$ cd thefolder
$ find . -name *.pdf | xargs -I {} cp -iv {} .
# find all files
# which end in .pdf
# recursively from
# the current folder
# |
# for each emitted line
# copy the output (captured by {}) to
# the specified path ('.' is the current directory)
# copy should be verbose and should ask,
# in case a file would be overwritten
This should copy your files to /thefolder/. If you want to move them, replace cpwith mv.
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