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.

Author: domdomegg

Makefile

@@ -14,7 +14,7 @@ publisher: ## Build the publisher tool
 
 # Test targets
 test-unit: ## Run unit tests with coverage
-	go test -v -race -coverprofile=coverage.out -covermode=atomic ./internal/...
+	go test -v -race -coverprofile=coverage.out -covermode=atomic -coverpkg=./internal/... ./internal/...
 	go tool cover -html=coverage.out -o coverage.html
 	@echo "Coverage report generated: coverage.html"
 

cmd/registry/main.go

@@ -14,9 +14,9 @@ import (
 	"github.com/modelcontextprotocol/registry/internal/api"
 	"github.com/modelcontextprotocol/registry/internal/config"
 	"github.com/modelcontextprotocol/registry/internal/database"
+	"github.com/modelcontextprotocol/registry/internal/importer"
 	"github.com/modelcontextprotocol/registry/internal/service"
 	"github.com/modelcontextprotocol/registry/internal/telemetry"
-	apiv0 "github.com/modelcontextprotocol/registry/pkg/api/v0"
 )
 
 func main() {
@@ -46,7 +46,7 @@ func main() {
 	// Initialize services based on environment
 	switch cfg.DatabaseType {
 	case config.DatabaseTypeMemory:
-		db = database.NewMemoryDB(map[string]*apiv0.ServerJSON{})
+		db = database.NewMemoryDB()
 		registryService = service.NewRegistryServiceWithDB(db)
 	case config.DatabaseTypePostgreSQL:
 		// Use PostgreSQL for real registry service
@@ -84,7 +84,8 @@ func main() {
 		ctx, cancel := context.WithTimeout(context.Background(), 5*time.Minute)
 		defer cancel()
 
-		if err := db.ImportSeed(ctx, cfg.SeedFrom); err != nil {
+		importerService := importer.NewService(db)
+		if err := importerService.ImportFromPath(ctx, cfg.SeedFrom); err != nil {
 			log.Printf("Failed to import seed data: %v", err)
 		} else {
 			log.Println("Data import completed successfully")

go.mod

@@ -38,7 +38,6 @@ require (
 	github.com/prometheus/common v0.65.0 // indirect
 	github.com/prometheus/otlptranslator v0.0.0-20250717125610-8549f4ab4f8f // indirect
 	github.com/prometheus/procfs v0.17.0 // indirect
-	github.com/stretchr/objx v0.5.2 // indirect
 	go.opentelemetry.io/auto/sdk v1.1.0 // indirect
 	go.opentelemetry.io/otel/trace v1.37.0 // indirect
 	golang.org/x/crypto v0.41.0 // indirect