.repositoryUrl);
+        updateSyncFailureContext(syncFailureContext, {
+          phase: "evaluating_github_status",
           repositoryUrl: pullRequestRepository.url,
-          pullRequestNumber: pullRequestLink.data.githubPullRequestNumber,
-          pullRequestUrl: pullRequestResponse.data.html_url ?? pullRequestLink.data.githubPullRequestUrl,
-          pullRequestTitle: pullRequestResponse.data.title || pullRequestLink.data.title || `Pull request #${pullRequestLink.data.githubPullRequestNumber}`,
-          pullRequestState: livePullRequestState
+          githubIssueNumber: void 0
+        });
+        const pullRequestResponse = await octokit.rest.pulls.get({
+          owner: pullRequestRepository.owner,
+          repo: pullRequestRepository.repo,
+          pull_number: pullRequestLink.data.githubPullRequestNumber,
+          headers: {
+            "X-GitHub-Api-Version": GITHUB_API_VERSION
+          }
         });
+        const livePullRequestLifecycleState = getPullRequestApiState({
+          state: pullRequestResponse.data.state,
+          merged: pullRequestResponse.data.merged
+        });
+        const livePullRequestLinkState = livePullRequestLifecycleState === "open" ? "open" : "closed";
+        if (livePullRequestLinkState !== pullRequestLink.data.githubPullRequestState || pullRequestResponse.data.html_url !== pullRequestLink.data.githubPullRequestUrl || pullRequestResponse.data.title !== pullRequestLink.data.title) {
+          await upsertGitHubPullRequestLinkRecord(ctx, {
+            companyId: pullRequestLink.data.companyId ?? mappingCompanyId,
+            projectId: pullRequestLink.data.paperclipProjectId ?? mappingProjectId,
+            issueId: pullRequestLink.paperclipIssueId,
+            repositoryUrl: pullRequestRepository.url,
+            pullRequestNumber: pullRequestLink.data.githubPullRequestNumber,
+            pullRequestUrl: pullRequestResponse.data.html_url ?? pullRequestLink.data.githubPullRequestUrl,
+            pullRequestTitle: pullRequestResponse.data.title || pullRequestLink.data.title || `Pull request #${pullRequestLink.data.githubPullRequestNumber}`,
+            pullRequestState: livePullRequestLinkState
+          });
+        }
+        if (livePullRequestLifecycleState === "open") {
+          const pullRequest = await getGitHubPullRequestStatusSnapshot(
+            octokit,
+            pullRequestRepository,
+            pullRequestLink.data.githubPullRequestNumber,
+            pullRequestStatusCache
+          );
+          pullRequestSnapshots.push({
+            pullRequestLink,
+            repository: pullRequestRepository,
+            lifecycleState: "open",
+            pullRequest
+          });
+        } else {
+          pullRequestSnapshots.push({
+            pullRequestLink,
+            repository: pullRequestRepository,
+            lifecycleState: livePullRequestLifecycleState
+          });
+        }
+      } catch (error) {
+        if (isGitHubRateLimitError(error)) {
+          throw error;
+        }
+        groupHadFailure = true;
+        recordRecoverableSyncFailure(ctx, failures, error, syncFailureContext);
+      } finally {
+        completedIssueCount += 1;
+        if (onProgress) {
+          await onProgress({
+            pullRequestLink,
+            completedIssueCount,
+            totalIssueCount
+          });
+        }
       }
-      if (livePullRequestState !== "open") {
-        continue;
+    }
+    if (groupHadFailure || pullRequestSnapshots.length === 0) {
+      continue;
+    }
+    const primaryRepository = pullRequestSnapshots[0]?.repository;
+    try {
+      if (assertNotCancelled) {
+        await assertNotCancelled();
       }
-      const pullRequest = await getGitHubPullRequestStatusSnapshot(
-        octokit,
-        pullRequestRepository,
-        pullRequestLink.data.githubPullRequestNumber,
-        pullRequestStatusCache
-      );
