wip: Make cross-module visibility explicit via Visibles structs

All access is/will be through interfaces accessed through these structs.

This introduces several distinct storage units:
+ DB for server state
+ DB for codeql databases
+ query pack store

The steps for manually creating needed databases are in the README

cmd/server/main.go

@@ -74,38 +74,89 @@ func main() {
 		ss := storage.NewStorageSingle(config.Storage.StartingID)
 		sr := agent.NewRunnerSingle(2, sq) // FIXME take value from configuration
 
-		state := server.State{
-			Commander: sc,
-			Logger:    sl,
-			Queue:     sq,
-			Storage:   ss,
-			Runner:    sr,
+		qp, err := storage.NewQueryPackStore(config.Storage.StartingID)
+		if err != nil {
+			slog.Error("Unable to initialize query pack storage")
+			os.Exit(1)
 		}
 
-		sc.Setup(&state) // sc is part of state and dereferences it
+		ql, err := storage.NewQLDBStore()
+		if err != nil {
+			slog.Error("Unable to initialize ql database storage")
+			os.Exit(1)
+		}
+
+		sc.Setup(&server.CommanderVisibles{
+			Logger:         sl,
+			Queue:          sq,
+			ServerStore:    ss,
+			QueryPackStore: qp,
+			QLDBStore:      ql,
+		})
+
+		sl.Setup(&logger.LoggerVisibles{})
+
+		sq.Setup(&queue.QueueVisibles{
+			Logger: sl,
+		})
+
+		ss.Setup(&storage.ServerStorageVisibles{})
+
+		sr.Setup(&agent.RunnerVisibles{
+			Logger:         sl,
+			Queue:          sq,
+			QueryPackStore: qp,
+			QLDBStore:      ql,
+		})
 
 	case "container":
 		// Assemble container version
 		sq := queue.NewQueueSingle(2) // FIXME take value from configuration
 		sc := server.NewCommanderSingle(nil, sq)
 		sl := logger.NewLoggerSingle()
+
 		ss, err := storage.NewStorageContainer(config.Storage.StartingID)
 		if err != nil {
-			slog.Error("Unable to initialize storage")
+			slog.Error("Unable to initialize server storage")
+			os.Exit(1)
+		}
+
+		qp, err := storage.NewQueryPackStore(config.Storage.StartingID)
+		if err != nil {
+			slog.Error("Unable to initialize query pack storage")
+			os.Exit(1)
+		}
+
+		ql, err := storage.NewQLDBStore()
+		if err != nil {
+			slog.Error("Unable to initialize ql database storage")
 			os.Exit(1)
 		}
 
 		sr := agent.NewRunnerSingle(2, sq) // FIXME take value from configuration
 
-		state := server.State{
-			Commander: sc,
-			Logger:    sl,
-			Queue:     sq,
-			Storage:   ss,
-			Runner:    sr,
-		}
+		sc.Setup(&server.CommanderVisibles{
+			Logger:         sl,
+			Queue:          sq,
+			ServerStore:    ss,
+			QueryPackStore: qp,
+			QLDBStore:      ql,
+		})
 
-		sc.Setup(&state) // sc is part of state and dereferences it
+		sl.Setup(&logger.LoggerVisibles{})
+
+		sq.Setup(&queue.QueueVisibles{
+			Logger: sl,
+		})
+
+		ss.Setup(&storage.ServerStorageVisibles{})
+
+		sr.Setup(&agent.RunnerVisibles{
+			Logger:         sl,
+			Queue:          sq,
+			QueryPackStore: qp,
+			QLDBStore:      ql,
+		})
 
 	case "cluster":
 		// Assemble cccluster