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git-filter-branch: leave directory structure
|-repository/
|  |  |-repository/fileOne
|  |
|  |-subOne/
|  |  |-subOne/fileTwo
|  |
|  |-subTwo/
|     |-subTwo/fileThree

$ git filter-branch --subdirectory-filter subOne --prune-empty

$ git log --oneline
0c0ea11 subOne history
6318bba subOne history
c96fddb Initial commit

$ ls
fileOne
$ pwd
/this/is/a/path/repository

To move the whole tree into a subdirectory, or remove it from there:
       git filter-branch --index-filter
               'git ls-files -s | sed "s-t"*-&newsubdir/-" |
                       GIT_INDEX_FILE=$GIT_INDEX_FILE.new
                               git update-index --index-info &&
                mv "$GIT_INDEX_FILE.new" "$GIT_INDEX_FILE"' HEAD