cmd/run: remove superfluous [flags] from usageTemplate

Before vs after:

   $ opa run --help | grep flags
     opa run [flags] [flags] [files]
   $ ./opa_darwin_amd64 run --help | grep flags
     opa_darwin_amd64 run [flags] [files]

Signed-off-by: Stephan Renatus <srenatus@chef.io>