Update README.md with prune command, delete-branch option, and TOML configuration

[bjester]

Observed Behavior

README.md contains outdated and missing documentation for features released in v0.5.0:

1. The new prune command is completely omitted from both the Table of Contents and the Commands section.
2. The remove command documentation lacks mention of the new --delete-branch option.
3. The Directory Structure and Templates sections still reference config.json instead of config.toml and allowed_hooks.json.

Expected Behavior

README.md should accurately document all available CLI subcommands, flags, and configuration file formats.

Steps to Reproduce

1. Open README.md.
2. Check Table of Contents (#table-of-contents) and Commands (#commands): notice prune is absent.
3. Check remove command details: --delete-branch is missing.
4. Check lines 80 and 136: config.json is referenced instead of config.toml.

Minimal Reproduction Environment / Conditions

• Version / Branch / Commit: release-v0.5.x@6d07c0c
• File: README.md

Deliverables & Testing Requirements

• Add prune command documentation to Table of Contents and Commands collapsible sections.
• Document --delete-branch parameter under remove command.
• Update directory structure diagram and variable description to reference config.toml.
• Verify markdown rendering and anchor link integrity.

Technical Pointers & Root Cause Clues

• Suspected Components: README.md:15-32, 70-84, 136, 203-213
• Related Commits: bd7ed4c, c953c29, f96f3fb

Notes & Edge Cases

• Keeps documentation synchronized with the CLI before final tag release.

Metadata

Severity / Priority: P2 (Medium)
Area: documentation

AI Usage

Drafted with Gemini following the DEEP framework based on code review findings against release-v0.5.x. Reproduction conditions and code references were verified in the codebase.