Where in an Eclipse workspace is the list of projects stored?

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Windows:

<workspace>\.metadata\.plugins\org.eclipse.core.resources\.projects\

Linux / osx:

<workspace>/.metadata/.plugins/org.eclipse.core.resources/.projects/

Your project can exist outside the workspace, but all Eclipse-specific metadata are stored in that org.eclipse.core.resources\.projects directory
As noted in the comments by tk421storm, and in Jeegar Patel‘s answer:

In order for manual changes to take effect, make sure to do File -> Refresh afterwards.

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