rsync does not copy files recursively when -a and --files-from are used together:

adi@stargate:~$ mkdir src dst; touch src/testfile; echo src > files
adi@stargate:~$ rsync -a --files-from=files . dst
adi@stargate:~$ find dst/
dst/
dst/src

But it it's doing is recursively, when an additional -r is given:

adi@stargate:~$ rm -rf dst/; mkdir dst
adi@stargate:~$ rsync -ra --files-from=files . dst
adi@stargate:~$ find dst/
dst/
dst/src
dst/src/testfile