feat: comprehensive audit + Tier 3 wiring (security/correctness/features)

Multi-agent audit + fix pass covering bugs, security, dead config wiring,
and missing features. All quality gates green: build/vet/test -race/govulncheck/
golangci-lint. Frontend tests 47/47.

SECURITY & CORRECTNESS

- Scanner pipeline fail-closed: cache.go scan timeout now 503 (was goto servePkg);
  scanner.go all-scanners-fail saves ScanStatusError; CheckVulnerabilities blocks
  on missing/error result instead of allowing.
- Scanner argv corrections: govulncheck source-mode + go.mod discovery;
  npm-audit generates lockfile via npm install --package-lock-only --ignore-scripts;
  pip-audit per-extension dispatch (wheel direct / sdist extract+pyproject).
- GHSA version-range filtering implemented (was always-include); url.QueryEscape
  on package name.
- pypi SSRF closed via host allowlist on original_url; url.QueryEscape on
  rewriteURL output.
- Path traversal: cache temp file uses os.CreateTemp; smb keyToPath sanitized;
  filesystem keyToPath returns error + filepath.Abs prefix-verify.
- Goroutine leaks plugged: cache.cleanupWorker stop channel; auth.ValidationCache
  Stop() with sync.Once; ws.unregister buffered with non-blocking send.
- WebSocket double-close panic fixed via sync.Once Client.closeSend().
- Race conditions: gormstore.registryCache sync.RWMutex (was concurrent map
  panic); auth.LastUsedAt no longer mutated under RLock; analytics strict
  lock-ordering invariant (statsMu before downloadsMu).
- Auth validator fails CLOSED on transport/unknown-status errors (was returning
  true,err 'allow cache fallback').
- Credential cache hash full SHA256 (was 8-byte truncate; eliminates 2^32
  collision risk).
- filesystem.fs.used incremented after successful rename (no quota inflation
  race).
- gormstore aggregation events deleted in same tx as insert (no double-counting).
- gormstore.SavePackage uses Updates(map) so zero-value security flags
  (RequiresAuth=false) can be cleared.
- partition_manager validates partition name regex before DROP TABLE.
- vcs/git: version regex validation rejects --option-injection; checkout uses
  --detach -- separator; removed TrimPrefix(repo,'v') that corrupted vault/
  vitess/vim-go.
- WebSocket CheckOrigin allowlist (was return true; CSWSH closed); same-origin
  default + ServerConfig.AllowedOrigins.
- fiber CVE GO-2026-4543 patched (v2.52.10 -> v2.52.12).

FUNCTIONAL FEATURES

- API key DB persistence: APIKeyModel + migration 202604280002, full CRUD,
  async LastUsedAt updates with WaitGroup-tracked goroutines drained on Close.
- Admin bootstrap via GOHOARDER_BOOTSTRAP_ADMIN_KEY env var; idempotent
  (skipped when non-revoked admin already exists).
- Auth middleware factory in pkg/app: RequireAuth, RequireRole, RequirePermission,
  OptionalAuth. Mounted on proxy + read APIs when Auth.Enabled=true.
  DELETE /api/packages/* requires admin role. /health public for k8s probes.
- NFS storage backend: pkg/storage/nfs wraps filesystem with /proc/mounts
  detection (Linux), post-write fsync, read-after-write health probe.
- WebSocket real-time pipeline: pkg/events Broadcaster interface; cache + scanner
  managers emit EventPackageCached / EventPackageDownloaded / EventScanComplete;
  app.go runs 30s EventStatsUpdate ticker. Frontend has full WS client (reconnect
  with exponential backoff 1s->30s, 25s heartbeat, subscriber pattern), Pinia
  realtime store, Dashboard live indicator + activity feed + reactive stats
  override.
- TLS termination: fiber.ListenTLS when Server.TLS.Enabled.
- Pre-warming: Prewarming.Enabled flag wired (was hardcoded false); Interval,
  MaxConcurrent, TopPackages plumbed.
- NetworkConfig wired (timeouts, retry, rate-limit, circuit-breaker).
- AuthConfig.BcryptCost wired.
- Security.Scanners.Static.MaxPackageSize plumbed to cache.io.LimitReader.
- Handlers.{Go,NPM,PyPI}.Enabled gates route mounting.
- Graceful shutdown: authManager.Close drains async writes.

