Update configuration behaviour

[Vladyslav-Kuksiuk]

This PR updates how multiple embedding configurations are set. Resolves this issue.

Changes:

• Replaced the ambiguous embed-mappings structure with explicit top-level embeddings.
• Made each embedding a complete, named configuration with unique names and isolated fragment output under fragments-path/<embedding-name>.
• Improved validation and CLI output for multi-embedding configs, including warnings for shared docs-path values.