-      const paperclipIssue = await ctx.issues.get(pullRequestLink.paperclipIssueId, mapping.companyId);
+      const paperclipIssue = await ctx.issues.get(paperclipIssueId, mapping.companyId);
       if (!paperclipIssue) {
         continue;
       }
@@ -9794,12 +9868,12 @@ async function synchronizePaperclipPullRequestIssueStatuses(ctx, octokit, mappin
         paperclipIssueSyncContext,
         advancedSettings
       );
-      let nextStatus = resolvePaperclipPullRequestIssueStatus({
+      let nextStatus = resolvePaperclipDirectPullRequestIssueStatus({
         currentStatus: paperclipIssue.status,
-        pullRequest,
+        pullRequests: pullRequestSnapshots,
         hasExecutorHandoffTarget: Boolean(executorTransitionAssignee)
       });
-      if (paperclipIssue.status === "blocked" && nextStatus !== "blocked" && await hasUnresolvedPaperclipIssueBlocker(ctx, paperclipIssue, mapping.companyId)) {
+      if (paperclipIssue.status === "blocked" && nextStatus !== "blocked" && pullRequestSnapshots.some((entry) => entry.lifecycleState === "open") && await hasUnresolvedPaperclipIssueBlocker(ctx, paperclipIssue, mapping.companyId)) {
         nextStatus = "blocked";
       }
       const shouldPreserveMaintainerWaitRouting = isHealthyMaintainerWaitTransition({
@@ -9807,6 +9881,10 @@ async function synchronizePaperclipPullRequestIssueStatuses(ctx, octokit, mappin
         nextStatus,
         syncContext: paperclipIssueSyncContext
       });
+      const shouldClearCompletedExecutionPolicy = shouldClearCompletedSyncExecutionPolicy({
+        nextStatus,
+        syncContext: paperclipIssueSyncContext
+      });
       const nextTransitionAssignee = resolveSyncTransitionAssignee({
         currentStatus: paperclipIssue.status,
         nextStatus,
@@ -9817,20 +9895,20 @@ async function synchronizePaperclipPullRequestIssueStatuses(ctx, octokit, mappin
       const nextAssigneeChanged = nextTransitionAssignee ? !doesPaperclipIssueAssigneeMatch(paperclipIssueSyncContext.assignee, nextTransitionAssignee.principal) : false;
       const shouldWakeTransitionAssignee = paperclipIssue.status !== nextStatus && nextTransitionAssignee?.principal.kind === "agent" && isActionablePaperclipIssueStatus(nextStatus) && (nextAssigneeChanged || paperclipIssue.status !== nextStatus);
       if (paperclipIssue.status === nextStatus) {
-        if (shouldClearTransitionAssignee) {
+        if (shouldClearTransitionAssignee || shouldClearCompletedExecutionPolicy) {
           updateSyncFailureContext(syncFailureContext, {
             phase: "updating_paperclip_status",
-            repositoryUrl: pullRequestRepository.url,
+            repositoryUrl: primaryRepository?.url,
             githubIssueNumber: void 0
           });
           await updatePaperclipIssueState(ctx, {
             companyId: mapping.companyId,
-            issueId: pullRequestLink.paperclipIssueId,
+            issueId: paperclipIssueId,
             currentStatus: paperclipIssue.status,
             syncContext: paperclipIssueSyncContext,
             nextStatus,
-            clearAssignee: true,
-            ...shouldPreserveMaintainerWaitRouting ? { clearExecutionPolicy: true } : {},
+            ...shouldClearTransitionAssignee ? { clearAssignee: true } : {},
+            ...shouldPreserveMaintainerWaitRouting || shouldClearCompletedExecutionPolicy ? { clearExecutionPolicy: true } : {},
             transitionComment: "",
             paperclipApiBaseUrl
           });
@@ -9840,22 +9918,22 @@ async function synchronizePaperclipPullRequestIssueStatuses(ctx, octokit, mappin
       const transitionComment = buildPaperclipPullRequestIssueStatusTransitionComment({
         previousStatus: paperclipIssue.status,
         nextStatus,
-        pullRequest
+        pullRequests: pullRequestSnapshots
       });
       updateSyncFailureContext(syncFailureContext, {
         phase: "updating_paperclip_status",
