[DOCS] Standardized CLI Guide and Command Reference for RuFlo

[shadowshan125]

Currently, the CLI surface for RuFlo has expanded significantly (referencing #1791 regarding CLI gaps), but there is no centralized "Quick Start" or command reference in the README. To help new users and contributors, we should document the core commands and their expected behavior.

Below is a proposed list of commands that need official documentation/verification:

1. Initialization & Setup
   npx ruflo init — Should document the creation of .mcp.json and how it handles the legacy claude-flow keys (ref: init writes .mcp.json with legacy claude-flow key, causing duplicate MCP registration alongside ruflo #1779).

ruflo login — Authentication workflow for agent federation.

2. Agent Execution
   ruflo spawn --claude — Usage for starting a new agent instance.

ruflo run [task] — Executing specific tasks or goals.

--plan-only — Clarifying the behavior between planning and auto-execution (ref: #1694).

3. Federation & Management
   ruflo daemon start — Running the background service (noting current Windows + Node 25 known issues daemon start (background) still dies on Windows + Node 25 in v3.6.30 — IPC channel keeps fork tied to parent #1766).

ruflo federate — Setting up cross-installation agent federation.

4. Metrics & Diagnostics
   ruflo metrics — Viewing hook metrics and outcome persistence.

ruflo memory stats — Checking embedding provider activity (ref: #1622).

Proposed Action:

Create a COMMANDS.md or update the main README.

Add a --help audit to ensure all lazy-loaded commands (ref: #1651) display short flags correctly.