UMAP enhancement: subcommand, idempotent indexing, and interactive improvements

[cpetersen]

Summary

• Refactor train-umap / apply-umap top-level CLI commands into a ragnar umap train / ragnar umap apply Thor subcommand group
• Add idempotent indexing with file hash tracking to skip unchanged files and update only modified files
• Upgrade thor-interactive to support option parsing in interactive mode
• Auto-apply UMAP model to new embeddings during indexing when a trained model exists
• Make topics command use the cached LLM manager for better interactive mode performance
• Clean up unused config options and remove deprecated labeling method option from topics

Test plan

• Verify bundle exec rspec passes (270 examples, only pre-existing config cosmetic test failure)
• Verify ragnar umap train --help shows train options
• Verify ragnar umap apply --help shows apply options
• Verify ragnar umap --help lists available subcommands
• Verify ragnar help shows umap as a subcommand group
• Verify interactive mode routes /umap train and /umap apply correctly

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