docs: add CLI reference table for mcp dev/run/install flags

[RudrenduPaul]

The -t, --transport flag and all other mcp CLI flags were undocumented
in the README. Users and LLMs connecting to MCP servers had no reference
for available options without reading the source code.

Added a ### CLI Reference subsection under ## Running Your Server
with complete flag tables for mcp dev, mcp run, mcp install, and
mcp version. Flags sourced directly from src/mcp/cli/cli.py.

Motivation and Context

Users trying to connect external clients (e.g. Cursor, Claude Desktop) to
a locally-running MCP server need to know which transport to specify. The
-t, --transport flag for mcp run was only discoverable by reading the
source — it was absent from the README entirely. This adds a single
reference table so users don't have to grep the code.

How Has This Been Tested?

Documentation-only change. Verified flag names and types against
src/mcp/cli/cli.py directly. No code paths changed.

Breaking Changes

None.

Types of changes

• Documentation update

Checklist

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