Improve --output CLI help and deprecate --file

[tgerla]

Based on the discussion in #1062, we want to improve the CLI help text for the --output parameter, and deprecate the --file parameter. The --output text currently looks like:

  -o, --output stringArray       report output format, options=[syft-json cyclonedx-xml cyclonedx-json github-json spdx-tag-value spdx-json syft-table syft-text template] (default [syft-table])

...and it's not clear from that help text that you can do:

-o json=sbom.syft.json -o spdx-json=sbom.spdx.json (as described in https://github.com/anchore/syft#multiple-outputs)

This means that the --file parameter is kind of redundant and confusing, so we should deprecate that option.