feat(discover): support three versioning models in multi-module detection

[indaco]

Description

Enhances the discover command to properly recognize and configure three distinct versioning models:

1. Single-root: One .version file at project root with optional manifest syncing (package.json, Cargo.toml, etc.)
2. Coordinated versioning: Multiple .version files that stay synchronized via dependency-check plugin with format: raw
3. Independent versioning: Multiple .version files with different versions managed as a workspace

Key changes:

• Improved detection logic to distinguish between versioning models
• Updated prompts to guide users toward the appropriate configuration
• Added tests covering all three scenarios

Related Issue

N/A

Notes for Reviewers

• The dependency-check plugin now supports format: raw for syncing submodule .version files in coordinated versioning