logging: unify pkg/log and plugin/log (#2245)

Default to using pkg/log for all logging and use a fixed time prefix
which is RFC3339Millli (doesn't exist in time, so we just extended
RFC3339), i.e. Nano might be pushing it.

Logs go from:

2018/10/30 19:14:55 [INFO] CoreDNS-1.2.5
2018/10/30 19:14:55 [INFO] linux/amd64, go1.11,

to:

2018-10-30T19:10:07.547Z [INFO] CoreDNS-1.2.5
2018-10-30T19:10:07.547Z [INFO] linux/amd64, go1.11,

Which includes the timezone - which oddly the std log package doesn't
natively do.

Signed-off-by: Miek Gieben <miek@miek.nl>

coremain/run.go

@@ -62,7 +62,7 @@ func Run() {
 	}
 
 	log.SetOutput(os.Stdout)
-	log.SetFlags(log.LstdFlags)
+	log.SetFlags(0) // Set to 0 because we're doing our own time, with timezone
 
 	if version {
 		showVersion()