Let's say you have a Mule application server named myAppServer, and the root directory of the application server is /opt/MuleSoft/myAppServer. One of the sub directories is apps.

drwxr-sr-x 28 root root 4096 Jun 17 22:49 apps

You will place a .zip file that contains the app in the apps directory, like this.

/opt/MuleSoft/myAppServer/app/myApp.zip

As long as the Mule application server is running, Mule should unzip the file, and create a directory and anchor.txt file for the app. Additionally, the .zip file will be removed.

drwxr-sr-x 4 root root 4096 Aug 15  2019 myApp
-rw-r--r-- 1 root root   77 Jun 17 22:44 myApp-anchor.txt

The mule_ee.log should contain the following.

INFO yyyy-mm-dd hh:mm:ss,sss [Mule.app.deployer.monitor.1.thread.1] org.mule.module.launcher.ArtifactArchiveInstaller: Exploding a Mule artifact archive: file:/opt/MuleSoft/myMuleAppServer/apps/myApp.zip

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ New app 'myApp'                                          +
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

* Started app 'myApp' *

If you already have an old version of the application deployed, and you want to deploy a new version of the application, you will simply place the new .zip file in the apps directory, and Mule should replace the old version of the application with the new version of the application.