LINT/HYGIENE

- 80 golangci-lint issues resolved: errcheck (Close/Write/RemoveAll wrapped),
  gofmt, gosec G104/G306, govet shadow renames + fieldalignment reorders,
  staticcheck ST1000 pkg comments + QF1003 tagged switches + QF1008 embedded
  field selectors + QF1001 De Morgan's law.

BEHAVIOR CHANGES

- Scanner now fail-closed: deployments without scanner binaries
  (trivy/govulncheck/npm-audit/pip-audit/grype) BLOCK packages instead of
  serving unscanned. Add binaries or plan a future allow-on-scan-error flag.
- WS origin defaults to same-origin; cross-origin dashboards must set
  server.allowed_origins.
- Validator no longer fails open; private packages won't serve from cache when
  validation can't be performed.
- download_events retention dropped from 24h to ~5min (deleted in agg tx).
  Migration 202604280001 purges pre-upgrade events.
- DELETE /api/packages/* requires admin role when auth enabled.

NEW PACKAGES

- pkg/events  - Broadcaster interface
- pkg/storage/nfs  - NFS-aware filesystem wrapper

DEFERRED (out of scope this pass)

- Static scanner implementation (config defines AllowedLicenses/MaxPackageSize/
  BlockSuspicious but pkg/scanner/static/ does not exist).
- AuthConfig.AuditLog wiring (no audit log infra yet).
- CacheConfig.TTLOverrides passthrough (would touch cache.Config beyond
  integrator scope).

pkg/analytics/analytics.go

@@ -1,3 +1,5 @@
+// Package analytics tracks and analyzes package download events with
+// in-memory aggregation and periodic background flushing.
 package analytics
 
 import (
@@ -46,15 +48,22 @@ type PopularPackage struct {
 	Trend           float64 // Growth rate
 }
 
-// Engine tracks and analyzes package downloads
+// Engine tracks and analyzes package downloads.
+//
+// Lock ordering: never hold both downloadsMu and statsMu at the same time.
+// Code paths must acquire only one of the two; if they need both views, they
+// must take a snapshot under the first lock and release it before taking the
+// second.
 type Engine struct {
 	stats       map[string]*PackageStats
 	flushTicker *time.Ticker
 	stopChan    chan struct{}
+	doneChan    chan struct{}
 	downloads   []PackageDownload
 	maxEvents   int
 	downloadsMu sync.RWMutex
 	statsMu     sync.RWMutex
+	closeOnce   sync.Once
 }
 
 // Config holds analytics engine configuration
@@ -78,6 +87,7 @@ func NewEngine(cfg Config) *Engine {
 		maxEvents:   cfg.MaxEvents,
 		flushTicker: time.NewTicker(cfg.FlushInterval),
 		stopChan:    make(chan struct{}),
+		doneChan:    make(chan struct{}),
 	}
 
 	// Load existing stats from metadata store
@@ -94,19 +104,26 @@ func NewEngine(cfg Config) *Engine {
 	return engine
 }
 
-// TrackDownload records a package download event
+// TrackDownload records a package download event.
+//
+// Locks are taken sequentially (never nested) to avoid the lock-ordering
+// inversion between downloadsMu and statsMu that exists elsewhere in the
+// engine: append to the buffer under downloadsMu, release it, then update
+// stats under statsMu.
 func (e *Engine) TrackDownload(download PackageDownload) {
+	// Append to buffer and decide whether buffer is full.
 	e.downloadsMu.Lock()
-	defer e.downloadsMu.Unlock()
-
-	// Add to event buffer
 	e.downloads = append(e.downloads, download)
+	bufferFull := len(e.downloads) >= e.maxEvents
+	e.downloadsMu.Unlock()
 
-	// Update in-memory stats
+	// Update in-memory stats outside downloadsMu to keep the two locks
+	// strictly disjoint.
 	e.updateStats(download)
 
