Fix CLI reliability issues

[itsflaid]

Summary

• retry Groq rate limits up to three times with exponential backoff
• reject malformed snapshot fileIndex entries and invalid config schemas
• read the doctor version from package metadata
• standardize the DevMap AGENTS.md marker while recognizing legacy files
• document schema v1 file-count semantics
• add regression tests and update private development notes

Verification

• pnpm test:cli (47/47)
• pnpm build:cli
• pnpm build:web
• pnpm test:package-e2e
• git diff --check