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Though example.com is full crawled.
Looking at example.com/folder indicates
No pages from your site are currently included in Google's index.
I guess it doesn't matter because those pages were already crawled and indexed, and they are visible in example.com
But I wonder if there may be negative aspects because of "duplication" ? I put a sitemap.xml with files on /folder in the /folder directory. Those files are also on
sitemap.xml on root.
I did all because that allows you to set a different country to target when your site has different languages.
IE: /folder targeting a different country than files in root.
It is surprising that the data was all ready to populate your newly set up directory - it would be if you set up a new domain. I guess the GWT back end needs to do some number crunching first to sort out the data for just one directory.