In java EE, which jars should I put in the library dir?

Question

I have a Java EE project. The project is built using maven into an .ear archive. There is a library jar containing a JPA 2 persistence unit, which is located in the library directory of the ear (so multiple other modules can use it).

While adding an implementation of Shiro's Permission interface as an entity in this persistence unit, I had trouble getting the ear to deploy correctly, because the shiro classes where unavailable in the persistence unit. I eventually figured out that I needed to put all dependencies (applied also to transitive deps) of the library jar in the library directory to get it to deploy.

So the final layout look roughly like this:

ear
`- lib
   `- persistence-unit.jar
    - shiro-core.jar
    - slf4j-api.jar
 - module1
 - moduleN
 - library1.jar
 - libraryN.jar

Now, for the questions:

1. Are there any guide lines for what should be put in the library directory, and is my solution generally acceptable?
2. Why aren't the libraries in the root of the ear available to the jars in the lib directory?
3. Why doesn't maven figure this out automatically?

EDIT: pom.xml for the ear

<?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>

    <artifactId>ear</artifactId>
    <packaging>ear</packaging>

    <parent>
        <groupId>com.example</groupId>
        <artifactId>project</artifactId>
        <version>1.0-SNAPSHOT</version>
    </parent>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-ear-plugin</artifactId>
                <version>2.7</version>
                <configuration>
                    <modules>
                        <webModule>
                            <!-- ... -->
                        </webModule>
                        <ejbModule>
                            <!-- ... -->
                        </ejbModule>
                        <jarModule>
                            <groupId>com.example</groupId>
                            <artifactId>persistence-unit</artifactId>
                            <bundleDir>lib</bundleDir>
                        </jarModule>

                        <-- I added these to get the deployment working -->
                        <jarModule>
                            <groupId>org.apache.shiro</groupId>
                            <artifactId>shiro-core</artifactId>
                            <bundleDir>lib</bundleDir>
                        </jarModule>
                        <jarModule>
                            <groupId>org.slf4j</groupId>
                            <artifactId>slf4j-api</artifactId>
                            <bundleDir>lib</bundleDir>
                        </jarModule>
                    </modules>
                </configuration>
            </plugin>
        </plugins>
    </build>

    <dependencies>
        <dependency>
            <groupId>com.example</groupId>
            <artifactId>persistence-unit</artifactId>
        </dependency>
        <dependency>
            <!-- ... -->
            <type>war</type>
        </dependency>
        <dependency>
            <!-- ... -->
            <type>ejb</type>
        </dependency>

        <dependency>
            <groupId>org.apache.shiro</groupId>
            <artifactId>shiro-core</artifactId>
        </dependency>
    </dependencies>
</project>

And for the persistence unit:

<?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>

    <artifactId>persistence-unit</artifactId>
    <packaging>jar</packaging>

    <parent>
        <groupId>com.example</groupId>
        <artifactId>project</artifactId>
        <version>1.0-SNAPSHOT</version>
    </parent>

    <dependencies>
        <dependency>
            <groupId>org.jboss.spec</groupId>
            <artifactId>jboss-javaee-6.0</artifactId>
            <type>pom</type>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>org.apache.shiro</groupId>
            <artifactId>shiro-core</artifactId>
        </dependency>
    </dependencies>
</project>

Answer 1

This article has a great table explaining things:

Table 2 A standard archive may load classes either packaged inside it or from any other archives it is dependent on.

Module      Code Sources
EAR 
            All JARs in the /lib directory of the EAR
            Manifest Class-Path of any JARs in 1
EJB-JAR 
            EJB-JAR file itself
            JARs referenced by manifest Class-Path of EJB-JAR
            JARs referenced by manifest Class-Path of above JARs (in 2)
WAR 
            WEB-INF/classes
            JARs in WEB-INF/lib
            JARs referenced by manifest Class-Path of WAR
            JARs referenced by manifest Class-Path of JARs in 2 and 3