-	// Flush if buffer is full
-	if len(e.downloads) >= e.maxEvents {
+	// Flush if buffer is full. The flush goroutine acquires downloadsMu
+	// itself; we must not hold any lock when spawning it.
+	if bufferFull {
 		go e.flush()
 	}
 
@@ -183,28 +200,47 @@ func (e *Engine) GetTopPackages(limit int) []PopularPackage {
 	return packages
 }
 
-// GetTrendingPackages returns packages with growing popularity
+// GetTrendingPackages returns packages with growing popularity.
+//
+// The implementation takes a snapshot of stats under statsMu, releases it,
+// and only then queries the downloads buffer. This preserves the invariant
+// that downloadsMu and statsMu are never held simultaneously.
 func (e *Engine) GetTrendingPackages(limit int) []PopularPackage {
+	// Snapshot stats under statsMu only.
+	type statsSnapshot struct {
+		registry  string
+		name      string
+		downloads int64
+	}
 	e.statsMu.RLock()
-	defer e.statsMu.RUnlock()
+	snapshot := make([]statsSnapshot, 0, len(e.stats))
+	for _, stats := range e.stats {
+		snapshot = append(snapshot, statsSnapshot{
+			registry:  stats.Registry,
+			name:      stats.Name,
+			downloads: stats.TotalDownloads,
+		})
+	}
+	e.statsMu.RUnlock()
 
 	sevenDaysAgo := time.Now().Add(-7 * 24 * time.Hour)
 
-	packages := make([]PopularPackage, 0)
-	for _, stats := range e.stats {
-		// Calculate recent downloads (last 7 days)
-		recent := e.getRecentDownloads(stats.Registry, stats.Name, sevenDaysAgo)
+	packages := make([]PopularPackage, 0, len(snapshot))
+	for _, s := range snapshot {
+		// Calculate recent downloads (last 7 days). Acquires downloadsMu
+		// only; statsMu is no longer held here.
+		recent := e.getRecentDownloads(s.registry, s.name, sevenDaysAgo)
 
 		// Calculate trend (simple growth rate)
 		trend := 0.0
-		if stats.TotalDownloads > 0 {
-			trend = float64(recent) / float64(stats.TotalDownloads) * 100
+		if s.downloads > 0 {
+			trend = float64(recent) / float64(s.downloads) * 100
 		}
 
 		packages = append(packages, PopularPackage{
-			Registry:        stats.Registry,
-			Name:            stats.Name,
-			Downloads:       stats.TotalDownloads,
+			Registry:        s.registry,
+			Name:            s.name,
+			Downloads:       s.downloads,
 			RecentDownloads: recent,
 			Trend:           trend,
 		})
@@ -297,8 +333,10 @@ func (e *Engine) GetTotalStats() map[string]interface{} {
 	}
 }
 
-// flushLoop periodically flushes download events to metadata store
+// flushLoop periodically flushes download events to metadata store.
+// Closes doneChan after the final flush so Close can wait for it.
 func (e *Engine) flushLoop() {
+	defer close(e.doneChan)
 	for {
 		select {
 		case <-e.flushTicker.C:
@@ -336,12 +374,22 @@ func (e *Engine) loadStats() {
 	log.Debug().Msg("Loading analytics stats from metadata store")
 }
 
-// Close stops the analytics engine
+// Close stops the analytics engine. Safe to call multiple times.
+//
+// Shutdown sequence:
+//  1. signal stopChan (sync.Once-guarded so we never close twice)
+//  2. stop the ticker
+//  3. wait for flushLoop to drain and run its final flush via doneChan
+//
+// We do not call flush() directly here — flushLoop owns the final flush, so
+// there is exactly one flush at shutdown.
 func (e *Engine) Close() {
-	close(e.stopChan)
-	e.flushTicker.Stop()
-	e.flush() // Final flush
-	log.Info().Msg("Analytics engine stopped")
+	e.closeOnce.Do(func() {
+		close(e.stopChan)
+		e.flushTicker.Stop()
+		<-e.doneChan
+		log.Info().Msg("Analytics engine stopped")
+	})
 }
 
 // GetRegistryStats returns per-registry statistics