fix: classify missing repositories as not found

[jlitola]

Summary

• map GraphQL REPOSITORY_NOT_FOUND to code-navigation target not found errors
• preserve repository URL and requested ref details in MCP/unified-search error payloads
• keep REF_NOT_FOUND classification unchanged for missing refs on existing repos

Tests

• bun test packages/core-internal/src/services/code-navigation-service.test.ts packages/mcp/src/shared/code-navigation-error-map.test.ts packages/mcp/src/shared/unified-search-response.test.ts
• bun run build

Backend follow-up for githits-com/pkgseer-backend#1437.