How to pull only one branch from remote?

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I want to copy all of the code and folder structure to the master branch but still keep my changes in the develop branch. That's because I'd like to compare the branches and then merge them.

Sadly, when I use the clone command in Git bash the new code is also displayed when I switch to the develop branch, isn't the pupose of branches that you should be able to change one of them and the others are kept unaffected?

What am I doing wrong? (I'm using Eclipse if it's helpful) :)

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