Do not discover properties resource in the classpath to avoid missing resources registration in native mode

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

@@ -83,6 +83,7 @@
 import io.quarkus.runtime.configuration.ConfigDiagnostic;
 import io.quarkus.runtime.configuration.ConfigRecorder;
 import io.quarkus.runtime.configuration.DisableableConfigSource;
+import io.quarkus.runtime.configuration.NativeConfigBuilder;
 import io.quarkus.runtime.configuration.QuarkusConfigValue;
 import io.quarkus.runtime.configuration.RuntimeConfigBuilder;
 import io.quarkus.runtime.configuration.RuntimeOverrideConfigSource;
@@ -162,6 +163,14 @@ void buildTimeRunTimeConfig(
         runTimeConfigBuilder.produce(new RunTimeConfigBuilderBuildItem(builderClassName));
     }
 
+    @BuildStep(onlyIf = NativeOrNativeSourcesBuild.class)
+    void nativeConfig(
+            BuildProducer<StaticInitConfigBuilderBuildItem> staticInitConfigBuilder,
+            BuildProducer<RunTimeConfigBuilderBuildItem> runTimeConfigBuilder) {
+        staticInitConfigBuilder.produce(new StaticInitConfigBuilderBuildItem(NativeConfigBuilder.class.getName()));
+        runTimeConfigBuilder.produce(new RunTimeConfigBuilderBuildItem(NativeConfigBuilder.class.getName()));
+    }
+
     @BuildStep(onlyIfNot = { IsNormal.class }) // for dev or test
     void runtimeOverrideConfig(
             BuildProducer<StaticInitConfigBuilderBuildItem> staticInitConfigBuilder,

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

@@ -0,0 +1,37 @@
+package io.quarkus.runtime.configuration;
+
+import static io.smallrye.config.PropertiesConfigSourceLoader.inFileSystem;
+
+import java.nio.file.Paths;
+
+import io.smallrye.config.SmallRyeConfigBuilder;
+
+/**
+ * Do not register classpath resources lookup in native mode to avoid missing resources registration errors, which
+ * became a strict check during native image execution.
+ * <p>
+ * Configuration coming from classpath resources is recoded during build time in a low ordinal source, so the
+ * configuration will still be available. If the users change the ordinals of the sources in runtime, it may
+ * cause unexpected values to be returned by the config, but this has always been the case. The classpath configuration
+ * resources were never registered in the native image.
+ */
+public class NativeConfigBuilder implements ConfigBuilder {
+    @Override
+    public SmallRyeConfigBuilder configBuilder(final SmallRyeConfigBuilder builder) {
+        builder
+                .setAddDefaultSources(false)
+                .setAddSystemSources(true)
+                .setAddPropertiesSources(false);
+
+        builder.withSources(inFileSystem(
+                Paths.get(System.getProperty("user.dir"), "config", "application.properties").toUri().toString(), 260,
+                builder.getClassLoader()));
+
+        return builder;
+    }
+
+    @Override
+    public int priority() {
+        return Integer.MIN_VALUE + 100;
+    }
+}

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

@@ -1,6 +1,11 @@
 package io.quarkus.runtime.configuration;
 
+import java.net.URI;
+import java.util.Collections;
+import java.util.List;
+
 import org.eclipse.microprofile.config.spi.ConfigProviderResolver;
+import org.eclipse.microprofile.config.spi.ConfigSource;
 
 import com.oracle.svm.core.annotate.Alias;
 import com.oracle.svm.core.annotate.RecomputeFieldValue;
@@ -9,6 +14,7 @@
 import com.oracle.svm.core.annotate.TargetElement;
 
 import io.smallrye.common.constraint.Assert;
+import io.smallrye.config.AbstractLocationConfigSourceLoader;
 import io.smallrye.config.ConfigMappingInterface;
 import io.smallrye.config.ConfigMappingLoader;
 import io.smallrye.config.ConfigMappingMetadata;
@@ -99,4 +105,12 @@ public byte[] getClassBytes() {
             return null;
         }
     }
+
+    @TargetClass(value = AbstractLocationConfigSourceLoader.class)
+    static final class Target_AbstractLocationConfigSourceLoader {
+        @Substitute
+        protected List<ConfigSource> tryClassPath(final URI uri, final int ordinal, final ClassLoader classLoader) {
+            return Collections.emptyList();
+        }
+    }
 }

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

@@ -5,7 +5,9 @@
 public class SystemOnlySourcesConfigBuilder implements ConfigBuilder {
     @Override
     public SmallRyeConfigBuilder configBuilder(final SmallRyeConfigBuilder builder) {
-        return builder.setAddDefaultSources(false).addSystemSources();
+        return builder.setAddDefaultSources(false)
+                .setAddPropertiesSources(false)
+                .addSystemSources();
     }
 
