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You can either upload and activate the plugin through UI or just place it in a specific folder on Server. Either option works fine.

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Upload and Activate Plugins using UI

The FlexDeploy installation comes with plugins which are automatically loaded on startup. To install additional plugins or plugin versions, select Integrations-> Plugins from the menu. Image
You can download new plugin versions from http://support.flexagon.com or download link provided on Plugins page see screen shot below for example.
Image To upload a new plugin or new version of an existing plugin, click the Upload button.  On the upload plugin popup, click on the text field to find the plugin jar file on your local drive or drag and drop the jar file onto the text field in the popup directly. Then click on UPLOAD in the popup to load your plugin. Image If the upload of plugin completes successfully, you will see new row in plugins table. The plugin is now installed in the FlexDeploy server but is not yet ready for use. To make it available for use you must click on the button in the Active column for the plugin version you uploaded. Only one version of a particular plugin can be active at one time. To revert to an older version, simply activate that version. Select the newly uploaded plugin version and make it active through the button in the Active column. See screenshots below for example. Image
One version of each plugin is active for use in FlexDeploy at a time. This process does not require any restart.
If you are installing a new plugin for the first time you must now associate one or more of its operations to one or more Target Groups. See the Target Groups section of the Topology chapter for details. Flexagon may from time to time provide new plugins, or provide updates to existing plugins, and make them available independent of a FlexDeploy upgrade. This approach allows faster plugin delivery which is not tied to product release timelines.

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Uninstall Plugin Versions

@Since 11.2.0.0 You can uninstall inactive plugin versions from Administration > Plugins. Uninstall requires Plugin Upload permission. The active version cannot be uninstalled. Uninstall is available from the plugins list and from a plugin version detail page. After uninstalling from the detail page, you return to the plugins list. Uninstalling an inactive version removes it from Administration > Plugins and deletes that version’s folder on the server. Plugin property sets and the remaining active version are not changed.

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Auto Upload Plugins

This is useful when you are upgrading FlexDeploy, as there may be many new plugins or versions available as part of new FlexDeploy release. This option can also be used for one single plugin version upload as well.
  • Locate flexagon.fd.install.root folder for your FlexDeploy installation. This is specified on Java command line. For example, -Dflexagon.fd.install.root=c:/temp/flexdeploy/application.
  • Create plugins folder, if it does not exist under this folder.
  • Download new plugins from Flexagon support site and save in plugins folder.
  • Start FlexDeploy, and all plugin jar files from plugins folder will be uploaded and files will be moved to uploadedplugins folder.
  • Now go to Administration - Plugins in FlexDeploy and activate plugin versions as necessary.