fix: stop server startup from auto-failing in-flight workflow runs (#1216)

CHANGELOG.md

@@ -7,8 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Fixed
+
+- **Server startup no longer marks actively-running workflows as failed.** The `failOrphanedRuns()` call has been removed from `packages/server/src/index.ts` to match the CLI precedent (`packages/cli/src/cli.ts:256-258`). Per the new CLAUDE.md principle "No Autonomous Lifecycle Mutation Across Process Boundaries", a stuck `running` row is now transitioned explicitly by the user: via the per-row Cancel/Abandon buttons on the dashboard workflow card, or `archon workflow abandon <run-id>` from the CLI. (`archon workflow cleanup` is a separate command that deletes OLD terminal runs for disk hygiene — it does not handle stuck `running` rows.) Closes #1216.
+
 ### Changed
 
+- **Dashboard nav tab** now shows a numeric count of running workflows instead of a binary pulse dot. Reads from the existing `/api/dashboard/runs` `counts.running` field; same 10s polling interval.
+- **Workflow run destructive actions** (Abandon, Cancel, Delete, Reject) now use a proper confirmation dialog matching the codebase-delete UX, replacing the browser's native `window.confirm()` popups. Each dialog includes context-appropriate copy describing what the action does to the run record.
+
 - **Claude Code binary resolution** (breaking for compiled binary users): Archon no longer embeds the Claude Code SDK into compiled binaries. In compiled builds, you must install Claude Code separately (`curl -fsSL https://claude.ai/install.sh | bash` on macOS/Linux, `irm https://claude.ai/install.ps1 | iex` on Windows, or `npm install -g @anthropic-ai/claude-code`) and point Archon at the executable via `CLAUDE_BIN_PATH` env var or `assistants.claude.claudeBinaryPath` in `.archon/config.yaml`. The Claude Agent SDK accepts either the native compiled binary (from the curl/PowerShell installer at `~/.local/bin/claude`) or a JS `cli.js` (from the npm install). Dev mode (`bun run`) is unaffected — the SDK resolves via `node_modules` as before. The Docker image ships Claude Code pre-installed with `CLAUDE_BIN_PATH` pre-set, so `docker run` still works out of the box. Resolves silent "Module not found /Users/runner/..." failures on macOS (#1210) and Windows (#1087).
 
 ### Added

packages/docs-web/src/content/docs/guides/authoring-workflows.md

@@ -474,7 +474,7 @@ This means a single transient crash may trigger up to **3 SDK retries** before a
 
 ## DAG Resume on Failure
 
-When a `nodes:` (DAG) workflow fails (including due to a server restart), the next invocation automatically resumes from where it left off — no `--resume` flag required.
+When a `nodes:` (DAG) workflow fails, the next invocation automatically resumes from where it left off — no `--resume` flag required.
 
 **How it works:**
 
@@ -483,7 +483,14 @@ When a `nodes:` (DAG) workflow fails (including due to a server restart), the ne
 3. Completed nodes are skipped; only failed and not-yet-run nodes are executed.
 4. You receive a platform message like: `Resuming workflow — skipping 3 already-completed node(s).`
 
-**Server restart**: If a server restart leaves runs in `running` status, they are automatically marked as `failed` on the next startup (with `metadata.failure_reason = 'server_restart'`). The next invocation of the same workflow at the same path auto-resumes from completed nodes.
+**Crashed servers / orphaned runs**: Archon does **not** auto-fail `running` rows on server startup — that would kill workflows actively executing in another process (CLI, adapter). If a server crash leaves a row stuck as `running`, it remains visible in the dashboard (the Dashboard nav tab shows a count of running workflows). Transition it to a terminal status explicitly:
+
+- **Web UI**: click the Abandon or Cancel button on the workflow card. Abandon marks the run `cancelled` and keeps completed-node history. Cancel also terminates any in-flight subprocess.
+- **CLI**: `archon workflow abandon <run-id>` (equivalent to the dashboard Abandon button). Run IDs are listed by `archon workflow status`.
+
+Once the row reaches a terminal status, the next invocation of the same workflow at the same path auto-resumes from completed nodes via the mechanism above.
+
+> Not to be confused with `archon workflow cleanup [days]`, which **deletes** old terminal runs (`completed`/`failed`/`cancelled`) from the database for disk hygiene. It does not transition `running` rows.
 
