Directories and executables files in an APEX have x bit set

Files under /bin and all directories in an APEX now have x (executable)
bit set correctly.

Bug: 117580281
Test: m apex.test, push it to /data/apex and reboot.
adb shell ls -al /apex/com.android.example.apex@1 shows that the
directories have x bit set

Change-Id: I76e4188d86dc9cdf65e9f8e52be1981e25441a6e