score:1
that tab within eclipse is all put onto the buildpath at runtime and is going to be organized based on the library you are putting onto the path not where in the eclipse ui you designate it.
as you mentioned it is more for a logical easier to use ui as opposed to any actual change to where it is located. personally i prefer using the "native library" in the source tab but that is just out of preference.
Source: stackoverflow.com
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