feat: improve search freshness follow-ups

[jlitola]

Summary

• Preserve floating repo targets for discovery search while keeping code read/list/grep targets exact.
• Thread freshness/progress metadata through search and search_status with concise warnings and agent-ready follow-up commands.
• Sanitize GraphQL schema mismatch errors by default while keeping raw details behind debug flags.

Verification

• bun run typecheck
• bun test
• bun run build
• Production smoke: package/repo search, mixed targets, code_read follow-ups, search_status indexing progress

Notes

• The local implementation plan remains untracked and is intentionally excluded from this PR.