assuming

bin/run.[bat/sh]
lib/*.jar
etc/


run.bat
------------------------------------------------------
setlocal ENABLEDELAYEDEXPANSION

set CLASSPATH=

FOR /R .\lib %%G IN (*.jar) DO set CLASSPATH=!CLASSPATH!;%%G

set CLASSPATH=.\etc\;.\lib\;%CLASSPATH%

echo "%JAVA_HOME%\bin\java" %OPTS% -cp "%CLASSPATH%" com.mycompany.Main

------------------------------------------------------

run.sh
------------------------------------------------------
if [[ $UBD_HOME == "" ]]; then
  echo ERROR: UBD_HOME not set - setting default
  UBD_HOME=$( cd `dirname $0`/.. ; pwd )
  #echo $UBD_HOME
fi

CLASSPATH=

for i in `ls -1 ./lib/*.jar`
do
  CLASSPATH=$CLASSPATH:${i}
done

CLASSPATH=./etc/:./lib/:$CLASSPATH

#OPTS=-Xdebug -Xnoagent -Djava.compiler=NONE -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5005

echo "INFO  *** Starting UBD ***"
"$JAVA_HOME/bin/java" $OPTS -cp  $CLASSPATH no.bbc.bagdrop.client.Start

------------------------------------------------------

src/assemble/bin.xml
------------------------------------------------------
  [...]
  <dependencySets>
    <dependencySet>
      <outputDirectory>lib</outputDirectory>
      <unpack>false</unpack>
      <scope>runtime</scope>
    </dependencySet>
  </dependencySets>
</assembly>



pom.xml
------------------------------------------------------
[...]
  <build>
    <defaultGoal>install</defaultGoal>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-assembly-plugin</artifactId>
        <executions>
          <execution>
            <phase>install</phase>
            <goals><goal>assembly</goal></goals>
          </execution>
        </executions>
        <configuration>
          <descriptor>src/assemble/bin.xml</descriptor>
          <finalName>XXX-${version}</finalName>
        </configuration>
      </plugin>
    </plugins>
------------------------------------------------------