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Eclipse Web Tools Guide
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Clean projects published on the server

You can use the clean option available in the Servers view to remove any invalid resources from the server before doing a full republish. This helps remove by-products generated as a result of the publishing process. When you find there is old code or an invalid state of code running on the server, try using this clean option to see if this helps remove these invalid states from the server.

To clean projects published on the server, complete the following steps:
  1. In the Servers view, right-click a server.
  2. In the pop-up menu, select Clean.
  3. The following message dialog box displays:
    Clean will discard all publish state and republish from scratch.  Are you sure you 
    want to clean all published projects?
  4. Select OK.

 
 
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