fix(server): call server.init after setting server options - #4003
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Call server.init from runApp only after final ServerOptions are applied, and from JoobyExtension before start, so the service registry does not retain stale defaults from bootstrap. Fixes jooby-project#3995
Call server.init after test server options are finalized and before start for integration tests that no longer rely on Jooby constructor init.
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Summary
server.initfrom theJoobyconstructor during bootstrap (it ran beforerunAppapplied config-derivedServerOptions).server.initfor each app inrunAppafter final options are set, and inJoobyExtensionbeforestart.ServerOptionsmatch the configured instance after init.Fixes #3995
Test plan
mvn -pl jooby -am test -Dtest=Issue3995,JoobyRunnerTest,ServerTest(Java 21, Maven 3.8+)