refactor(dir/store): flatten store config and move name verification to naming

[paralta]

Simplify config before #1490.

OCI is the only supported store backend, so the store.provider field and the store.oci.* nesting are gone. store.oci.* is now store.* everywhere (Go, YAML, Helm, env vars), and store.verification.enabled moves to naming.enabled next to naming.ttl.

Warning

Breaking config changes — update your config before redeploying:

• YAML: drop store.provider; rename store.oci.<field> → store.<field>; rename store.verification.enabled → naming.enabled.
• Env vars: drop DIRECTORY_SERVER_STORE_PROVIDER; rename DIRECTORY_SERVER_STORE_OCI_* → DIRECTORY_SERVER_STORE_*; rename DIRECTORY_SERVER_STORE_VERIFICATION_ENABLED → DIRECTORY_SERVER_NAMING_ENABLED.
• Helm values: drop apiserver.config.store.provider; rename apiserver.config.store.oci.<field> → apiserver.config.store.<field>.
• Go callers: server/store/config is deleted — read cfg.Store.<field> instead of cfg.Store.OCI.<field>.

• Deleted server/store/config; server.Config.Store is oci.Config directly and store.New calls oci.New with no provider switch.
• Moved store.verification.enabled to naming.enabled (default true) next to naming.ttl.
• Flattened store.oci.* → store.* in cli/cmd/daemon/daemon.config.yaml, every e2e/integration testenv, install/docker/apiserver.env, and the Helm chart values, templates, and configmap.
• Updated callers (server/controller/sync.go, server/routing/test_utils.go, tests/integration/server/setup.go, cli/cmd/daemon/{config,start,daemon_test}.go) to read cfg.Store.<field> and rebound viper keys to server.store.*.
• Renamed env vars in server/config/config_test.go and deployment.yaml from DIRECTORY_SERVER_STORE_OCI_* to DIRECTORY_SERVER_STORE_*.

[github-actions]

The latest Buf updates on your PR. Results from workflow Buf CI / verify-proto (pull_request).

Build	Format	Lint	Breaking	Updated (UTC)
✅ passed	⏩ skipped	⏩ skipped	✅ passed	May 20, 2026, 9:28 AM

[codecov]

Codecov Report

❌ Patch coverage is 91.42857% with 3 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
server/store/store.go	50.0%	1 Missing and 1 partial ⚠️
cli/cmd/daemon/start.go	80.0%	0 Missing and 1 partial ⚠️

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