Create entire wordpress as a github repositery?

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In my IDE (Flash Builder for PHP), I can’t find a way to create sub project inside WordPress project as I did with NetBeans. Seems I need to make entire WordPress as a github local repo in order to add version control for my small plugin. Is there other ways I can import git repo as a project inside main project?

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  1. There are two ways to make this easier:

    1. Set WordPress as a separate project and associate it with your current sub project as shown in this answer.
    2. If 1. isn’t possible manage the Git repository from a terminal and don’t use the limited build-in Git manager in Flash Builder.