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I need to install 2 version of Eclipse. One for Java and one for PHP. Should I expect that some hidden folder/file is gonna be overridden by both installation? I downloaded to standalone installation package from the eclipse download page.

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Eclipse installation is actually a zip file that can be extracted into some folder of your choice. You may have two Eclipse installed by naming the directories with a different name (e.g. eclipse_java and eclipse_php).
There is no problem with that because Eclipse doesn't store anything outside of its directory and the Workspace directory.

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I do have a .eclipse folder in my /home –  luso Oct 12 '12 at 17:48
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Typically, you don't need to have separate Eclipse installations for different environments. The persepctive concept is made to switch from different tasks, and you can easily download different plugins.

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yeah that's absoluely true but since I'm gonna need in total like 9 plugins, if I install them on the same installation it's gonna be slow, trust me. I usually keep separated installation for every language to keep the bootstrap thin. –  dierre Mar 5 '12 at 9:51
    
Like Yossile said - if you change your Workspace folder you're changing your set of plugins ( check <workspace_name>/.metadata/.plugins ). You should be fine with a single installation and 2 workspaces. –  racamirko Mar 5 '12 at 12:31
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