The one in the project folder is your generic TS lint file that applies globally.
The one in the src folder is a project specific TS lint file that extends the other one, allowing you to tweak TS lint settings for the specific project.
Remember with Angular, you can have multiple projects and you may want slightly different TS lint settings for those projects.
If you only have one project, I think it is fairly safe to delete the TS lint file in the src folder. In the project I am working on we seem to have done just that.
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