 **Known limitation**: AI session context from prior nodes is not restored. If a downstream node relies on in-context knowledge from a prior run's session (rather than artifacts), it may need to re-read those artifacts explicitly.
 

packages/server/src/index.ts

@@ -77,7 +77,6 @@ import {
   loadConfig,
   logConfig,
   getPort,
-  createWorkflowStore,
 } from '@archon/core';
 import type { IPlatformAdapter } from '@archon/core';
 import { createLogger, logArchonPaths, validateAppDefaultsPaths } from '@archon/paths';
@@ -208,12 +207,17 @@ export async function startServer(opts: ServerOptions = {}): Promise<void> {
   // Start cleanup scheduler
   startCleanupScheduler();
 
-  // Mark workflow runs orphaned by previous process termination as failed
-  void createWorkflowStore()
-    .failOrphanedRuns()
-    .catch(err => {
-      getLog().error({ err }, 'workflow.fail_orphans_failed');
-    });
+  // Note: orphaned-run cleanup intentionally NOT called at server startup.
+  // Running it here killed parallel workflow runs from other processes
+  // (CLI, adapters) by flipping their `running` rows to `failed` mid-flight.
+  // Same lesson the CLI already learned — see packages/cli/src/cli.ts:256-258.
+  // Per CLAUDE.md "No Autonomous Lifecycle Mutation Across Process Boundaries":
+  // surface ambiguous state to users and provide a one-click action instead.
+  // Users transition a stuck `running` row via the per-row Cancel/Abandon
+  // buttons in the Web UI dashboard, or `archon workflow abandon <run-id>`.
+  // (`archon workflow cleanup` is a separate command that deletes OLD terminal
+  // rows for disk hygiene — it does not handle stuck `running` rows.)
+  // See #1216.
 
   // Log Archon paths configuration
   logArchonPaths();

packages/web/src/components/dashboard/ConfirmRunActionDialog.tsx

@@ -0,0 +1,76 @@
+import type { ReactNode } from 'react';
+import {
+  AlertDialog,
+  AlertDialogAction,
+  AlertDialogCancel,
+  AlertDialogContent,
+  AlertDialogDescription,
+  AlertDialogFooter,
+  AlertDialogHeader,
+  AlertDialogTitle,
+  AlertDialogTrigger,
+} from '@/components/ui/alert-dialog';
+
+interface Props {
+  /** The element that opens the dialog when clicked (typically a button). */
+  trigger: ReactNode;
+  /** Dialog title (e.g. "Abandon workflow?"). */
+  title: string;
+  /** Body text — supports rich children (e.g. wrapping the workflow name in <strong>). */
+  description: ReactNode;
+  /** Confirm-button label (e.g. "Abandon", "Delete"). */
+  confirmLabel: string;
+  /** Invoked when the user confirms. The current callsites are all
+   *  fire-and-forget wrappers around React Query mutations whose error
+   *  handling lives at the page level (`runAction` in `DashboardPage.tsx`).
+   *  Widen to `Promise<void>` only if a caller needs to await the action. */
+  onConfirm: () => void;
+}
+
+/**
+ * Confirmation dialog for destructive workflow-run actions.
+ *
+ * Wraps shadcn's AlertDialog with the trigger included as a slot, so callers
+ * pass their existing action button as the `trigger` prop. The Action button
+ * is destructive-styled by default (per `AlertDialogAction` in
+ * `@/components/ui/alert-dialog`), which is appropriate for every workflow
+ * lifecycle action this is used for (Abandon, Cancel, Delete, Reject).
+ *
+ * Replaces previous use of `window.confirm()` for these actions to match the
+ * codebase-delete UX in `sidebar/ProjectSelector.tsx`.
+ */
+export function ConfirmRunActionDialog({
+  trigger,
+  title,
+  description,
+  confirmLabel,
+  onConfirm,
+}: Props): React.ReactElement {
+  return (
+    <AlertDialog>
+      <AlertDialogTrigger asChild>{trigger}</AlertDialogTrigger>
+      <AlertDialogContent>
+        <AlertDialogHeader>
+          <AlertDialogTitle>{title}</AlertDialogTitle>
+          <AlertDialogDescription asChild>
+            <div>{description}</div>
+          </AlertDialogDescription>
+        </AlertDialogHeader>
+        <AlertDialogFooter>
+          <AlertDialogCancel>Cancel</AlertDialogCancel>
+          <AlertDialogAction
+            onClick={(): void => {
+              // Caller's onConfirm is fire-and-forget over a parent-level
+              // runAction helper that surfaces errors via component state.
+              // We do NOT catch here; swallowing would hide failures the
+              // parent is positioned to display.
+              onConfirm();
+            }}
+          >
+            {confirmLabel}
+          </AlertDialogAction>
+        </AlertDialogFooter>
+      </AlertDialogContent>
+    </AlertDialog>
+  );
+}

