src/a/  tgt/aye/
src/b   tgt/b/
src/c/  tgt/c

/tmp/testzone/src/a/afile.txt
/tmp/testzone/src/b/bfile.txt
/tmp/testzone/src/c/cfile.txt

cut -f 2 mapping.txt | tr 'n' '' | xargs -0 mkdir -p

/tmp/testzone/tgt/aye/
/tmp/testzone/tgt/b/
/tmp/testzone/tgt/c/

xargs --arg-file mapping2.txt cp -a

/tmp/testzone/tgt/aye/
/tmp/testzone/tgt/b/
/tmp/testzone/tgt/c/a/afile.txt
/tmp/testzone/tgt/c/aye/
/tmp/testzone/tgt/c/b/bfile.txt
/tmp/testzone/tgt/c/c/cfile.txt