docs: Update --help output to reflect new command pattern

[swinney]

Summary

Updates the CLI help output to accurately reflect the current state of the project after the Phase 2 refactoring, which introduced a command pattern architecture while maintaining backward compatibility.

Changes

• Enhanced help output to show both new command pattern and legacy flag-based approaches
• Added comprehensive examples for all available commands and their aliases
• Updated main() function to recognize all command aliases (g, gen, r, std, s, lm, lp, clean, etc.)
• Clear documentation marking the new command pattern as recommended while maintaining legacy support

Key Improvements

1. Clarity: Users now immediately understand there are two ways to use the CLI
2. Discoverability: All command aliases are documented in the help output
3. Migration Path: Shows equivalent commands in both patterns to help users transition
4. Complete Coverage: Documents the test command and all utility commands

Testing

• ✅ Verified doc-gen --help shows updated output
• ✅ Tested command aliases work (e.g., doc-gen g --help for generate)
• ✅ All CLI tests pass with updated help content

Backward Compatibility

✅ All legacy flag-based commands continue to work exactly as before
✅ No breaking changes - purely additive improvements to help documentation

This addresses the user's request to update the out-of-date help output to reflect current capabilities.