fix: set PRAGMA busy_timeout on all RW SQLite connections (#707)

## Problem

`SQLITE_BUSY` contention between the ingestor and server's async
persistence goroutine drops `resolved_path` and `neighbor_edges`
updates. The DSN parameter `_busy_timeout=10000` may not be honored by
the modernc/sqlite driver.

## Fix

- **`openRW()` now sets `PRAGMA busy_timeout = 5000`** after opening the
connection, guaranteeing SQLite retries for up to 5 seconds before
returning `SQLITE_BUSY`
- **Refactored `PruneOldPackets` and `PruneOldMetrics`** to use
`openRW()` instead of duplicating connection setup — all RW connections
now get consistent busy_timeout handling
- Added test verifying the pragma is set correctly

## Changes

| File | Change |
|------|--------|
| `cmd/server/neighbor_persist.go` | `openRW()` sets `PRAGMA
busy_timeout = 5000` after open |
| `cmd/server/db.go` | `PruneOldPackets` and `PruneOldMetrics` use
`openRW()` instead of inline `sql.Open` |
| `cmd/server/neighbor_persist_test.go` | `TestOpenRW_BusyTimeout`
verifies pragma is set |

## Performance

No performance impact — `PRAGMA busy_timeout` is a connection-level
setting with zero overhead on uncontended writes. Under contention, it
converts immediate `SQLITE_BUSY` failures into brief retries (up to 5s),
which is strictly better than dropping data.

Fixes #705

---------

Co-authored-by: you <you@example.com>

cmd/server/db.go

@@ -1704,12 +1704,10 @@ func nullInt(ni sql.NullInt64) interface{} {
 // Returns the number of transmissions deleted.
 // Opens a separate read-write connection since the main connection is read-only.
 func (db *DB) PruneOldPackets(days int) (int64, error) {
-	dsn := fmt.Sprintf("file:%s?_journal_mode=WAL&_busy_timeout=10000", db.path)
-	rw, err := sql.Open("sqlite", dsn)
+	rw, err := openRW(db.path)
 	if err != nil {
 		return 0, err
 	}
-	rw.SetMaxOpenConns(1)
 	defer rw.Close()
 
 	cutoff := time.Now().UTC().AddDate(0, 0, -days).Format(time.RFC3339)
@@ -2053,12 +2051,10 @@ func (db *DB) GetMetricsSummary(since string) ([]MetricsSummaryRow, error) {
 
 // PruneOldMetrics deletes observer_metrics rows older than retentionDays.
 func (db *DB) PruneOldMetrics(retentionDays int) (int64, error) {
-	dsn := fmt.Sprintf("file:%s?_journal_mode=WAL&_busy_timeout=10000", db.path)
-	rw, err := sql.Open("sqlite", dsn)
+	rw, err := openRW(db.path)
 	if err != nil {
 		return 0, err
 	}
-	rw.SetMaxOpenConns(1)
 	defer rw.Close()
 
 	cutoff := time.Now().UTC().AddDate(0, 0, -retentionDays).Format(time.RFC3339)

cmd/server/neighbor_persist.go

@@ -584,12 +584,18 @@ func extractEdgesFromObs(obs *StoreObs, tx *StoreTx, pm *prefixMap) []edgeCandid
 
 // openRW opens a read-write SQLite connection (same pattern as PruneOldPackets).
 func openRW(dbPath string) (*sql.DB, error) {
-	dsn := fmt.Sprintf("file:%s?_journal_mode=WAL&_busy_timeout=10000", dbPath)
+	dsn := fmt.Sprintf("file:%s?_journal_mode=WAL", dbPath)
 	rw, err := sql.Open("sqlite", dsn)
 	if err != nil {
 		return nil, err
 	}
 	rw.SetMaxOpenConns(1)
+	// DSN _busy_timeout may not be honored by all drivers; set via PRAGMA
+	// to guarantee SQLite retries for up to 5s before returning SQLITE_BUSY.
+	if _, err := rw.Exec("PRAGMA busy_timeout = 5000"); err != nil {
+		rw.Close()
+		return nil, fmt.Errorf("set busy_timeout: %w", err)
+	}
 	return rw, nil
 }
 

cmd/server/neighbor_persist_test.go

@@ -532,3 +532,31 @@ func TestPersistSemaphoreTryAcquireSkipsBatch(t *testing.T) {
 
 	<-persistSem // release
 }
+
+func TestOpenRW_BusyTimeout(t *testing.T) {
+	dir := t.TempDir()
+	dbPath := filepath.Join(dir, "test.db")
+
+	// Create the DB file first
+	db, err := sql.Open("sqlite", "file:"+dbPath+"?_journal_mode=WAL")
+	if err != nil {
+		t.Fatal(err)
+	}
+	db.Exec("CREATE TABLE dummy (id INTEGER)")
+	db.Close()
+
+	// Open via openRW and verify busy_timeout is set
+	rw, err := openRW(dbPath)
+	if err != nil {
+		t.Fatalf("openRW failed: %v", err)
+	}
+	defer rw.Close()
+
+	var timeout int
+	if err := rw.QueryRow("PRAGMA busy_timeout").Scan(&timeout); err != nil {
+		t.Fatalf("query busy_timeout: %v", err)
+	}
+	if timeout != 5000 {
+		t.Errorf("expected busy_timeout=5000, got %d", timeout)
+	}
+}