Code Intelligence Tool Selection

Need	Tool	Example
Package/module overview	codebase_navigate MCP (L0→L1→L2)	"What packages exist?"
Symbol definition/signature	Serena find_symbol	"Where is Router defined?"
Who calls/references X	Serena find_referencing_symbols	"Who calls _set_output?"
File symbol overview	Serena get_symbols_overview	"What's in engine.py?"
What breaks if I change X	GitNexus impact	"Blast radius of renaming Router"
End-to-end execution flow	GitNexus query	"How does task submission work?"
Architecture/clusters	GitNexus context or clusters resource	"What's in the memory package?"
String pattern / non-Python	Grep	"Find all TODO comments"
File by name	Glob	"Find all *_hook.py files"

Escalation Path

Start cheap, escalate as needed:

1. codebase_navigate for orientation (always available, fast)
2. Serena for precise symbol work (LSP-powered, Python-only)
3. GitNexus for relationships and impact (knowledge graph, needs index)
4. Grep/Glob for everything else

Availability

• Serena: Always available. 1-2s init per session.
• GitNexus: Requires index. Check freshness: npx gitnexus status. PostToolUse hook auto-detects staleness after commits.
• codebase_navigate: Always available (Genesis health MCP).