The problems happens if, in a commit which already committed to the subversion server, a branch has been merged into
trunk that where some files are added.

Who or what is merging the branch into trunk?

  • A developer, on their own machine, which is then committed to svn.

And what if you checkout the trunk with command line svn - is the content duplicated, too?

  • no, if you use the command line tools, the checkout is as expected, with no duplicated content.
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