docs: fix incorrect CLI commands, flags, and API examples

[KellyJDavis]

This commit fixes numerous documentation errors to ensure all examples and command references accurately reflect the actual implementation:

CLI Commands:

• Change http start to http serve (correct command name)
• Change mcp start to mcp serve (correct command name)
• Fix default port from 8000 to 8001 for HTTP server
• Fix default host from 127.0.0.1 to localhost for HTTP server
• Fix default limit from 10 to 5 for search command

CLI Flags:

• Change --pkg to --package (or -p) for search command
• Remove non-existent --log-level from mcp serve command
• Fix chat command flags: use --backend, --lean-api-key, --debug instead of non-existent --model and --api-key

CLI Subcommands:

• Remove non-existent configure show and configure reset subcommands
• Remove non-existent data list and data status subcommands
• Document actual subcommands: configure api-key, configure openai-key, data fetch, data clean

API Examples:

• Fix field access: results.items → results.results
• Fix field name: item.informal_name → item.informal_description
• Fix method name: get_citations() → get_dependencies()
• Update all port references from 8000 to 8001

HTTP Server Documentation:

• Fix endpoint: /api/v1/citations/{item_id} → /api/v1/statement_groups/{group_id}/dependencies
• Update response JSON examples to match actual API structure

MCP Server Documentation:

• Fix tool names: remove incorrect lean_explore_ prefixes
• Use correct tool names: search, get_by_id, get_dependencies
• Fix parameter names to match actual tool signatures

All documentation now accurately reflects the codebase implementation.