cleanConf Gradle task deletes the wrong directory in projects with non-standard layout

jmix-gradle-plugin/src/main/groovy/io/jmix/gradle/JmixPlugin.groovy

@@ -27,6 +27,8 @@ import java.util.jar.Manifest
 
 class JmixPlugin implements Plugin<Project> {
 
+    public static final String DEFAULT_CONF_DIR = '.jmix/conf'
+
     public static final String PROVIDED_RUNTIME_CONFIGURATION_NAME = 'providedRuntime'
     public static final String PRODUCTION_RUNTIME_CLASSPATH_CONFIGURATION_NAME = 'productionRuntimeClasspath'
 
@@ -314,7 +316,7 @@ class JmixPlugin implements Plugin<Project> {
                         def confDir = resolveConfDir(project, mainProperties)
 
                         project.logger.lifecycle("Delete directory: {}", confDir)
-                        delete "${confDir}"
+                        delete confDir
                     } else {
                         project.logger.lifecycle("Resource directory not found")
                         return
@@ -396,26 +398,47 @@ class JmixPlugin implements Plugin<Project> {
         }
     }
 
-    private static String resolveConfDir(Project project, Properties mainProperties) {
+    /**
+     * Resolves the directory used by the application as 'jmix.core.conf-dir' at runtime.
+     *
+     * The runtime resolves this property against its working directory, which is the project directory
+     * both for the Gradle 'bootRun' task and for Studio run configurations. So relative paths and the
+     * '${user.dir}' placeholder are resolved against the project directory, not the build root directory:
+     * these are different directories when the application is a subproject with a custom 'projectDir'.
+     */
+    private static File resolveConfDir(Project project, Properties mainProperties) {
         def profilesList = resolveActiveProfiles(project, mainProperties)
 
         def confDir = null
         if (!profilesList.isEmpty()) {
             for (def profileName : profilesList) {
                 project.logger.lifecycle("Check profile: {}", profileName)
                 def profileProperties = loadProperties(project, profileName)
-                confDir = profileProperties.getProperty("jmix.core.conf-dir") ?: profileProperties.getProperty("jmix.core.confDir") ?: null
+                confDir = getConfDirProperty(profileProperties)
                 if (confDir != null) {
                     break
                 }
             }
         }
 
         if (confDir == null) {
-            confDir = mainProperties.getProperty("jmix.core.conf-dir") ?: mainProperties.getProperty("jmix.core.confDir") ?: "${project.rootDir}/.jmix/conf"
+            confDir = getConfDirProperty(mainProperties) ?: DEFAULT_CONF_DIR
         }
 
-        return confDir
+        return project.file(expandPathPlaceholders(project, confDir))
+    }
+
+    private static String getConfDirProperty(Properties properties) {
+        return properties.getProperty("jmix.core.conf-dir") ?: properties.getProperty("jmix.core.confDir") ?: null
+    }
+
+    /**
+     * Replaces the placeholders that the running application resolves in path properties.
+     * '${user.dir}' becomes the project directory because that is the working directory of the application.
+     */
+    private static String expandPathPlaceholders(Project project, String path) {
+        return path.replace('${user.dir}', project.projectDir.absolutePath)
+                .replace('${user.home}', System.getProperty('user.home'))
     }
 
     private static List<String> resolveActiveProfiles(Project project, Properties mainProperties) {

