Você está procurando
diff -rq (dir1) (dir2)
Prova de conceito:
#!/bin/sh
#create our test
mkdir -p /tmp/a/b
echo "test" >> /tmp/a/c
mkdir -p /tmp/a/d/e
echo "blah" >> /tmp/a/d/e/f #only exists here
mkdir -p /tmp/q/b
echo "testing" >> /tmp/q/c #/tmp/a/c shouldnt match
mkdir -p /tmp/q/d/e
echo "blah" >> /tmp/q/d/e/g #only exists here
diff -rq /tmp/a /tmp/q
resulta em:
Files /tmp/a/c and /tmp/q/c differ
Only in /tmp/a/d/e: f
Only in /tmp/q/d/e: g