At the moment Sencha Cmd 5.1 is out.
- 
Download and install Sencha Cmd 5.1 as described in getting started. Also take a look at the Cmd 5.x docs.
 - 
Generate new ExtJS 5.1 application:
$ sencha generate app -ext MyApp src/main/application
 
I don't recommend to add "ext" directory with all ExtJS framework files to our Git repository.
In order to compile your project from Maven use exec-maven-plugin:
<plugin>
    <groupId>org.codehaus.mojo</groupId>
    <artifactId>exec-maven-plugin</artifactId>
    <version>1.3.2</version>
    <executions>
        <execution>
            <id>sencha-compile</id>
            <phase>compile</phase>
            <goals>
                <goal>exec</goal>
            </goals>
            <configuration>
                <!-- Set path to your Sencha Cmd executable-->
                <executable>${env.SENCHA_CMD}</executable>
                <workingDirectory>${project.basedir}/src/main/application</workingDirectory>
                <arguments>
                    <argument>app</argument>
                    <argument>build</argument>
                    <argument>--clean</argument>
                    <argument>--environment</argument>
                    <argument>${sencha.env}</argument>
                </arguments>
            </configuration>
        </execution>
    </executions>
</plugin>
And run:
$ export SENCHA_CMD="/path/to/your/Sencha/Cmd/5.1.2.52/sencha"
$ mvn compile
If you want to make SENCHA_CMD permanent then add it to your /etc/profile or ~/.bashrc file.
Note: ${sencha.env} determines your current maven profile: development or production. Take a look at pom.xml.
Your compiled ExtJS project will be located at src/main/application/build/production. You may change it to any other location.
Use maven-war-plugin to package WAR file.
<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-war-plugin</artifactId>
    <version>2.4</version>
    <configuration>
        <failOnMissingWebXml>false</failOnMissingWebXml>
        <webResources>
            <resource>
                <directory>src/main/application/build/${sencha.env}/MyApp</directory>
                <excludes>
                    <exclude>**/Readme.md</exclude>
                </excludes>
            </resource>
        </webResources>
    </configuration>
</plugin>
Now you have fully funtional Java web application.
- 
Create new artifact and add
src/main/applicationfolder to it instead ofsrc/main/application/build/testing/MyApp - 
Configure web server to deploy your newly created artifact.
 - 
In
rebel.xmlchange root web folder tosrc/main/application: 
See more info about JRebel configuration: