JSHint in javascript is not showing all warnings for code to be corrected

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I have the JSHint plugin running in eclipse to see code corrections I need to make as I go then also generate a report from the JSHint CLI tool when I make a release.

In eclipse I get told that there are 53 corrections that need to be made for JSHint none at all concerning indents or white space. However when I run the CLI JSHint tool I get told there are 350 corrections that need to be made mainly concerning white spacing and indentation that are not showing up in eclipse.

Why are these warnings not being displayed in the eclipse JSHint plugin but being displayed in the report for JSHint?

Also yes they are both using the same configuration file so that is not the problem.

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