fix: three bug fixes for MCP tools and background embedding generation

[syn-zhu]

/kind fix

Description

Three bug fixes found while integrating AgentRegistry into a production Kubernetes platform.

1. auth.WithSystemContext for background embedding goroutines — bare context.Background() lacks the system auth session, causing embedding updates to fail silently. Matches the pattern already used in embeddings_sse.go and embeddings.go.

2. Nil Config map initialization — get_deployment and list_deployments MCP tools return null for Config when the map is nil, breaking downstream JSON consumers. Also adds case-insensitive resource_type filtering.

3. Default port 3000 for stdio transport — the kagent translator leaves Deployment.Port at 0 for stdio servers, which is invalid. Defaults to 3000 to match the KMCP CLI.

Fixes #217

Changes

File	Change
internal/registry/service/registry_service.go	context.Background() → auth.WithSystemContext(context.Background()) in 2 goroutines
internal/mcp/registryserver/server.go	Init nil Config maps, strings.EqualFold for resource type filter
internal/runtime/translation/kagent/kagent_translator.go	Default port 3000 for stdio transport

Test plan

• Publish a server with EMBEDDINGS_ENABLED=true → verify embedding column is populated (not NULL)
• Call get_deployment for a deployment with no config → verify Config is {} not null
• Call list_deployments with resource_type=server (lowercase) → verify results returned
• Deploy a stdio MCP server via kagent translator → verify port is 3000

Fix background embedding generation silently failing due to missing auth context, nil Config map in deployment MCP tool responses, and missing default port for stdio transport in kagent translator.

[syn-zhu]

Hi, @ilackarms gentle bump on this :)

Should be a super quick review!

[inFocus7]

nit: i'm personally a bit iffy on this. it makes sense, but as far as I could tell this is the only place in the code we'd support case-insensitive

[inFocus7]

to avoid a nil Config, would it be better to update the list method so it gets instantiated there and we wouldn't need to do this check here?

so in registry_service.go, when listing k8s deployments listKubernetesDeployments, we'd simply

config := labels
if config == nil {
  config = make(map[string]string)
}
d := {
...
  config: config
...
}

for what it's worth, our db listing code already does something similar to this, so we'd essentially be matching its behavior in the k8s listing

		if d.Config == nil {
			d.Config = make(map[string]string)
		}