Limit external configuration sources parsing in native-mode

`SmallryeConfigBuilder` tries to access properties files from various
sources, despite them not being available at run-time nor supported in
native-mode, see #41994

This patch also avoids getting a `MissingRegistrationError` when using
`-H:+ThrowMissingRegistrationErrors` or `--exact-reachability-metadata`.

Related to #41994 and
#41995

core/deployment/src/main/java/io/quarkus/deployment/steps/ConfigBuildSteps.java

@@ -15,7 +15,9 @@
 import io.quarkus.deployment.builditem.StaticInitConfigBuilderBuildItem;
 import io.quarkus.deployment.builditem.nativeimage.RuntimeInitializedClassBuildItem;
 import io.quarkus.deployment.builditem.nativeimage.ServiceProviderBuildItem;
+import io.quarkus.deployment.pkg.steps.NativeOrNativeSourcesBuild;
 import io.quarkus.deployment.util.ServiceUtil;
+import io.quarkus.runtime.configuration.FileSystemOnlySourcesConfigBuilder;
 import io.quarkus.runtime.configuration.SystemOnlySourcesConfigBuilder;
 import io.quarkus.runtime.graal.InetRunTime;
 import io.smallrye.config.ConfigSourceInterceptor;
@@ -62,6 +64,16 @@ void systemOnlySources(BuildProducer<StaticInitConfigBuilderBuildItem> staticIni
         runTimeConfigBuilder.produce(new RunTimeConfigBuilderBuildItem(SystemOnlySourcesConfigBuilder.class.getName()));
     }
 
+    /**
+     * Limit external configuration sources parsing for native executables since they are not supported see
+     * https://github.com/quarkusio/quarkus/issues/41994
+     */
+    @BuildStep(onlyIf = NativeOrNativeSourcesBuild.class)
+    void nativeNoSources(BuildProducer<StaticInitConfigBuilderBuildItem> staticInitConfigBuilder,
+            BuildProducer<RunTimeConfigBuilderBuildItem> runTimeConfigBuilder) {
+        runTimeConfigBuilder.produce(new RunTimeConfigBuilderBuildItem(FileSystemOnlySourcesConfigBuilder.class.getName()));
+    }
+
     private static class SystemOnlySources implements BooleanSupplier {
         ConfigBuildTimeConfig configBuildTimeConfig;
 

core/deployment/src/main/java/io/quarkus/deployment/steps/ConfigGenerationBuildStep.java

@@ -58,6 +58,7 @@
 import io.quarkus.deployment.builditem.ShutdownContextBuildItem;
 import io.quarkus.deployment.builditem.StaticInitConfigBuilderBuildItem;
 import io.quarkus.deployment.builditem.SuppressNonRuntimeConfigChangedWarningBuildItem;
+import io.quarkus.deployment.builditem.nativeimage.NativeImageResourceBuildItem;
 import io.quarkus.deployment.builditem.nativeimage.ReflectiveClassBuildItem;
 import io.quarkus.deployment.builditem.nativeimage.ReflectiveMethodBuildItem;
 import io.quarkus.deployment.configuration.BuildTimeConfigurationReader;
@@ -391,6 +392,17 @@ public void setupConfigOverride(
 
     @BuildStep
     public void watchConfigFiles(BuildProducer<HotDeploymentWatchedFileBuildItem> watchedFiles) {
+        for (String configWatchedFile : getConfigFiles()) {
+            watchedFiles.produce(new HotDeploymentWatchedFileBuildItem(configWatchedFile));
+        }
+    }
+
+    @BuildStep
+    public NativeImageResourceBuildItem nativeConfigFiles() {
+        return new NativeImageResourceBuildItem(getConfigFiles());
+    }
+
+    private List<String> getConfigFiles() {
         List<String> configWatchedFiles = new ArrayList<>();
 
         SmallRyeConfig config = ConfigProvider.getConfig().unwrap(SmallRyeConfig.class);
@@ -432,10 +444,7 @@ public void watchConfigFiles(BuildProducer<HotDeploymentWatchedFileBuildItem> wa
                 }
             }
         });
-
-        for (String configWatchedFile : configWatchedFiles) {
-            watchedFiles.produce(new HotDeploymentWatchedFileBuildItem(configWatchedFile));
-        }
+        return configWatchedFiles;
     }
 
     @BuildStep

core/runtime/src/main/java/io/quarkus/runtime/configuration/FileSystemOnlySourcesConfigBuilder.java

@@ -0,0 +1,22 @@
+package io.quarkus.runtime.configuration;
+
+import static io.smallrye.config.PropertiesConfigSourceLoader.inFileSystem;
+
+import java.nio.file.Paths;
+
+import io.smallrye.config.SmallRyeConfigBuilder;
+
+public class FileSystemOnlySourcesConfigBuilder implements ConfigBuilder {
+    @Override
+    public SmallRyeConfigBuilder configBuilder(final SmallRyeConfigBuilder builder) {
+        return builder.withSources(
+                inFileSystem(Paths.get(System.getProperty("user.dir"), "config", "application.properties").toUri().toString(),
+                        260, Thread.currentThread().getContextClassLoader()));
+    }
+
+    @Override
+    public int priority() {
+        return Integer.MAX_VALUE;
+    }
+
+}

extensions/config-yaml/deployment/src/main/java/io/quarkus/config/yaml/deployment/ConfigYamlProcessor.java

@@ -14,6 +14,7 @@
 import io.quarkus.deployment.builditem.HotDeploymentWatchedFileBuildItem;
 import io.quarkus.deployment.builditem.RunTimeConfigBuilderBuildItem;
 import io.quarkus.deployment.builditem.StaticInitConfigBuilderBuildItem;
+import io.quarkus.deployment.builditem.nativeimage.NativeImageResourceBuildItem;
 import io.smallrye.config.SmallRyeConfig;
 
 public final class ConfigYamlProcessor {
@@ -34,10 +35,23 @@ public void yamlConfig(
 
     @BuildStep
     void watchYamlConfig(BuildProducer<HotDeploymentWatchedFileBuildItem> watchedFiles) {
+        for (String configWatchedFile : getConfigWatchedFiles()) {
+            watchedFiles.produce(new HotDeploymentWatchedFileBuildItem(configWatchedFile));
+        }
+    }
+
+    @BuildStep
+    NativeImageResourceBuildItem nativeYamlConfig() {
+        return new NativeImageResourceBuildItem(getConfigWatchedFiles());
+    }
+
+    private static List<String> getConfigWatchedFiles() {
         List<String> configWatchedFiles = new ArrayList<>();
         String userDir = System.getProperty("user.dir");
 
         // Main files
+        configWatchedFiles.add("META-INF/microprofile-config.yaml");
+        configWatchedFiles.add("META-INF/microprofile-config.yml");
         configWatchedFiles.add("application.yaml");
         configWatchedFiles.add("application.yml");
         configWatchedFiles.add(Paths.get(userDir, "config", "application.yaml").toAbsolutePath().toString());
@@ -53,9 +67,6 @@ void watchYamlConfig(BuildProducer<HotDeploymentWatchedFileBuildItem> watchedFil
             configWatchedFiles.add(
                     Paths.get(userDir, "config", String.format("application-%s.yml", profile)).toAbsolutePath().toString());
         }
-
-        for (String configWatchedFile : configWatchedFiles) {
-            watchedFiles.produce(new HotDeploymentWatchedFileBuildItem(configWatchedFile));
-        }
+        return configWatchedFiles;
     }
 }