Classes found in the wrong directory error when packaging a plugin.

[Jakub Skurek]

I started getting this error when running atlas-run or atlas-package after importing the com.atlassian.confluence package into my project.

Compilation completes successfully; however, the subsequent package generation always terminates at the 

Generating a manifest for this plugin
using maven-bundle-plugin v2.5.3

stage, with the following error:

[ERROR] Manifest com.atlassian.plugins.api.rest.extension:RestExtension:atlassian-plugin:1.0 : Classes found in the wrong directory: {edu/oswego/cs/dl/util/concurrent/ConcurrentReaderHashMap$1.class=EDU.oswego.cs.dl.util.concurrent.ConcurrentReaderHashMap$1...} [ERROR] Error(s) found in manifest configuration

The error lists out the entire edu.oswego package (give or take a hundred files), which located in my project's target folder. No doubt it is a dependency of the com.atlassian.confluence package. The edu.oswego package has the following structure:

C:\Projects\Plugins\REST\RestExtension\target\classes\edu\oswego\cs\dl\util\concurrent

The script does not seem to provide any helpful troubleshooting information, for example where the files were expected...

Thank you in advance for any support or advice you can offer.

Cheers, Jacob

PS: I am including my pom.xml file here, in case it is of any use:

<?xml version="1.0" encoding="UTF-8"?>

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
    <modelVersion>4.0.0</modelVersion>
    <groupId>com.atlassian.plugins.api.rest.extension</groupId>
    <artifactId>RestExtension</artifactId>
    <version>1.0</version>
    <organization>
        <name>Example Company</name>
        <url>http://www.example.com/</url>
    </organization>
    <name>RestExtension</name>
    <description>This is the com.atlassian.plugins.api.rest.extension:RestExtension plugin for Atlassian Refapp.</description>
    <packaging>atlassian-plugin</packaging>
    <dependencies>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>javax.servlet</groupId>
            <artifactId>javax.servlet-api</artifactId>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>com.atlassian.plugin</groupId>
            <artifactId>atlassian-spring-scanner-annotation</artifactId>
            <version>${atlassian.spring.scanner.version}</version>
            <scope>compile</scope>
        </dependency>
        <dependency>
            <groupId>com.atlassian.plugin</groupId>
            <artifactId>atlassian-spring-scanner-runtime</artifactId>
            <version>${atlassian.spring.scanner.version}</version>
            <scope>runtime</scope>
        </dependency>
        <dependency>
            <groupId>javax.inject</groupId>
            <artifactId>javax.inject</artifactId>
            <version>1</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-simple</artifactId>
        </dependency>
        <!-- WIRED TEST RUNNER DEPENDENCIES -->
        <dependency>
            <groupId>com.atlassian.plugins</groupId>
            <artifactId>atlassian-plugins-osgi-testrunner</artifactId>
            <version>${plugin.testrunner.version}</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>javax.ws.rs</groupId>
            <artifactId>jsr311-api</artifactId>
            <version>1.1.1</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>com.google.code.gson</groupId>
            <artifactId>gson</artifactId>
            <version>2.2.2-atlassian-1</version>
        </dependency>
        <dependency>
            <groupId>javax.servlet</groupId>
            <artifactId>servlet-api</artifactId>
            <version>2.4</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>javax.xml.bind</groupId>
            <artifactId>jaxb-api</artifactId>
            <version>2.1</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>com.atlassian.plugins.rest</groupId>
            <artifactId>atlassian-rest-common</artifactId>
            <version>1.0.2</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>org.apache.wink</groupId>
            <artifactId>wink-client</artifactId>
            <version>1.1.3-incubating</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.mockito</groupId>
            <artifactId>mockito-all</artifactId>
            <version>1.8.5</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>com.atlassian.confluence</groupId>
            <artifactId>confluence</artifactId>
            <version>6.7.1</version>
        </dependency>
        <dependency>
            <groupId>com.atlassian.sal</groupId>
            <artifactId>sal-api</artifactId>
            <version>3.1.0</version>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.junit.jupiter</groupId>
            <artifactId>junit-jupiter-api</artifactId>
            <version>RELEASE</version>
        </dependency>
    </dependencies>
    <dependencyManagement>
        <dependencies>
            <dependency>
                <groupId>com.atlassian.platform</groupId>
                <artifactId>platform</artifactId>
                <version>${platform.version}</version>
                <type>pom</type>
                <scope>import</scope>
            </dependency>
            <dependency>
                <groupId>com.atlassian.platform</groupId>
                <artifactId>third-party</artifactId>
                <version>${platform.version}</version>
                <type>pom</type>
                <scope>import</scope>
            </dependency>
        </dependencies>
    </dependencyManagement>
    <build>
        <plugins>
 
            <plugin>
                <groupId>com.atlassian.maven.plugins</groupId>
                <artifactId>maven-refapp-plugin</artifactId>
                <version>${amps.version}</version>
                <extensions>true</extensions>
                <configuration>
               
                    <productVersion>${refapp.version}</productVersion>
                    <enableQuickReload>true</enableQuickReload>
                    <enableFastdev>false</enableFastdev>
                    <!-- See here for an explanation of default instructions: -->
                    <!-- https://developer.atlassian.com/docs/advanced-topics/configuration-of-instructions-in-atlassian-plugins -->
                    <instructions>
                        <Atlassian-Plugin-Key>${atlassian.plugin.key}</Atlassian-Plugin-Key>
                        <!-- Add package to export here -->
                        <Export-Package>com.atlassian.plugins.api.rest.extension.api,</Export-Package>
                        <!-- Add package import here -->
                        <Import-Package>org.springframework.osgi.*;resolution:="optional", org.eclipse.gemini.blueprint.*;resolution:="optional", *</Import-Package>
                        <!-- Ensure plugin is spring powered -->
                        <Spring-Context>*</Spring-Context>
                    </instructions>
               <jvmArgs>-Xms1g -Xmx2g -XX:MaxPermSize=1g -XX:-UseGCOverheadLimit -server</jvmArgs>
            </configuration>
            </plugin>
            <plugin>
                <groupId>com.atlassian.plugin</groupId>
                <artifactId>atlassian-spring-scanner-maven-plugin</artifactId>
                <version>${atlassian.spring.scanner.version}</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>atlassian-spring-scanner</goal>
                        </goals>
                        <phase>process-classes</phase>
                    </execution>
                </executions>
                <configuration>
                    <scannedDependencies>
                        <dependency>
                            <groupId>com.atlassian.plugin</groupId>
                            <artifactId>atlassian-spring-scanner-external-jar</artifactId>
                        </dependency>
                    </scannedDependencies>
                    <verbose>false</verbose>
                </configuration>
            </plugin>
        </plugins>
    </build>
    <properties>
        <platform.version>3.0.0</platform.version>
        <refapp.version>3.3.6</refapp.version>
        <amps.version>6.3.15</amps.version>
        <plugin.testrunner.version>1.2.3</plugin.testrunner.version>
        <atlassian.spring.scanner.version>1.2.13</atlassian.spring.scanner.version>
        <!-- This key is used to keep the consistency between the key in atlassian-plugin.xml and the key to generate bundle. -->
        <atlassian.plugin.key>${project.groupId}.${project.artifactId}</atlassian.plugin.key>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
        <maven.compiler.source>1.8</maven.compiler.source>
        <maven.compiler.target>1.8</maven.compiler.target>
    </properties>
</project>

[Mikael Carlsson]

Did you ever solve this? I'm having the same problem.