I found that there is an easy solution for this problem. You can add a <Class-Path> element to <manifestEntries> element, and set <addClassPath>true</addClassPath> to <manifest> element. So value of <Class-Path> element is added to class-path automatically. Example:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>true</addDefaultImplementationEntries>
<addClasspath>true</addClasspath>
<mainClass>your.main.Class</mainClass>
</manifest>
<manifestEntries>
<Class-Path>../conf/</Class-Path>
</manifestEntries>
</archive>
</configuration>
</plugin>