Maven not compiling or including Scala .class files in jar only when using resources plugin - scala

Question

I have a Scala application that I'm trying to package as a .jar file using Maven. There is an application.conf file that I'm trying to package into the jar as a resource. However, when I use the resources plugin, either automatically by putting the resources in src/main/resources, or explicitly by adding it to pom.xml from some other folder, Maven then stops compiling and packaging the .class files in the jar.
So long as I don't use the resources plugin, everything works 100%. Maven runs the Scala compiler, puts the .class files into the jar, and after manually adding my resources via 7zip the program executes just fine.
A few additional details:
I'm using the scala-maven-plugin with the Artima Supersafe compiler plugin
I'm also using the maven-shade-plugin to generate a fat jar, concatenate akka reference.conf files, and generate the manifest. This still works when using the resources plugin, its just my .class files are missing. I've tried running without this plugin but the results are the exact same.
I am manually specifying the sourceDirectory as src/main/scala
When not using the resource plugin, the Scala compiles and the console output displays [INFO] --- scala-maven-plugin:3.2.0:compile (default) # batchmanager --- followed by compiler warnings, etc. However, when using the resource plugin it instead always insists: [INFO] Nothing to compile - all classes are up to date
The application.conf file does actually appear in the jar correctly when using the resource plugin
I'm running Maven through Eclipse, not the CLI
I have a feeling there is something about the resource plugin that I do not understand. Any help would be much appreciated.
The full pom.xml (removing the resources definition is the only difference between the working and non-working versions of the file)
<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.digitalalbatross</groupId>
<artifactId>batchmanager</artifactId>
<version>0.0.1</version>
<name>${project.artifactId}</name>
<inceptionYear>2017</inceptionYear>
<licenses>
<license>
<name>My License</name>
<url>http://....</url>
<distribution>repo</distribution>
</license>
</licenses>
<properties>
<maven.compiler.source>1.6</maven.compiler.source>
<maven.compiler.target>1.6</maven.compiler.target>
<encoding>UTF-8</encoding>
<scala.version>2.12.2</scala.version>
<scala.compat.version>2.12</scala.compat.version>
</properties>
<repositories>
<repository>
<id>artima</id>
<name>Artima Maven Repository</name>
<url>http://repo.artima.com/releases</url>
</repository>
</repositories>
<dependencies>
<!-- Test -->
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-http_2.12</artifactId>
<version>10.0.7</version>
<exclusions>
<exclusion>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.iq80.leveldb</groupId>
<artifactId>leveldb</artifactId>
<version>0.9</version>
</dependency>
<dependency>
<groupId>org.fusesource.leveldbjni</groupId>
<artifactId>leveldbjni-all</artifactId>
<version>1.8</version>
</dependency>
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-actor_2.12</artifactId>
<version>2.5.1</version>
<exclusions>
<exclusion>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-persistence_2.12</artifactId>
<version>2.5.1</version>
<exclusions>
<exclusion>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-stream_2.12</artifactId>
<version>2.5.1</version>
<exclusions>
<exclusion>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.typesafe.akka</groupId>
<artifactId>akka-http-spray-json_2.12</artifactId>
<version>10.0.6</version>
<exclusions>
<exclusion>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.12</artifactId>
<version>3.0.3</version>
<exclusions>
<exclusion>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
<version>2.12.2</version>
</dependency>
</dependencies>
<build>
<sourceDirectory>src/main/scala</sourceDirectory>
<testSourceDirectory>src/test/scala</testSourceDirectory>
<resources>
<resource>
<directory>res</directory>
<includes>
<include>application.conf</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<!-- see http://davidb.github.com/scala-maven-plugin -->
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>3.2.0</version>
<executions>
<execution>
<goals>
<goal>compile</goal>
<goal>testCompile</goal>
</goals>
<configuration>
<compilerPlugins>
<compilerPlugin>
<groupId>com.artima.supersafe</groupId>
<artifactId>supersafe_${scala.version}</artifactId>
<version>1.1.2</version>
</compilerPlugin>
</compilerPlugins>
<args>
<arg>-dependencyfile</arg>
<arg>${project.build.directory}/.scala_dependencies</arg>
</args>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.18.1</version>
<configuration>
<useFile>false</useFile>
<disableXmlReport>true</disableXmlReport>
<!-- If you have classpath issue like NoDefClassError,... -->
<!-- useManifestOnlyJar>false</useManifestOnlyJar -->
<includes>
<include>**/*Test.*</include>
<include>**/*Suite.*</include>
</includes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.0.0</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<shadedArtifactAttached>true</shadedArtifactAttached>
<shadedClassifierName>allinone</shadedClassifierName>
<artifactSet>
<includes>
<include>*:*</include>
</includes>
</artifactSet>
<transformers>
<transformer
implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
<resource>reference.conf</resource>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<manifestEntries>
<Main-Class>com.digitalalbatross.batchmanager.Boot</Main-Class>
</manifestEntries>
</transformer>
</transformers>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<description>Batch Manager for IMAX</description>
<organization>
<name>Digital Albatross Design and Consulting</name>
<url>digitalalbatross.com</url>
</organization>
</project>

Answer 1

I managed to solve my issue in the course of solving another. My eclipse workbench kept crashing on boot, so I deleted the .plugins folder to try and solve the issue. Not only did this fix my eclipse setup, but Maven decided to cooperate and started to actually include both resource and class files in the jar. After some confusion over which of the generated jar files actually had a working manifest, I've verified that it is now working as expected.
To summarize, it was most likely some bizarre bug caused by something in my .plugins folder for eclipse. Deleting that folder and reconfiguring my setup fixed the issue.