packages/web/src/components/dashboard/WorkflowHistoryTable.tsx

@@ -3,6 +3,7 @@ import { Globe, Terminal, Hash, Send, GitBranch, Trash2 } from 'lucide-react';
 import type { DashboardRunResponse } from '@/lib/api';
 import { cn } from '@/lib/utils';
 import { formatDuration, formatStarted } from '@/lib/format';
+import { ConfirmRunActionDialog } from './ConfirmRunActionDialog';
 
 interface WorkflowHistoryTableProps {
   runs: DashboardRunResponse[];
@@ -101,21 +102,27 @@ export function WorkflowHistoryTable({
                     View Logs
                   </Link>
                   {onDelete && (
-                    <button
-                      onClick={(): void => {
-                        if (
-                          window.confirm(
-                            `Delete workflow run "${run.workflow_name}"? This cannot be undone.`
-                          )
-                        ) {
-                          onDelete(run.id);
-                        }
+                    <ConfirmRunActionDialog
+                      trigger={
+                        <button
+                          className="text-text-tertiary hover:text-error transition-colors"
+                          title="Delete run"
+                        >
+                          <Trash2 className="h-3 w-3" />
+                        </button>
+                      }
+                      title="Delete workflow run?"
+                      description={
+                        <>
+                          Permanently delete the run record for <strong>{run.workflow_name}</strong>{' '}
+                          and its events. This cannot be undone.
+                        </>
+                      }
+                      confirmLabel="Delete"
+                      onConfirm={(): void => {
+                        onDelete(run.id);
                       }}
-                      className="text-text-tertiary hover:text-error transition-colors"
-                      title="Delete run"
-                    >
-                      <Trash2 className="h-3 w-3" />
-                    </button>
+                    />
                   )}
                 </div>
               </td>

packages/web/src/components/dashboard/WorkflowRunCard.tsx

@@ -22,6 +22,7 @@ import { cn } from '@/lib/utils';
 import { formatDuration } from '@/lib/format';
 import { useWorkflowStore } from '@/stores/workflow-store';
 import type { WorkflowState } from '@/lib/types';
+import { ConfirmRunActionDialog } from './ConfirmRunActionDialog';
 
 interface WorkflowRunCardProps {
   run: DashboardRunResponse;
@@ -318,17 +319,25 @@ export function WorkflowRunCard({
             </button>
           )}
           {run.status === 'paused' && onReject && (
-            <button
-              onClick={(): void => {
-                if (window.confirm(`Reject workflow "${run.workflow_name}"?`)) {
-                  onReject(run.id);
-                }
+            <ConfirmRunActionDialog
+              trigger={
+                <button className="flex items-center gap-1 rounded-md px-2 py-1 text-xs text-error/80 hover:bg-error/10 hover:text-error transition-colors">
+                  <XCircle className="h-3.5 w-3.5" />
+                  Reject
+                </button>
+              }
+              title="Reject workflow?"
+              description={
+                <>
+                  Reject the paused workflow <strong>{run.workflow_name}</strong>. The run will be
+                  marked as failed and any pending iterations will not continue.
+                </>
+              }
+              confirmLabel="Reject"
+              onConfirm={(): void => {
+                onReject(run.id);
               }}
-              className="flex items-center gap-1 rounded-md px-2 py-1 text-xs text-error/80 hover:bg-error/10 hover:text-error transition-colors"
-            >
-              <XCircle className="h-3.5 w-3.5" />
-              Reject
-            </button>
+            />
           )}
           {run.status === 'failed' && onResume && (
             <button
@@ -342,47 +351,67 @@ export function WorkflowRunCard({
             </button>
           )}
           {run.status === 'running' && onAbandon && (
-            <button
-              onClick={(): void => {
-                if (window.confirm(`Abandon workflow "${run.workflow_name}"?`)) {
-                  onAbandon(run.id);
-                }
+            <ConfirmRunActionDialog
+              trigger={
+                <button className="flex items-center gap-1 rounded-md px-2 py-1 text-xs text-warning/80 hover:bg-warning/10 hover:text-warning transition-colors">
+                  <Ban className="h-3.5 w-3.5" />
+                  Abandon
+                </button>
+              }
+              title="Abandon workflow?"
+              description={
+                <>
+                  Mark <strong>{run.workflow_name}</strong> as cancelled. Already-completed nodes
+                  remain in the database; the run will not continue.
+                </>
+              }
+              confirmLabel="Abandon"
+              onConfirm={(): void => {
+                onAbandon(run.id);
               }}
-              className="flex items-center gap-1 rounded-md px-2 py-1 text-xs text-warning/80 hover:bg-warning/10 hover:text-warning transition-colors"
-            >
-              <Ban className="h-3.5 w-3.5" />
-              Abandon
-            </button>
+            />
           )}
           {(run.status === 'running' || run.status === 'pending') && (
-            <button
-              onClick={(): void => {
-                if (window.confirm(`Cancel workflow "${run.workflow_name}"?`)) {
-                  onCancel(run.id);
-                }
+            <ConfirmRunActionDialog
+              trigger={
+                <button className="flex items-center gap-1 rounded-md px-2 py-1 text-xs text-error/80 hover:bg-error/10 hover:text-error transition-colors">
+                  <XCircle className="h-3.5 w-3.5" />
+                  Cancel
+                </button>
+              }
+              title="Cancel workflow?"
+              description={
+                <>
+                  Cancel <strong>{run.workflow_name}</strong>. The run will be marked as cancelled
+                  and any in-flight subprocess will be terminated.
+                </>
+              }
+              confirmLabel="Cancel workflow"
+              onConfirm={(): void => {
+                onCancel(run.id);
               }}
-              className="flex items-center gap-1 rounded-md px-2 py-1 text-xs text-error/80 hover:bg-error/10 hover:text-error transition-colors"
-            >
-              <XCircle className="h-3.5 w-3.5" />
-              Cancel
-            </button>
+            />
           )}
           {onDelete && run.status !== 'running' && run.status !== 'pending' && (
-            <button
-              onClick={(): void => {
-                if (
-                  window.confirm(
-                    `Delete workflow run "${run.workflow_name}"? This cannot be undone.`
-                  )
-                ) {
-                  onDelete(run.id);
-                }
+            <ConfirmRunActionDialog
+              trigger={
+                <button className="flex items-center gap-1 rounded-md px-2 py-1 text-xs text-text-tertiary hover:bg-error/10 hover:text-error transition-colors">
+                  <Trash2 className="h-3.5 w-3.5" />
+                  Delete
+                </button>
+              }
+              title="Delete workflow run?"
+              description={
+                <>
+                  Permanently delete the run record for <strong>{run.workflow_name}</strong> and its
+                  events. This cannot be undone.
+                </>
+              }
+              confirmLabel="Delete"
+              onConfirm={(): void => {
+                onDelete(run.id);
               }}
-              className="flex items-center gap-1 rounded-md px-2 py-1 text-xs text-text-tertiary hover:bg-error/10 hover:text-error transition-colors"
-            >
-              <Trash2 className="h-3.5 w-3.5" />
-              Delete
-            </button>
+            />
           )}
         </div>
       </div>

