Why does Jira plugin JAR size differ when it is packaged with Jira running/not running?

I have a Jira plugin built against Jira 7.2.2 with Atlassian SDK 6.2.14.

When I run atlas-mvn package I get a Jar file of ~5,5 Mb.

When I run a Jira instance with atlas-run and run atlas-mvn package after that I get a Jar file of ~100 Kb. Both plugins seem to work fine when installed on a local Jira instance.

Smaller jar contains only class files that were created by me. Bigger jar also includes dependencies from pom.xml not marked as provided.

Can someone please explain what kind of magic happens when the plugin is being packaged providing two different sets of *.class files and which dependencies should actually be packaged with the plugin?

Below is the contents of my pom.xml:

<?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>xxx</groupId>
    <artifactId>xxx</artifactId>
    <version>1.0.0-SNAPSHOT</version>
    <organization>
        <name>xxx</name>
        <url>xxx</url>
    </organization>
    <name>xxx</name>
    <description>xxx</description>
    <packaging>atlassian-plugin</packaging>
    <dependencies>
        <dependency>
            <groupId>com.atlassian.jira</groupId>
            <artifactId>jira-api</artifactId>
            <version>${jira.version}</version>
            <scope>provided</scope>
        </dependency>

        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.10</version>
            <scope>test</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>com.atlassian.jwt</groupId>
            <artifactId>jwt-plugin</artifactId>
            <version>1.6.2</version>
        </dependency>
        <dependency>
            <groupId>org.springframework</groupId>
            <artifactId>spring-context</artifactId>
            <version>4.1.6.RELEASE</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>com.atlassian.sal</groupId>
            <artifactId>sal-api</artifactId>
            <version>3.0.7</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>commons-logging</groupId>
            <artifactId>commons-logging</artifactId>
            <version>1.2</version>
        </dependency>
        <dependency>
            <groupId>com.atlassian.templaterenderer</groupId>
            <artifactId>atlassian-template-renderer-api</artifactId>
            <version>1.3.1</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>com.sun.jersey</groupId>
            <artifactId>jersey-client</artifactId>
            <version>1.8-atlassian-15</version>
            <scope>provided</scope>
        </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>org.mockito</groupId>
            <artifactId>mockito-all</artifactId>
            <version>1.8.5</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>com.sun.xml.bind</groupId>
            <artifactId>jaxb-impl</artifactId>
            <version>2.2.1.1</version>
        </dependency>
    </dependencies>
    <build>
        <plugins>
            <plugin>
                <groupId>com.atlassian.maven.plugins</groupId>
                <artifactId>maven-jira-plugin</artifactId>
                <version>${amps.version}</version>
                <extensions>true</extensions>
                <configuration>
                    <productVersion>${jira.version}</productVersion>
                    <productDataVersion>${jira.version}</productDataVersion>                    
                    <enableQuickReload>true</enableQuickReload>
                    <enableFastdev>false</enableFastdev>                    
                    <instructions>
                        <Atlassian-Plugin-Key>${atlassian.plugin.key}</Atlassian-Plugin-Key>                        
                        <Export-Package>xxx,</Export-Package>                        
                        <Import-Package>org.springframework.osgi.*;resolution:="optional", org.eclipse.gemini.blueprint.*;resolution:="optional", *;version="0";resolution:=optional</Import-Package>                        
                        <Spring-Context>*</Spring-Context>
                    </instructions>
                </configuration>
            </plugin>
            <plugin>
                <groupId>com.atlassian.plugin</groupId>
                <artifactId>atlassian-spring-scanner-maven-plugin</artifactId>
                <version>${atlassian.spring.scanner.version}</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>atlassian-spring-scanner</goal>
                        </goals>
                        <phase>process-classes</phase>
                    </execution>
                </executions>
                <configuration>
                    <scannedDependencies>
                        <dependency>
                            <groupId>com.atlassian.plugin</groupId>
                            <artifactId>atlassian-spring-scanner-external-jar</artifactId>
                        </dependency>
                    </scannedDependencies>
                    <verbose>false</verbose>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <configuration>
                    <source>1.8</source>
                    <target>1.8</target>
                </configuration>
            </plugin>
        </plugins>
    </build>
    <properties>
        <jira.version>7.2.2</jira.version>
        <amps.version>6.2.11</amps.version>
        <plugin.testrunner.version>1.2.3</plugin.testrunner.version>
        <atlassian.spring.scanner.version>1.2.13</atlassian.spring.scanner.version>
        <atlassian.plugin.key>${project.groupId}.${project.artifactId}</atlassian.plugin.key>
        <testkit.version>6.3.11</testkit.version>
    </properties>
</project>