refactor: wave 2 - split atlas, auto-update-checker, session-recovery, todo-enforcer, background-task hooks

- Extract atlas/ into 15 focused modules (hook, event handler, tool policies, types, etc.)
- Split auto-update-checker into checker/ and hook/ subdirectories with single-purpose files
- Decompose session-recovery into separate recovery strategy files per error type
- Extract todo-continuation-enforcer from monolith to directory with dedicated modules
- Split background-task/tools.ts into individual tool creator files
- Extract command-executor, tmux-utils into focused sub-modules
- Split config/schema.ts into domain-specific schema files
- Decompose cli/config-manager.ts into focused modules
- Rollback skill-mcp-manager, model-availability, index.ts splits that broke tests
- Fix all import path depths for moved files (../../ -> ../../../)
- Add explicit type annotations to resolve TS7006 implicit any errors

Typecheck: 0 errors
Tests: 2359 pass, 5 fail (all pre-existing)

src/hooks/atlas/verification-reminders.ts

@@ -0,0 +1,83 @@
+import { VERIFICATION_REMINDER } from "./system-reminder-templates"
+
+function buildVerificationReminder(sessionId: string): string {
+  return `${VERIFICATION_REMINDER}
+
+---
+
+**If ANY verification fails, use this immediately:**
+\`\`\`
+task(session_id="${sessionId}", prompt="fix: [describe the specific failure]")
+\`\`\``
+}
+
+export function buildOrchestratorReminder(
+  planName: string,
+  progress: { total: number; completed: number },
+  sessionId: string
+): string {
+  const remaining = progress.total - progress.completed
+  return `
+---
+
+**BOULDER STATE:** Plan: \`${planName}\` | ${progress.completed}/${progress.total} done | ${remaining} remaining
+
+---
+
+${buildVerificationReminder(sessionId)}
+
+**STEP 4: MARK COMPLETION IN PLAN FILE (IMMEDIATELY)**
+
+RIGHT NOW - Do not delay. Verification passed → Mark IMMEDIATELY.
+
+Update the plan file \`.sisyphus/tasks/${planName}.yaml\`:
+- Change \`- [ ]\` to \`- [x]\` for the completed task
+- Use \`Edit\` tool to modify the checkbox
+
+**DO THIS BEFORE ANYTHING ELSE. Unmarked = Untracked = Lost progress.**
+
+**STEP 5: COMMIT ATOMIC UNIT**
+
+- Stage ONLY the verified changes
+- Commit with clear message describing what was done
+
+**STEP 6: PROCEED TO NEXT TASK**
+
+- Read the plan file to identify the next \`- [ ]\` task
+- Start immediately - DO NOT STOP
+
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+**${remaining} tasks remain. Keep bouldering.**`
+}
+
+export function buildStandaloneVerificationReminder(sessionId: string): string {
+  return `
+---
+
+${buildVerificationReminder(sessionId)}
+
+**STEP 4: UPDATE TODO STATUS (IMMEDIATELY)**
+
+RIGHT NOW - Do not delay. Verification passed → Mark IMMEDIATELY.
+
+1. Run \`todoread\` to see your todo list
+2. Mark the completed task as \`completed\` using \`todowrite\`
+
+**DO THIS BEFORE ANYTHING ELSE. Unmarked = Untracked = Lost progress.**
+
+**STEP 5: EXECUTE QA TASKS (IF ANY)**
+
+If QA tasks exist in your todo list:
+- Execute them BEFORE proceeding
+- Mark each QA task complete after successful verification
+
+**STEP 6: PROCEED TO NEXT PENDING TASK**
+
+- Identify the next \`pending\` task from your todo list
+- Start immediately - DO NOT STOP
+
+━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
+
+**NO TODO = NO TRACKING = INCOMPLETE WORK. Use todowrite aggressively.**`
+}