fix(atlas): stop stalled boulder continuations

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

src/hooks/atlas/boulder-continuation-injector.ts

@@ -9,6 +9,7 @@ import { createInternalAgentContinuationTextPart, resolveInheritedPromptTools }
 import { dispatchInternalPrompt } from "../shared/prompt-async-gate"
 import { HOOK_NAME } from "./hook-name"
 import { BOULDER_CONTINUATION_PROMPT } from "./system-reminder-templates"
+import { markContinuationInjectedAwaitingToolProgress } from "./tool-progress"
 import { resolveRecentPromptContextForSession } from "./recent-model-resolver"
 import type { BackgroundTaskStatusProvider, SessionState } from "./types"
 
@@ -122,6 +123,7 @@ export async function injectBoulderContinuation(input: {
     }
 
     sessionState.promptFailureCount = 0
+    markContinuationInjectedAwaitingToolProgress(sessionState)
     log(`[${HOOK_NAME}] Boulder continuation injected`, { sessionID })
     return "injected"
   } catch (err) {

src/hooks/atlas/event-handler.ts

@@ -96,6 +96,7 @@ export function createAtlasEventHandler(input: {
         const deletedState = sessions.get(sessionID)
         if (deletedState?.pendingRetryTimer) {
           clearTimeout(deletedState.pendingRetryTimer)
+          deletedState.pendingRetryTimer = undefined
         }
         sessions.delete(sessionID)
         log(`[${HOOK_NAME}] Session deleted: cleaned up`, { sessionID })
@@ -109,6 +110,7 @@ export function createAtlasEventHandler(input: {
         const compactedState = sessions.get(sessionID)
         if (compactedState?.pendingRetryTimer) {
           clearTimeout(compactedState.pendingRetryTimer)
+          compactedState.pendingRetryTimer = undefined
         }
         sessions.delete(sessionID)
         log(`[${HOOK_NAME}] Session compacted: cleaned up`, { sessionID })

src/hooks/atlas/idle-event.ts

@@ -25,6 +25,11 @@ import { injectBoulderContinuation } from "./boulder-continuation-injector"
 import { HOOK_NAME } from "./hook-name"
 import { resolveActiveBoulderSession } from "./resolve-active-boulder-session"
 import { BOULDER_COMPLETE_PROMPT } from "./system-reminder-templates"
+import {
+  markContinuationStalled,
+  shouldAbortForNoToolProgress,
+  updateNoToolProgressIterations,
+} from "./tool-progress"
 import type { AtlasHookOptions, SessionState } from "./types"
 
 const CONTINUATION_COOLDOWN_MS = 5000
@@ -172,6 +177,7 @@ function scheduleRetry(input: {
     sessionState.pendingRetryTimer = undefined
 
     if (sessionState.promptFailureCount >= MAX_CONSECUTIVE_PROMPT_FAILURES) return
+    if (sessionState.stalledContinuationReason) return
     if (sessionState.waitingForFinalWaveApproval) return
 
     const now = Date.now()
@@ -352,6 +358,30 @@ export async function handleAtlasSessionIdle(input: {
     return
   }
 
+  if (sessionState.stalledContinuationReason) {
+    log(`[${HOOK_NAME}] Skipped: boulder continuation stalled`, {
+      sessionID,
+      reason: sessionState.stalledContinuationReason,
+    })
+    return
+  }
+
+  const noProgressIterations = updateNoToolProgressIterations(sessionState)
+  if (shouldAbortForNoToolProgress(sessionState)) {
+    markContinuationStalled(sessionState, boulderState.plan_name)
+    if (sessionState.pendingRetryTimer) {
+      clearTimeout(sessionState.pendingRetryTimer)
+      sessionState.pendingRetryTimer = undefined
+    }
+    log(`[${HOOK_NAME}] Aborting boulder continuation after repeated no-tool-progress iterations`, {
+      sessionID,
+      plan: boulderState.plan_name,
+      noProgressIterations,
+      reason: sessionState.stalledContinuationReason,
+    })
+    return
+  }
+
   if (sessionState.lastEventWasAbortError) {
     sessionState.lastEventWasAbortError = false
     log(`[${HOOK_NAME}] Skipped: abort error immediately before idle`, { sessionID })

src/hooks/atlas/tool-execute-after.ts

@@ -22,6 +22,7 @@ import { DIRECT_WORK_REMINDER } from "./system-reminder-templates"
 import { isOmoPath } from "./omo-path"
 import { resolvePreferredSessionId, resolveTaskContext } from "./task-context"
 import { extractSessionIdFromMetadata, extractSessionIdFromOutput, validateSubagentSessionId } from "./subagent-session-id"
+import { didToolMakeProgress, isTangibleProgressTool, recordToolProgress } from "./tool-progress"
 import {
   buildCompletionGate,
   buildFinalWaveApprovalReminder,
@@ -142,6 +143,10 @@ export function createToolExecuteAfterHandler(input: {
       return
     }
 
+    if (toolInput.sessionID && isTangibleProgressTool(toolInput.tool) && didToolMakeProgress(toolOutput)) {
+      recordToolProgress(getState(toolInput.sessionID))
+    }
+
     if (!(await resolveIsCallerOrchestrator(toolInput.sessionID))) {
       return
     }