项目的目录结构如图：

下面是主要的配置文件内容：

assembly.xml

<?xml version="1.0" encoding="UTF-8"?>
<assembly>
	<id>package</id>
	<formats>
		<format>zip</format>
		<format>dir</format>
	</formats>
	<includeBaseDirectory>false</includeBaseDirectory>
	<fileSets>
		<fileSet>
			<directory>target/appassembler</directory>
			<outputDirectory>/</outputDirectory>
			<excludes>
				<exclude>**/spring-boot-devtools*</exclude>
			</excludes>
		</fileSet>
		<fileSet>
			<directory>src/main/resources</directory>
			<outputDirectory>/conf</outputDirectory>
			<excludes>
				<exclude>*.yml</exclude>
				<exclude>logback.xml</exclude>
			</excludes>
		</fileSet>
	</fileSets>
</assembly>

deploy目录存放不同环境下的配置文件

pom.xml添加如下配置：

<profiles>
        <profile>
            <id>dev</id>
            <activation>
                <activeByDefault>true</activeByDefault>
            </activation>
            <properties>
                <jvm.args>-Xms3g -Xmx3g</jvm.args>
                <app.resources>src/main/resources</app.resources>
            </properties>
        </profile>
        <profile>
            <id>test</id>
            <properties>
                <jvm.args>-Xms3g -Xmx3g</jvm.args>
                <app.resources>src/main/deploy/test</app.resources>
            </properties>
        </profile>
        <profile>
            <id>prod</id>
            <properties>
                <jvm.args>-Xms3g -Xmx3g</jvm.args>
                <app.resources>src/main/deploy/prod</app.resources>
            </properties>
        </profile>
    </profiles>


    <build>
        <finalName>${project.artifactId}</finalName>

        <resources>
            <!--指定src/main/resources资源要过滤-->
            <resource>
                <directory>src/main/resources</directory>
                <filtering>true</filtering>
            </resource>
        </resources>

        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <version>2.6</version>
                <configuration>
                    <archive>
                        <manifest>
                            <addClasspath>true</addClasspath>
                            <classpathPrefix>lib/</classpathPrefix>
                            <mainClass>com.xxg.Main</mainClass>
                        </manifest>
                    </archive>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>appassembler-maven-plugin</artifactId>
                <version>1.7</version>
                <configuration>
                    <repositoryLayout>flat</repositoryLayout>
                    <!-- 在脚本的classpath开始增加配置文件路径 -->
                    <includeConfigurationDirectoryInClasspath>true</includeConfigurationDirectoryInClasspath>
                    <!-- 生成配置文件路径 -->
                    <configurationDirectory>conf</configurationDirectory>
                    <!-- 配置文件原路径 -->
                    <configurationSourceDirectory>${app.resources}</configurationSourceDirectory>
                    <!-- 从原配置文件复制 -->
                    <copyConfigurationDirectory>true</copyConfigurationDirectory>
                    <includeConfigurationDirectoryInClasspath>true</includeConfigurationDirectoryInClasspath>

                    <!-- 生成哪几种平台的脚本 -->
                    <platforms>
                        <platform>windows</platform>
                        <platform>unix</platform>
                    </platforms>
                    <!-- 生成脚本的后缀 -->
                    <binFileExtensions>
                        <unix>.sh</unix>
                        <windows>.bat</windows>
                    </binFileExtensions>
                    <!-- 使用classpath通配符 -->
                    <useWildcardClassPath>true</useWildcardClassPath>
                    <!-- JVM参数 -->
                    <extraJvmArguments>${jvm.args}</extraJvmArguments>
                    <!-- 依赖包目录 -->
                    <repositoryName>lib</repositoryName>
                    <programs>
                        <program>
                            <!-- springboot项目主启动类 -->
                            <mainClass>xxxx.xxx.xx.xxx</mainClass>
                            <name>main</name>
                        </program>
                    </programs>
                </configuration>
                <!-- 绑定生命周期 -->
                <executions>
                    <execution>
                        <id>appassembler</id>
                        <phase>package</phase>
                        <goals>
                            <goal>assemble</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <version>2.4.1</version>
                <configuration>
                    <appendAssemblyId>false</appendAssemblyId>
                    <descriptors>
                        <descriptor>src/main/assembly/assembly.xml</descriptor>
                    </descriptors>
                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id>
                        <phase>package</phase>
                        <goals>
                            <goal>single</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <version>2.10</version>
                <executions>
                    <execution>
                        <id>copy-dependencies</id>
                        <phase>package</phase>
                        <goals>
                            <goal>copy-dependencies</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}/lib</outputDirectory>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

<!--             可执行jar插件-->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <configuration>
                    <archive>
                        <manifest>
                            <addClasspath>true</addClasspath>
                            <classpathPrefix>lib/</classpathPrefix>
                            <mainClass>ssp.lanxinpay.settlement.MainApp</mainClass>
                        </manifest>
                        <manifestEntries>
                            <Class-Path>.</Class-Path>
                        </manifestEntries>
                    </archive>
                    <excludes>
                        <exclude>**/*.xml</exclude>
                        <exclude>**/*.conf</exclude>
                        <exclude>**/*.properties</exclude>
                        <exclude>**/*.yml</exclude>
                    </excludes>

                </configuration>
            </plugin>
            <!-- maven资源文件复制插件 -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-resources-plugin</artifactId>
                <version>2.7</version>
                <executions>
                    <execution>
                        <id>copy-resources</id>
                        <!-- here the phase you need -->
                        <phase>package</phase>
                        <goals>
                            <goal>copy-resources</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}/etc</outputDirectory>
                            <resources>
                                <resource>
                                    <directory>src/main/resources</directory>
                                    <includes>
                                        <exclude>**/*.xml</exclude>
                                        <exclude>**/*.conf</exclude>
                                        <exclude>**/*.properties</exclude>
                                        <exclude>**/*.yml</exclude>
                                    </includes>
                                    <filtering>true</filtering>
                                </resource>
                            </resources>
                            <encoding>UTF-8</encoding>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <!-- 依赖包插件 -->
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-dependency-plugin</artifactId>
                <executions>
                    <execution>
                        <id>copy-dependencies</id>
                        <phase>package</phase>
                        <goals>
                            <goal>copy-dependencies</goal>
                        </goals>
                        <configuration>
                            <outputDirectory>${project.build.directory}/etc/lib</outputDirectory>
                            <!-- 是否不包含间接依赖 -->
                            <excludeTransitive>false</excludeTransitive>
                            <!-- 忽略版本 -->
                            <stripVersion>false</stripVersion>
                        </configuration>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.18.1</version>
                <configuration>
                    <skipTests>true</skipTests>
                </configuration>
            </plugin>
            <!--<plugin>
                <groupId>org.mybatis.generator</groupId>
                <artifactId>mybatis-generator-maven-plugin</artifactId>
                <version>1.3.2</version>
                <configuration>
                    <configurationFile>src/main/resources/generatorConfig.xml</configurationFile>
                    <verbose>true</verbose>
                    <overwrite>true</overwrite>
                </configuration>
                <executions>
                    <execution>
                        <id>Generate MyBatis Artifacts</id>
                        <goals>
                            <goal>generate</goal>
                        </goals>
                    </execution>
                </executions>
                <dependencies>
                    <dependency>
                        <groupId>org.mybatis.generator</groupId>
                        <artifactId>mybatis-generator-core</artifactId>
                        <version>1.3.5</version>
                    </dependency>
                </dependencies>
            </plugin>-->
        </plugins>
 </build>

按照这种配置打包出来会生成zip包和ja包。以及针对不同操作系统生成不同的启动脚本。