Only run refresh_db once per salt run

As presently contstructed, pkg.refresh_db is run for every call of every
pkg.installed and pkg.latest state, and the refresh param for these
states is ignored.

This commit fixes it so that the rtag isn't created for every call, and
that a pkg.refresh_db is only done when refresh == True and the rtag
exists. After the install is run, the rtag is removed, keeping
pkg.refresh_db from being run in subsequent pkg states within the same
state.sls or state.highstate.
Now that #5744 is merged, apply the same recipe to `SaltRunOptionParser`.
Quiet sphinx.
run not cp!
Make pkg state refresh if rtag exists

After further discussion with Tom, the intent is that there is a single
pkg.refresh_db each salt run. This commit reverts that particular change
from the previous commit.
utils.verify.zmq_version: fix pylint W0702 "No exception type(s) specified"
salt.utils: fix pylint W0702 "No exception type(s) specified"
states.sysctl: add spaces after commas to fix pylint C0324
salt.payload: fix pylint W0702 "No exception type(s) specified"
salt.crypt: fix pylint W0702 "No exception type(s) specified"
Merge pull request #5751 from terminalmage/issue5733

Limit to one pkg.refresh per salt run
minion: fix pylint W0702 "No exception type(s) specified"
Merge pull request #5755 from cvrebert/patch-3

states.sysctl: add spaces after commas to fix pylint C0324
Merge pull request #5757 from cvrebert/patch-5

salt.crypt: fix pylint W0702 "No exception type(s) specified"
Merge pull request #5756 from cvrebert/patch-4

salt.payload: fix pylint W0702 "No exception type(s) specified"
Merge pull request #5754 from cvrebert/patch-2

salt.utils: fix pylint W0702 "No exception type(s) specified"
Merge pull request #5753 from cvrebert/patch-1

utils.verify.zmq_version: fix pylint W0702 "No exception type(s) specified
Merge pull request #5758 from cvrebert/patch-6

minion: fix pylint W0702 "No exception type(s) specified"
modules.freebsd_shadow: rm unused import of the os module

************* Module salt.modules.freebsd_shadow
W0611:  6,0: Unused import os
modules.netbsd_shadow: rm unused import of the os module

************* Module salt.modules.netbsd_shadow
W0611:  7,0: Unused import os