Refactor: split monolithic CLI and MCP server into smaller modules

[selftwo]

Problem

Both src/cli/index.ts and src/mcp/server.ts are large monolithic files. This makes them hard to test and difficult for contributors to navigate.

Proposed structure

CLI

src/cli/
  index.ts        # Entry point + command registration
  commands/
    init.ts
    scan.ts
    classify.ts
    move.ts
    status.ts
    trace.ts
    undo.ts
    archive.ts

MCP Server

src/mcp/
  server.ts       # Server setup
  tools/
    status.ts
    scan.ts
    classify.ts
    move.ts
    # ...etc

Prerequisite

This refactor should happen after a test suite is in place (see #1) to avoid regressions.

Impact

Unblocks external contributions — contributors can add a single command or MCP tool without reading the entire file.