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I downloaded the the PHP tools for Eclipse and have created a new PHP project. I added a trivial hello world script with no dependencies and click Run As -> PHP Webscript.

Now for the weird part: My entire workspace gets rebuilt. This means that ALL my other projects in different languages like C,C++ and Java are being built and only THEN does the script run as a webpage.

Any ideas where I could reconfigure this or why its happening?

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Have you tried right-clicking on the PHP project and selecting "Close Unrelated Projects"? When you need to go back to one of the other projects, you can right-click on it and select "Open Project" to open it back up.

I have not tried this on projects with version control, though.

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Thanks. That works perfectly. Not sure why a Run As call to one project would try to compile all of them though.
It's what I think is commonly called a 'feature'. ;D

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