BREAKING CHANGE: Storage and system scans no longer create entries in update_logs
**Problem**
- Storage scans were appearing on Updates page (mixed with package updates)
- System scans were appearing on Updates page (mixed with package updates)
- Duplicate "Scan All" entries from collective + individual logging
**Root Cause**
Scan handlers were calling both ReportLog() and dedicated endpoints:
- reportLogWithAck → POST /api/v1/agents/:id/logs → update_logs table
- This caused storage/system metrics to appear alongside package updates
**Fix**
Removed ALL ReportLog() calls from scan handlers:
1. handleScanUpdatesV2 (lines 44-46): Removed collective logging
2. handleScanStorage (lines 103-105): Use only ReportStorageMetrics
3. handleScanSystem (lines 189-191): Use only ReportMetrics
4. handleScanDocker (lines 269-271): Use only ReportDockerImages
**Verification**
- All 4 handlers have working dedicated endpoints (verified via subagent)
- Routes already registered: POST /storage-metrics, POST /metrics, etc.
- Frontend queries correct endpoints (verified)
- No data loss: dedicated endpoints store in proper tables
**Result**
- Storage scans → storage_metrics table → Storage page only ✅
- System scans → system reporting → System page only ✅
- Package updates → update_logs table → Updates page only ✅
- No duplicate "Scan All" entries ✅
**Files Changed**
- aggregator-agent/cmd/agent/subsystem_handlers.go: Removed 20 lines of ReportLog calls
- internal/api/handlers/agents.go: Command recovery enhancements
- internal/api/handlers/updates.go: Subsystem extraction logic
- internal/database/queries/commands.go: GetStuckCommands query
Added circuit breakers with configurable timeouts for all subsystems (APT, DNF, Docker, Windows, Winget, Storage). Replaces cron-based scheduler with priority queue that should scale beyond 1000+ agents if your homelab is that big.
Command acknowledgment system ensures results aren't lost on network failures or restarts. Agent tracks pending acknowledgments with persistent state and automatic retry.
- Circuit breakers: 3 failures in 1min opens circuit, 30s cooldown
- Per-subsystem timeouts: 30s-10min depending on scanner
- Priority queue scheduler: O(log n), worker pool, jitter, backpressure
- Acknowledgments: at-least-once delivery, max 10 retries over 24h
- All tests passing (26/26)
