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You can create separate mounts as per suggested size requirements below. Both folders must be owned writable by user that will be used to run FlexDeploy server process.

FlexDeploy Working Directory

FlexDeploy uses a working directory for temporary files to be transferred between the server and its endpoints. This directory needs to have at least 4GB of space available on the FlexDeploy Server.

This directory will be specified on command line as -Dflexagon.fd.install.root.

As this file system contains only temporary files, there is no reason to backup this directory.
Availability of space within the server working directory is critical to functioning of the FlexDeploy platform. Therefore, the filesystem should be monitored and space should be allocated as necessary. In addition, it is recommended that this be a separate mount point.
Files in this directory which are older than one day will be purged automatically to help effectively manage the size.

If creating a separate working directory, you will need to copy the plugins folder (and the jars contained within it) from the applications folder that was created in the initial install to this new directory.

FlexDeploy Artifact Repository

The FlexDeploy artifact repository is a directory available on the FlexDeploy server where all build artifacts are stored, and later retrieved for the deployments. This directory needs to have at least 10GB of space available on the FlexDeploy Server.

Due to the importance of the artifact repository, this file system should be backed up regularly.

Customers should follow their standard practices for File System(Artifact Repository) backup. Files are never modified once added in the Artifacts directory, they are deleted based on purge settings, just wanted to mention that here for clarity. Incremental daily should be reasonable option. During upgrade procedure, we have defined steps to take complete backup of database and file system as well.

There is no need to stop Application during regular scheduled backup, but time with least activity should be used in such cases.

This directory will be specified on command line as -Dflexagon.fd.repository.root.

Availability of space within the Artifact Repository is critical to the creation of new build versions. It is highly recommended to have a file system size monitor in place for this directory, and size should be adjusted based on the number of builds created, and the size of the artifacts produced. In addition, it is recommended that this be a separate mount point.
Number of files in Artifact Repository will depend on Purge Settings, number of projects and build activity. As best practice, we are recommending 30 to 60 days setting for keeping Artifacts. There are other criteria that keep the Artifacts from being purged as well, for example, latest configurable number of versions are always kept. Size of file depends on type of packages being created, but for EBS artifact file is compressed and typically should be smaller in size.