Maven prefixing WEB-INF/classes into JAR dependency - maven-3

Question

Update: Solved! Posted solution as my own answer. Will be accepting it in two days when I'm allowed to.
A little back story
I've been chasing down this rabbit hole for the past few days, and my question has drastically changed shape over that time. Initially, I thought I had an issue with Spring Boot, because it failed to parse one of my #Configuration annotated classes. Debugging that, I determined that Spring was looking in all the right places for one of my JAR-bound dependencies, but was coming up with a FileNotFoundException when trying to load a class from the JAR.
I was thrown off by this, because the JAR in question was quite verifiably on the classpath. I could print out the classpath during app startup, and see my JAR living nice and cozy inside.
So I simplified. And simplified. Eventually, I got things down to a project with two Java source files, and a tiny placeholder JAR pulled through Maven. This JAR only contains one file: tiny/jar/BaseTest.class.
This worked perfectly. From there, I swapped the dependency JAR on this small project. . . and startup failed. So I compared the JARs and noticed something odd.
The realization
While my small JAR contained a folder hierarchy of:
tiny/jar/BaseTest.class
The larger JAR looked like:
WEB-INF/classes/com/company/...
This WEB-INF/classes prefix is the poison which is killing Spring Boot's class loader. It expects to find classes starting from the root: com/company/... -- no prefix allowed.
I believe that Maven's dependency management is doing something tricky here. When my JAR is created using the clean install goal, it has the com/company/... root inside of it. If I manually copy this version of the JAR into my servers WEB-INF/lib folder, everything works, recognizes, and fires up perfectly.
But when Maven is used to bring in the dependency, WEB-INF/classes is prefixed on to my folder hierarchy, breaking everything.
The question
Does anyone know how I can prevent Maven from altering the directory structure of my JAR? The JAR is 100% correct until Maven pulls it in as a dependency, and suddenly the WEB-INF/classes prefix appears.
Here are the three POM files for reference. I've cut out a large swath of dependencies, but left everything else intact for easier reading.
Tiny Jar POM
<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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>tiny</groupId>
<artifactId>jar</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.2.1.RELEASE</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>
<name>jar</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<java.version>1.8</java.version>
</properties>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
</dependency>
</dependencies>
</project>
Big Jar POM
<?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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>com.company</groupId>
<artifactId>company-foundation</artifactId>
<version>0.7.0-SNAPSHOT</version>
<packaging>jar</packaging>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.2.1.RELEASE</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>
<dependencies>
<dependency>
<groupId>org.springframework.ws</groupId>
<artifactId>spring-ws-core</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.ws</groupId>
<artifactId>spring-ws-security</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-logging</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-data-jpa</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-jdbc</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-security</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-mail</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.webflow</groupId>
<artifactId>spring-webflow</artifactId>
<version>2.4.0.RELEASE</version>
</dependency>
</dependencies>
<build>
<plugins>
<plugin> <!-- Sonar -->
<groupId>org.codehaus.mojo</groupId>
<artifactId>sonar-maven-plugin</artifactId>
<version>2.5</version>
</plugin>
</plugins>
</build>
<repositories>
<!-- To use snapshots, you must also use the Sonatype Snapshots respository -->
<repository>
<id>sonatype-snapshots</id>
<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
</repository>
<repository>
<id>spring-snapshots</id>
<name>Spring Snapshots</name>
<url>https://repo.spring.io/snapshot</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
<repository>
<id>spring-milestones</id>
<name>Spring Milestones</name>
<url>https://repo.spring.io/milestone</url>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
<pluginRepositories>
<pluginRepository>
<id>spring-snapshots</id>
<name>Spring Snapshots</name>
<url>https://repo.spring.io/snapshot</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
</pluginRepository>
<pluginRepository>
<id>spring-milestones</id>
<name>Spring Milestones</name>
<url>https://repo.spring.io/milestone</url>
<snapshots>
<enabled>false</enabled>
</snapshots>
</pluginRepository>
</pluginRepositories>
</project>
Project POM
<?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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.test</groupId>
<artifactId>dependency-issue</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>war</packaging>
<name>jar-dependency-issue</name>
<description>Barebones Spring Boot project used to demonstrate a JAR loading issue.</description>
<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>1.2.1.RELEASE</version>
<relativePath/> <!-- lookup parent from repository -->
</parent>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<start-class>demo.JarDependencyIssueApplication</start-class>
<java.version>1.8</java.version>
</properties>
<dependencies>
<!-- To run on a separate server, we need to mark tomcat starter as provided. -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-tomcat</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-web</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
<!--
<dependency>
<groupId>com.company</groupId>
<artifactId>company-foundation</artifactId>
<version>0.7.0-SNAPSHOT</version>
</dependency>
-->
<dependency>
<groupId>tiny</groupId>
<artifactId>jar</artifactId>
<version>0.0.1-SNAPSHOT</version>
</dependency>
</dependencies>
</project>

Answer 1

Solved my problem! I just got done poring over the configuring of my projects, comparing them for any suspicious deviations. Turns out that my larger JARs project in Eclipse had its Deployment Assembly (Found under Properties > Deployment Assembly) set to:
Source ============ Deploy Path
src/main/java --------> /WEB-INF/classes
src/main/resources -> /WEB-INF/classes
This caused my server to deploy the JAR into an internal /WEB-INF/classes folder.
Changing the Deploy Path setting to / fixed the problem! Everything is working perfectly now! Woo!