✨ chore: Add FastMCP stdio support, update CLI, docs, and dependencies

[Falamarcao]

✨ chore: Add FastMCP stdio support, update CLI, docs, and dependencies

We did the thing.
The stdio thing.
And a bunch of other things.

This PR:

• 🧑‍💻 Added FastMCP stdio server support (run_stdio and CLI integration)
• 🛠️ Refactored CLI helpers and constants for better modularity
• 🧹 Removed legacy CLI utils/helpers, migrated logic to new helpers
• 🏷️ Updated pyproject.toml and uv.lock with new dependencies (fastmcp, asgi-lifespan, etc.)
• 🐍 Improved logger to redirect to stderr in stdio mode
• 🧪 Added integration tests for stdio connect/disconnect and FastMCP in-memory client
• 🧪 Updated test fixtures to use new command discovery helpers
• 📦 Updated Dockerfile to use correct healthcheck and port
• 📚 Improved README and CONTRIBUTING docs for stdio, Docker, and Kubernetes usage
• 🏷️ Updated attribution, citation, and project metadata

✅ Local Tests: all 126 tests passed successfully.

So yes, it works.
No, I don’t know how.
But the tests passed, so we ship.

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🔐 refactor: replace API_TOKEN=SERVER_AUTH_DISABLED with AUTH_ENABLED flag for cleaner auth handling

Remember that time we used API_TOKEN=SERVER_AUTH_DISABLED to turn off auth?

Yeah… that was a phase.

We’ve matured now. We use real flags like adults.

Introducing: AUTH_ENABLED=false

• No more pretending a token value is a config flag
• No more explaining “no, really, it’s not a bug”
• Just clean, honest, AUTH_ENABLED=false energy

The server still starts.
The logs still scream in uppercase.
But now, at least, we’re not lying to ourselves.

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🤖 PR Message Note
Yes, an AI helped write this.
No, it didn’t question my life choices — but it probably should have.
The code? Mine.
The tests? Green.

But for now — we merge.
And we move on.