     @Override

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

@@ -6,14 +6,16 @@
 
 import org.eclipse.microprofile.config.ConfigProvider;
 
-import io.quarkus.config.yaml.runtime.YamlConfigBuilder;
+import io.quarkus.config.yaml.runtime.YamlInClassPathConfigBuilder;
+import io.quarkus.config.yaml.runtime.YamlInFileSystemConfigBuilder;
 import io.quarkus.deployment.Feature;
 import io.quarkus.deployment.annotations.BuildProducer;
 import io.quarkus.deployment.annotations.BuildStep;
 import io.quarkus.deployment.builditem.FeatureBuildItem;
 import io.quarkus.deployment.builditem.HotDeploymentWatchedFileBuildItem;
 import io.quarkus.deployment.builditem.RunTimeConfigBuilderBuildItem;
 import io.quarkus.deployment.builditem.StaticInitConfigBuilderBuildItem;
+import io.quarkus.deployment.pkg.NativeConfig;
 import io.smallrye.config.SmallRyeConfig;
 
 public final class ConfigYamlProcessor {
@@ -24,12 +26,18 @@ public FeatureBuildItem feature() {
     }
 
     @BuildStep
-    public void yamlConfig(
+    void yamlConfig(
+            NativeConfig nativeConfig,
             BuildProducer<StaticInitConfigBuilderBuildItem> staticInitConfigBuilder,
             BuildProducer<RunTimeConfigBuilderBuildItem> runTimeConfigBuilder) {
 
-        staticInitConfigBuilder.produce(new StaticInitConfigBuilderBuildItem(YamlConfigBuilder.class));
-        runTimeConfigBuilder.produce(new RunTimeConfigBuilderBuildItem(YamlConfigBuilder.class));
+        staticInitConfigBuilder.produce(new StaticInitConfigBuilderBuildItem(YamlInFileSystemConfigBuilder.class));
+        runTimeConfigBuilder.produce(new RunTimeConfigBuilderBuildItem(YamlInFileSystemConfigBuilder.class));
+
+        if (!nativeConfig.enabled()) {
+            staticInitConfigBuilder.produce(new StaticInitConfigBuilderBuildItem(YamlInClassPathConfigBuilder.class));
+            runTimeConfigBuilder.produce(new RunTimeConfigBuilderBuildItem(YamlInClassPathConfigBuilder.class));
+        }
     }
 
     @BuildStep

extensions/config-yaml/runtime/src/main/java/io/quarkus/config/yaml/runtime/YamlConfigBuilder.java → extensions/config-yaml/runtime/src/main/java/io/quarkus/config/yaml/runtime/YamlInClassPathConfigBuilder.java

@@ -4,10 +4,19 @@
 import io.smallrye.config.SmallRyeConfigBuilder;
 import io.smallrye.config.source.yaml.YamlConfigSourceLoader;
 
-public class YamlConfigBuilder implements ConfigBuilder {
+/**
+ * Only for JVM mode.
+ *
+ * @see io.quarkus.runtime.configuration.RuntimeConfigBuilder
+ */
+public class YamlInClassPathConfigBuilder implements ConfigBuilder {
     @Override
     public SmallRyeConfigBuilder configBuilder(final SmallRyeConfigBuilder builder) {
-        return builder.withSources(new YamlConfigSourceLoader.InFileSystem())
-                .withSources(new YamlConfigSourceLoader.InClassPath());
+        return builder.withSources(new YamlConfigSourceLoader.InClassPath());
+    }
+
+    @Override
+    public int priority() {
+        return Integer.MIN_VALUE + 100;
     }
 }

extensions/config-yaml/runtime/src/main/java/io/quarkus/config/yaml/runtime/YamlInFileSystemConfigBuilder.java

@@ -0,0 +1,25 @@
+package io.quarkus.config.yaml.runtime;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.eclipse.microprofile.config.spi.ConfigSourceProvider;
+
+import io.quarkus.runtime.configuration.ConfigBuilder;
+import io.smallrye.config.SmallRyeConfigBuilder;
+import io.smallrye.config.source.yaml.YamlConfigSourceLoader;
+
+public class YamlInFileSystemConfigBuilder implements ConfigBuilder {
+    @Override
+    public SmallRyeConfigBuilder configBuilder(final SmallRyeConfigBuilder builder) {
+        // Removes Yaml source providers added by the ServiceLoader to avoid double registration
+        List<ConfigSourceProvider> toRemove = new ArrayList<>();
+        for (ConfigSourceProvider sourceProvider : builder.getSourceProviders()) {
+            if (sourceProvider instanceof YamlConfigSourceLoader) {
+                toRemove.add(sourceProvider);
+            }
+        }
+        builder.getSourceProviders().removeAll(toRemove);
+        return builder.withSources(new YamlConfigSourceLoader.InFileSystem());
+    }
+}