-        repositoryUrl: pullRequestRepository.url,
+        repositoryUrl: primaryRepository?.url,
         githubIssueNumber: void 0
       });
       await updatePaperclipIssueState(ctx, {
         companyId: mapping.companyId,
-        issueId: pullRequestLink.paperclipIssueId,
+        issueId: paperclipIssueId,
         currentStatus: paperclipIssue.status,
         syncContext: paperclipIssueSyncContext,
         nextStatus,
         ...nextTransitionAssignee ? { nextAssignee: nextTransitionAssignee.principal } : {},
         ...shouldClearTransitionAssignee ? { clearAssignee: true } : {},
-        ...shouldPreserveMaintainerWaitRouting ? { clearExecutionPolicy: true } : {},
+        ...shouldPreserveMaintainerWaitRouting || shouldClearCompletedExecutionPolicy ? { clearExecutionPolicy: true } : {},
         transitionComment,
         paperclipApiBaseUrl
       });
@@ -9863,7 +9941,7 @@ async function synchronizePaperclipPullRequestIssueStatuses(ctx, octokit, mappin
       if (shouldWakeTransitionAssignee && nextTransitionAssignee?.principal.kind === "agent") {
         queuedIssueWakeups.push({
           assigneeAgentId: nextTransitionAssignee.principal.id,
-          paperclipIssueId: pullRequestLink.paperclipIssueId,
+          paperclipIssueId,
           reason: STATUS_TRANSITION_WAKE_REASON,
           mutation: "status_transition",
           previousStatus: paperclipIssue.status,
@@ -9875,16 +9953,6 @@ async function synchronizePaperclipPullRequestIssueStatuses(ctx, octokit, mappin
         throw error;
       }
       recordRecoverableSyncFailure(ctx, failures, error, syncFailureContext);
-      continue;
-    } finally {
-      completedIssueCount += 1;
-      if (onProgress) {
-        await onProgress({
-          pullRequestLink,
-          completedIssueCount,
-          totalIssueCount
-        });
-      }
     }
   }
   await mapWithConcurrency(
@@ -12909,19 +12977,24 @@ async function createProjectPullRequestPaperclipIssue(ctx, input) {
     };
   }
   const requestedTitle = typeof input.title === "string" && input.title.trim() ? input.title.trim() : pullRequest.title.trim();
-  const createdIssue = await ctx.issues.create({
-    companyId: scope.companyId,
-    projectId: scope.projectId,
-    title: requestedTitle,
-    originKind: GITHUB_PULL_REQUEST_ORIGIN_KIND,
-    originId: pullRequestUrl,
-    description: buildPaperclipIssueDescriptionFromPullRequest({
-      repository: scope.repository,
-      pullRequestNumber,
-      pullRequestUrl,
-      body: pullRequest.body
-    })
-  });
+  const createdIssue = await ensurePaperclipIssueStandardWorkMode(
+    ctx,
+    await ctx.issues.create({
+      companyId: scope.companyId,
+      projectId: scope.projectId,
+      title: requestedTitle,
+      status: "todo",
+      originKind: GITHUB_PULL_REQUEST_ORIGIN_KIND,
+      originId: pullRequestUrl,
+      description: buildPaperclipIssueDescriptionFromPullRequest({
+        repository: scope.repository,
+        pullRequestNumber,
+        pullRequestUrl,
+        body: pullRequest.body
+      })
+    }),
+    scope.companyId
+  );
   const resolvedIssue = await ctx.issues.get(createdIssue.id, scope.companyId) ?? createdIssue;
   await upsertGitHubPullRequestLinkRecord(ctx, {
     companyId: scope.companyId,

package/package.json

@@ -1,10 +1,10 @@
 {
   "name": "paperclip-github-plugin",
-  "version": "0.8.11",
+  "version": "0.9.0",
   "description": "Paperclip plugin for synchronizing GitHub issues into Paperclip projects.",
   "license": "Apache-2.0",
   "type": "module",
-  "packageManager": "pnpm@10.33.2",
+  "packageManager": "pnpm@11.0.9",
   "engines": {
     "node": ">=20"
   },
@@ -41,7 +41,7 @@
   },
   "dependencies": {
     "@octokit/rest": "^22.0.1",
-    "@paperclipai/plugin-sdk": "^2026.428.0",
+    "@paperclipai/plugin-sdk": "^2026.512.0",
     "react": "^19.2.6",
     "react-markdown": "^10.1.0",
     "rehype-raw": "^7.0.0",