Eclipse Juno does not auto update the changes (Clean and Rebuild not working too)

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I am currently using Eclipse Juno with detail shown below.

Eclipse Java EE IDE for Web Developers.

Version: Juno Service Release 2 Build id: 20130225-0426

I got 2 same project with different file changes. My problem is when I delete the existing file(old file) and import with another file(latest file), it does not detected my latest file, it keep run for the old version even thought I check the coding is already change with latest code in the IDE. I had try search thought online with method of clean project, rebuild project, clean server file& run again, tick for "built automatically", create new workplace and delete .metadata file . None of these can solve my problems. However, if I purposely open the changes file, changes the file and save it, it then only reflect to the changes which was very inefficient and wrong. Does any body face this problem? Thank you.

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