merge: integrate origin/dev into modular-enforcement branch

Resolves all merge conflicts, preserving our split module structure
while integrating all dev changes:
- Custom agent summaries support (parseRegisteredAgentSummaries)
- Background notification queue (enqueueNotificationForParent)
- Atlas shared git-worktree module (collectGitDiffStats, formatFileChanges)
- Ralph-loop withTimeout + DEFAULT_API_TIMEOUT=5000
- Session recovery assistant_prefill_unsupported error type
- Atlas agentOverrides forwarding
- Config handler plan model demotion (buildPlanDemoteConfig)
- Delegate-task agentOverrides, promptSyncWithModelSuggestionRetry, variant
- LSP init timeout + stale init detection
- isPlanFamily function + task-continuation-enforcer hook
- Handoff command

src/agents/atlas/default.ts

@@ -274,13 +274,13 @@ ACCUMULATED WISDOM:
 
 **For exploration (explore/librarian)**: ALWAYS background
 \`\`\`typescript
-task(subagent_type="explore", run_in_background=true, ...)
-task(subagent_type="librarian", run_in_background=true, ...)
+task(subagent_type="explore", load_skills=[], run_in_background=true, ...)
+task(subagent_type="librarian", load_skills=[], run_in_background=true, ...)
 \`\`\`
 
 **For task execution**: NEVER background
 \`\`\`typescript
-task(category="...", run_in_background=false, ...)
+task(category="...", load_skills=[...], run_in_background=false, ...)
 \`\`\`
 
 **Parallel task groups**: Invoke multiple in ONE message

src/agents/atlas/gpt.ts

@@ -231,12 +231,12 @@ ACCUMULATED WISDOM: [from notepad]
 <parallel_execution>
 **Exploration (explore/librarian)**: ALWAYS background
 \`\`\`typescript
-task(subagent_type="explore", run_in_background=true, ...)
+task(subagent_type="explore", load_skills=[], run_in_background=true, ...)
 \`\`\`
 
 **Task execution**: NEVER background
 \`\`\`typescript
-task(category="...", run_in_background=false, ...)
+task(category="...", load_skills=[...], run_in_background=false, ...)
 \`\`\`
 
 **Parallel task groups**: Invoke multiple in ONE message