Clean up deprecated and old flags in the CLI

[zlav]

Overview

This PR is intended to clean up old CLI flags and clearly state that deprecated functionality is deprecated

• --experimental-use-v3-go-resolver flag has been hidden. This behavior is now default
• MSB documentation cleaned up. The flags have been hidden with deprecation warnings and the public docs have been removed.

Acceptance criteria

The logic to deprecate flags and the behavior is correct.

Testing plan

Manually run the flags on the binaries and see that they output a deprecation message and that they no longer show up in the list of features.

Risks

There should be none. The flags are either being hidden or having a deprecation notice added

Checklist

• I added tests for this PR's change (or explained in the PR description why tests don't make sense).
• If this PR introduced a user-visible change, I added documentation into docs/.
• If this PR added docs, I added links as appropriate to the user manual's ToC in docs/README.ms and gave consideration to how discoverable or not my documentation is.
• If this change is externally visible, I updated Changelog.md. If this PR did not mark a release, I added my changes into an ## Unreleased section at the top.
• If I made changes to .fossa.yml or fossa-deps.{json.yml}, I updated docs/references/files/*.schema.json AND I have updated example files used by fossa init command. You may also need to update these if you have added/removed new dependency type (e.g. pip) or analysis target type (e.g. poetry).
• If I made changes to a subcommand's options, I updated docs/references/subcommands/<subcommand>.md.