jmix-gradle-plugin/src/test/groovy/io/jmix/gradle/CleanConfFunctionalTest.groovy

@@ -0,0 +1,144 @@
+/*
+ * Copyright 2026 Haulmont.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package io.jmix.gradle
+
+import org.gradle.testkit.runner.GradleRunner
+import org.junit.jupiter.api.Tag
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.io.TempDir
+
+import java.nio.file.Files
+import java.nio.file.Path
+import java.nio.file.StandardCopyOption
+
+import static org.junit.jupiter.api.Assertions.assertFalse
+import static org.junit.jupiter.api.Assertions.assertTrue
+
+/**
+ * The 'cleanConf' task must delete the directory that the application actually uses at runtime.
+ * The runtime resolves 'jmix.core.conf-dir' against its working directory, which for 'bootRun'
+ * is the application module dir - not the build root dir.
+ */
+class CleanConfFunctionalTest {
+
+    private static final String APP_MODULE_PATH = 'modules/backend/app'
+
+    @TempDir
+    Path testProjectDir
+
+    @Test
+    @Tag('slowTests')
+    void defaultConfDirIsResolvedAgainstApplicationModule() {
+        copyFixture('nonstandard-layout-conf-dir', testProjectDir)
+
+        Path rootConfDir = createConfDir('.jmix/conf')
+        Path appConfDir = createAppConfDir('.jmix/conf')
+
+        runCleanConf()
+
+        assertFalse(Files.exists(appConfDir), "conf dir of the application module must be deleted: ${appConfDir}")
+        assertTrue(Files.exists(rootConfDir), "conf dir of the build root must be left alone: ${rootConfDir}")
+    }
+
+    @Test
+    @Tag('slowTests')
+    void relativeConfDirPropertyIsResolvedAgainstApplicationModule() {
+        copyFixture('nonstandard-layout-conf-dir', testProjectDir)
+        appendAppProperty('jmix.core.conf-dir = custom-conf')
+
+        Path rootConfDir = createConfDir('custom-conf')
+        Path appConfDir = createAppConfDir('custom-conf')
+
+        runCleanConf()
+
+        assertFalse(Files.exists(appConfDir), "conf dir of the application module must be deleted: ${appConfDir}")
+        assertTrue(Files.exists(rootConfDir), "conf dir of the build root must be left alone: ${rootConfDir}")
+    }
+
+    @Test
+    @Tag('slowTests')
+    void userDirPlaceholderInConfDirPropertyIsExpanded() {
+        copyFixture('nonstandard-layout-conf-dir', testProjectDir)
+        appendAppProperty('jmix.core.conf-dir = ${user.dir}/.jmix/conf')
+
+        Path rootConfDir = createConfDir('.jmix/conf')
+        Path appConfDir = createAppConfDir('.jmix/conf')
+
+        runCleanConf()
+
+        assertFalse(Files.exists(appConfDir), "conf dir of the application module must be deleted: ${appConfDir}")
+        assertTrue(Files.exists(rootConfDir), "conf dir of the build root must be left alone: ${rootConfDir}")
+    }
+
+    @Test
+    @Tag('slowTests')
+    void absoluteConfDirPropertyIsUsedAsIs() {
+        copyFixture('nonstandard-layout-conf-dir', testProjectDir)
+
+        Path absoluteConfDir = Files.createDirectories(testProjectDir.resolve('outside/conf'))
+        Files.writeString(absoluteConfDir.resolve('marker.txt'), 'marker')
+        appendAppProperty("jmix.core.conf-dir = ${absoluteConfDir.toString().replace('\\', '/')}")
+
+        Path appConfDir = createAppConfDir('.jmix/conf')
+
+        runCleanConf()
+
+        assertFalse(Files.exists(absoluteConfDir), "conf dir given as an absolute path must be deleted: ${absoluteConfDir}")
+        assertTrue(Files.exists(appConfDir), "default conf dir must be left alone when the property is set: ${appConfDir}")
+    }
+
+    private void runCleanConf() {
+        GradleRunner.create()
+                .withProjectDir(testProjectDir.toFile())
+                .withArguments(':app:cleanConf', '--stacktrace')
+                .withPluginClasspath()
+                .forwardOutput()
+                .build()
+    }
+
+    private Path createConfDir(String relativePath) {
+        return createMarkedDir(testProjectDir.resolve(relativePath))
+    }
+
+    private Path createAppConfDir(String relativePath) {
+        return createMarkedDir(testProjectDir.resolve(APP_MODULE_PATH).resolve(relativePath))
+    }
+
+    private static Path createMarkedDir(Path dir) {
+        Files.createDirectories(dir)
+        Files.writeString(dir.resolve('marker.txt'), 'marker')
+        return dir
+    }
+
+    private void appendAppProperty(String line) {
+        Path propertiesFile = testProjectDir.resolve("${APP_MODULE_PATH}/src/main/resources/application.properties")
+        Files.writeString(propertiesFile, "${Files.readString(propertiesFile)}\n${line}\n")
+    }
+
+    private static void copyFixture(String name, Path target) {
+        Path source = Path.of(CleanConfFunctionalTest.getResource("/fixtures/${name}").toURI())
+
+        Files.walk(source).forEach { sourcePath ->
+            Path targetPath = target.resolve(source.relativize(sourcePath).toString())
+            if (Files.isDirectory(sourcePath)) {
+                Files.createDirectories(targetPath)
+            } else {
+                Files.copy(sourcePath, targetPath, StandardCopyOption.REPLACE_EXISTING)
+            }
+        }
+    }
+}

jmix-gradle-plugin/src/test/resources/fixtures/nonstandard-layout-conf-dir/modules/backend/app/build.gradle

@@ -0,0 +1,11 @@
+plugins {
+    id 'io.jmix'
+    id 'java'
+}
+
+jmix {
+    useBom = false
+    entitiesEnhancing {
+        enabled = false
+    }
+}

jmix-gradle-plugin/src/test/resources/fixtures/nonstandard-layout-conf-dir/modules/backend/app/src/main/resources/application.properties

@@ -0,0 +1 @@
+spring.application.name = app

jmix-gradle-plugin/src/test/resources/fixtures/nonstandard-layout-conf-dir/settings.gradle

@@ -0,0 +1,6 @@
+// The Jmix application is a subproject of the root build with a custom projectDir,
+// so the application module dir differs from the build root dir.
+rootProject.name = 'jmix-gradle-plugin-conf-dir'
+
+include ':app'
+project(':app').projectDir = file('modules/backend/app')