As of v7, using Upload All to upload plugins to the server will replace the plugins folder on the server rather than merging with what is there.
When the custom plugins are downloaded by clients (when they log in), the server plugins folder will normally be merged with what they have. To get a clean plugins folder on the client, delete the plugins folder prior to logging in.
If you will be adding and deleting custom plugins frequently, and want them cleanly synced to clients without accumulating old deleted ones on the clients and without the users having to manually delete the folder to clean up, there is a hidden option to have the cleanup performed automatically...
warning: do not use this option for users who might create their own custom forms or reports, because it will cause them to be lost.
To have a client machine replace it's custom plugins folder with the one from the server, when the server plugins change (rather than merge), you can set the hidden option clobberCustomPlugins on the client.
On Mac, use defaults write on the command line
defaults write nz.co.cognito.MoneyWorks.Gold clobberCustomPlugins YES
On Windows, use RegEdit to add a clobberCustomPlugins value in the MoneyWorks Gold Preferences tree with value 1