I already went into project properties > JavaScript > Include Path > Source and excluded my node_modules directory. But, when I run validation on the project it still tries to validate all of the javascript files in that folder.
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I was also annoyed by all sorts of validation errors (json, html, xml...) in the node_modules directory. I didn't had at least javascript validation errors because I added only /src/main/javascript to the JS build path.
For the other errors details are here: How to exclude specific folders or files from validation in Eclipse?, in particular check-out the comment from Jonatan Cloutier.
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I suggest you that you install 1.0.0-SNAPSHOT which provides the capability to exclude/include folders. To do that, configure those folder with JSDT JavaScript Include Path.
It's because tern.java doesn't support include/exclude path.