packages/web/src/components/layout/TopNav.tsx

@@ -1,7 +1,7 @@
 import { NavLink, Link } from 'react-router';
 import { useQuery } from '@tanstack/react-query';
 import { LayoutDashboard, MessageSquare, Workflow, Settings } from 'lucide-react';
-import { listWorkflowRuns, getUpdateCheck } from '@/lib/api';
+import { listDashboardRuns, getUpdateCheck } from '@/lib/api';
 import { cn } from '@/lib/utils';
 
 const tabs = [
@@ -12,12 +12,15 @@ const tabs = [
 ] as const;
 
 export function TopNav(): React.ReactElement {
-  const { data: runningRuns } = useQuery({
-    queryKey: ['workflowRuns', { status: 'running' }],
-    queryFn: () => listWorkflowRuns({ status: 'running', limit: 1 }),
+  // We only need `counts.running` — a server-side aggregate independent of
+  // the `runs` array. `limit: 1` minimises the `runs` payload that the API
+  // returns alongside the counts (we discard it).
+  const { data: dashboardRuns } = useQuery({
+    queryKey: ['dashboardRuns', { status: 'running', forCount: true }],
+    queryFn: () => listDashboardRuns({ status: 'running', limit: 1 }),
     refetchInterval: 10_000,
   });
-  const hasRunning = (runningRuns?.length ?? 0) > 0;
+  const runningCount = dashboardRuns?.counts.running ?? 0;
 
   const { data: updateCheck } = useQuery({
     queryKey: ['update-check'],
@@ -53,8 +56,13 @@ export function TopNav(): React.ReactElement {
         >
           <Icon className="h-4 w-4" />
           {label}
-          {to === '/dashboard' && hasRunning && (
-            <span className="flex h-2 w-2 rounded-full bg-primary animate-pulse" />
+          {to === '/dashboard' && runningCount > 0 && (
+            <span
+              className="ml-1 inline-flex min-w-[1.25rem] items-center justify-center rounded-full bg-primary px-1.5 py-0.5 text-[10px] font-medium text-primary-foreground"
+              aria-label={`${runningCount} workflows running`}
+            >
+              {runningCount}
+            </span>
           )}
         </NavLink>
       ))}