If I understand correctly, you have a large directory tree, and you want all the files inside it to be in the same directory. If this is correct, then I can do it in two lines:
dir /s /b "yourSourceDirectoryTreeHere" > filelist.txt for /f %f in (filelist.txt) do @copy %f "yourDestinationDirHere"
In the batch file compared to the command line, change% f to %% f
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