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

pkg/logger/types.go

@@ -1,9 +1,16 @@
 package logger
 
 type LoggerSingle struct {
+	modules *LoggerVisibles
 }
 
 func NewLoggerSingle() *LoggerSingle {
 	l := LoggerSingle{}
 	return &l
 }
+
+type LoggerVisibles struct{}
+
+func (l *LoggerSingle) Setup(v *LoggerVisibles) {
+	l.modules = v
+}