Make sure we get correct number (3) from wc by specifying line count.
Add "ls" to tools list, used in 10_files/03_transform/003.cf.
Fix sporadic failure of 10_files/03_transform/003.cf.

Don't use the same directory to hold the counter as the one who holds
the transformed files. Otherwise it may or may not be included
in the result, depending on file system order, since we use depth
search.