For code.cytognosis.org deployment and agent-accessible cross-repo code intelligence
| Feature | Zoekt (Sourcegraph) | GitNexus |
|---------|-------|----------|
| Primary use | Fast trigram-indexed code search | AST-based knowledge graph for code |
| Index type | Trigram (regex + substring) | AST + dependency graph |
| Agent integration | API/Web UI | MCP server (native) |
| Multi-repo | Yes (indexserver config) | Yes (global registry at ~/.gitnexus/) |
| Privacy | Self-hosted | Zero-server (local/WASM) |
| Search type | Text/regex/symbol | Structural (impact analysis, blast radius, coordinated rename) |
| Maintenance | Sourcegraph-maintained Go | Community-maintained |
| Deployment | Docker/systemd | CLI + MCP |
| License | Apache-2.0 | MIT/Apache-2.0 |
code.cytognosis.org for fast text/regex search across all reposcode.cytognosis.org``yaml`infrastructure/services/zoekt/config.json
{
"GitHubOrg": "cytognosis",
"GitHubToken": "${GITHUB_TOKEN}",
"Name": "code.cytognosis.org",
"Repos": [
"cytognosis/cytoskeleton",
"cytognosis/cytos",
"cytognosis/cytoskills",
"cytognosis/cytocast",
"cytognosis/Yar",
"cytognosis/CAP",
"cytognosis/cytoexplorer",
"cytognosis/infrastructure",
"cytognosis/org"
]
}
mermaid
graph LR
GH[GitHub cytognosis/*] -->|mirror| IS[zoekt-indexserver]
IS -->|index| IDX[SSD Index Store]
IDX --> WS[zoekt-webserver]
WS --> LB[Cloud Run / nginx]
LB --> DNS[code.cytognosis.org]
`
Cloud Run service with persistent SSD volume for index
Scheduled indexing every 15 minutes
Universal Ctags for symbol extraction
Estimated index size: ~500MB for all repos
Search Capabilities
Full regex search across all repos
Symbol search (functions, classes, types)
File path filtering
Language filtering
Repository filtering
Line-level results with context
3. GitNexus for Agent Intelligence
Why GitNexus is Critical for Cytognosis
Our multi-repo architecture creates cross-repo dependencies that text search cannot resolve:
cytoskeleton defines schemas → cytos imports them
cytocast generates packages → that depend on cytoskeleton
cytoskills wraps code → from cytos, cytoskeleton, Yar
GitNexus's AST-based knowledge graph can:
1. Impact analysis: "If I change
cytoskeleton.schemas.core.CytosEntity, what breaks?"
2. Coordinated rename: Rename a symbol across all repos atomically
3. Process-grouped search: Find all code that participates in "KG building" workflow
4. Change detection: Map a git diff to affected processes across repos
Integration
`yaml
Agent MCP config for GitNexus
{
"name": "gitnexus",
"command": "gitnexus",
"args": ["mcp-server"],
"env": {
"GITNEXUS_REPOS": "/home/mohammadi/repos/cytognosis/cytoskeleton,/home/mohammadi/repos/cytognosis/cytos,/home/mohammadi/repos/cytognosis/Yar"
}
}
`
Local Installation
`bash
Install GitNexus
cargo install gitnexus # or npm install -g gitnexus
Index all Cytognosis repos
gitnexus index /home/mohammadi/repos/cytognosis/cytoskeleton
gitnexus index /home/mohammadi/repos/cytognosis/cytos
gitnexus index /home/mohammadi/repos/cytognosis/Yar
gitnexus index /home/mohammadi/repos/cytognosis/cytoskills
gitnexus index /home/mohammadi/repos/cytognosis/cytocast
Start MCP server
gitnexus mcp-server
`
4. Comparison with Alternatives
| Tool | Type | Self-Hosted | MCP | Cost | Verdict |
|------|------|------------|-----|------|---------|
| Zoekt | Trigram search | ✅ | ❌ (API only) | Free | Deploy for web search |
| GitNexus | AST graph | ✅ (local) | ✅ Native | Free | Deploy for agent intelligence |
| Sourcegraph | Full platform | ✅ | Via API | $49/user/mo (Enterprise) | Overkill for our size |
| GitHub Code Search | Trigram | ❌ (hosted) | ❌ | Free (public) | Already available, but no self-hosted |
| Livegrep | In-memory regex | ✅ | ❌ | Free | Less capable than Zoekt |
| OpenGrok | Text + ctags | ✅ | ❌ | Free | Heavier, Java-based |
| Hound | Trigram | ✅ | ❌ | Free | Simpler than Zoekt |
5. Implementation Priority
| Step | Priority | Effort |
|------|----------|--------|
| Install GitNexus locally for agent use | P0 | 1 hour |
| Add GitNexus MCP to Antigravity config | P0 | 15 min |
| Deploy Zoekt on Cloud Run | P1 | 1 day |
| Configure
code.cytognosis.org` DNS | P1 | 15 min |