3 ways to generate the plugin-cfg.xml

Answer

There are 3 options to generate the plug-in file (plugin-cfg.xml).
You can generate the plug-in from:

1- The WebSphere Application Server console. Click: Environment > Update global Web Server plug-in configuration.

This option (new in WebSphere Application Server V6.1) picks up all applications mapped to servers in the entire cell. This approach will always be the "fullest". The plugin-cfg.xml produced is called the cell-wide or global plug-in config.
This option was created in order to be backward compatible with the plug-in generation option that was available in version 5.1 which only supports the concept of a global plugin-cfg.xml.
The plugin-cfg.xml will be generated at the following location:
%was_profile_home%/config/cells

2- The WebSphere Application Server console. Click servers > web servers, select your web server and click on "Generate Plug-in"

This option picks up only the applications that are mapped to the specified Web server.
The plugin-cfg.xml will be generated at the following location:
%was_profile_home%/config/cells/../nodes/.../servers/MyWebServerName

3- The command line. You can run the GenPluginCfg command %was_profile_home%/config/cells/GenPluginCfg.sh|bat
This option provides configuration parameters such as -cell.name -node.name -webserver.name. This approach can be used to generate the cell plug-in configuration file (plugin-cfg.xml that contains all apps in the cell), or webserver plug-in config. (For example: plugin-cfg.xml that contains only applications mapped to the specified webserver). By default, the plugin-cfg.xml will be generated at the following location:
%was_profile_home%/config/cells


For further information refer to:
Web server definition
Creating or updating a global Web server plug-in configuration file
Understanding Web server plug-ins