Add flags for publish subcommand

[Yuan325]

Add flags for publish subcommand.

Motivation and Context

We'll need to use the --file flag since we store our server.json in a folder.

The options that was noted in the docs here was not implemented. This PR added the 3 flags that was stated.

How Has This Been Tested?

Tested locally

Breaking Changes

No breaking changes. The existing way of defining file mcp-publisher publish server.json will still work.

Types of changes

• [x] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)
• [ ] Documentation update

Checklist

• [x] I have read the MCP Documentation
• [x] My code follows the repository's style guidelines
• [x] New and existing tests pass locally
• [x] I have added appropriate error handling
• [x] I have added or updated documentation as needed

Additional context

Fixes #767

[Yuan325]

@domdomegg @rdimitrov I am unable to add reviewers to this PR (and wasn't sure who should I request for reviews). Please take a look, thank you!! :)

[domdomegg]

Also I appreciate these flags are bizarrely in the docs, which seems like a mistake for something not implemented, so we do need to fix something (either the docs or the implementation). I'd lean towards removing the options from the docs.

cc @rdimitrov I wonder what you think here?