Really fix file and command collection regressions

Previous patch was missing the hunks for plugins other than
usb:

       modified:   sos/plugins/general.py
       modified:   sos/plugins/logs.py
       modified:   sos/plugins/networking.py
       modified:   sos/plugins/qpid.py
       modified:   sos/plugins/s390.py

The automation used to convert to add_copy_specs() and
add_cmd_outputs() left a few missing and stray commas in file
and command lists, for e.g. causing two lsusb commands to be
concatenated:

  Running 71/74: usb...
[plugin:usb] collecting path '/sys/bus/usb'
[plugin:usb] collecting output of 'lsusblsusb -v'
[plugin:usb] collecting output of 'lsusb -t'

Signed-off-by: Bryn M. Reeves <bmr@redhat.com>