fix: separate suggested repository refs

[jlitola]

Summary

• request and parse backend suggestedRefs separately from indexed availableRefs
• use suggestedRefs for REF_NOT_FOUND 'Did you mean' hints while keeping availableRefs as queryable retry candidates
• update target-resolution text, MCP tool descriptions, docs, and regression tests for the split

Verification

• bun test
• bun run typecheck
• bun run build
• GITHITS_MCP_URL=https://mcp-dev.githits.com GITHITS_API_URL=https://api-dev.githits.com PKGSEER_URL=https://pkgseer-backend-dev.fly.dev bun run smoke:cli
• GITHITS_MCP_URL=https://mcp-dev.githits.com GITHITS_API_URL=https://api-dev.githits.com PKGSEER_URL=https://pkgseer-backend-dev.fly.dev bun run smoke:mcp
• GITHITS_MCP_URL=https://mcp-dev.githits.com GITHITS_API_URL=https://api-dev.githits.com PKGSEER_URL=https://pkgseer-backend-dev.fly.dev bun run agent:e2e --agent claude --server local --workload eval/agentic/workloads/code-file-navigation.md
• dev checks: github:[feature request] Fliter events/actions in realtime n8n-io/n8n#2.26.5, github:Move Router dispatch to own GenServer module. Kill on response completion. phoenixframework/phoenix#1.7.0, github:Docs/Tutorial: Introducing a submit button in the comment form react/react#19.2.0