Database implementation cleanup (#335)

## Motivation and Context

The database logic was getting a bit unwieldy and fragile - especially
because business logic that should really have lived at the registry
service level was being pushed into the persistence level.

This PR tightens the interface, simplifies the code there, as well as
rips out a bunch of mocks etc. we don't need.

## How Has This Been Tested?

Locally everything works

## Breaking Changes

The list endpoint was surprisingly always filtering for isLatest only,
which seems like a bug? I have removed this filter.

tests/integration/main.go

@@ -217,7 +217,7 @@ func findServerIDByName(serverName string) (string, error) {
 
 	// Find the server with matching name
 	for _, server := range serverList.Servers {
-		if server.Name == serverName {
+		if server.Name == serverName && server.Meta.IOModelContextProtocolRegistry.IsLatest {
 			return server.Meta.IOModelContextProtocolRegistry.ID, nil
 		}
 	}