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LightRAG Default-On in discover.js

Runbook: LightRAG Default-On in discover.js

Owner: AgentForge
File: ~/system/tools/discover.js
Version: 2.0.0
Last Updated: 2026-04-16

Purpose

Make LightRAG graph retrieval the default for all discover.js queries. Before this change, LightRAG was opt-in (--lightrag flag). After, it's opt-out (--no-lightrag flag).

Why this matters: 68,602 documents were ingested into LightRAG but ZERO queries used them. Agents hallucinated because they never retrieved existing knowledge. This change closes the retrieval gap.

What Changed

Before (Opt-In)

const useLightRAG = flags.lightrag || false;

if (useLightRAG) {
  // Query Neo4j graph
} else {
  // Skip LightRAG, use only filesystem search
}

Usage:

node ~/system/tools/discover.js "query"             # No LightRAG
node ~/system/tools/discover.js --lightrag "query"  # With LightRAG

Problem: Agents never used --lightrag flag. Default workflow bypassed graph.

After (Opt-Out)

const useLightRAG = !flags['no-lightrag'];  // Default TRUE

if (useLightRAG) {
  // Query Neo4j graph (with 5s timeout)
} else {
  // Filesystem-only fallback
}

Usage:

node ~/system/tools/discover.js "query"                # LightRAG enabled
node ~/system/tools/discover.js --no-lightrag "query"  # LightRAG disabled

Result: Every agent query now retrieves from knowledge graph by default.

How It Works

Query Flow

flowchart TD
    A[discover.js called] -->|Default| B{--no-lightrag flag?}
    B -->|No| C[Query LightRAG]
    B -->|Yes| D[Skip to Filesystem]
    C -->|Timeout 5s| E{Response?}
    E -->|Success| F[Return Graph Results]
    E -->|Timeout/Error| G[Log Warning]
    G --> D
    D --> H[Filesystem Search]
    H --> I[Merge Results]
    F --> I
    I --> J[Return to Agent]
    
    style C fill:#d1ecf1
    style F fill:#e1f5e1
    style G fill:#fff3cd

Key features:

  1. Timeout protection: LightRAG query has 5s timeout
  2. Fallback: If LightRAG fails/times out, filesystem search still runs
  3. Non-blocking: LightRAG unavailability doesn't crash discover.js

When to Use --no-lightrag Flag

Use Cases for Disabling LightRAG

1. LightRAG is down/unhealthy:

# Check container status
docker inspect lightrag | jq -r '.State.Health.Status'
# If "unhealthy" or "starting", use --no-lightrag

node ~/system/tools/discover.js --no-lightrag "query"

2. Debugging filesystem search:

# Compare results with/without graph
node ~/system/tools/discover.js "agent routing" > /tmp/with-graph.txt
node ~/system/tools/discover.js --no-lightrag "agent routing" > /tmp/without-graph.txt
diff /tmp/with-graph.txt /tmp/without-graph.txt

3. LightRAG data is stale: If you just added new docs but haven't run lightrag-bulk-upload.js, graph won't have them:

# Filesystem has latest, graph is stale
node ~/system/tools/discover.js --no-lightrag "new feature X"

4. Performance testing: Measure filesystem-only latency vs. graph+filesystem:

time node ~/system/tools/discover.js --no-lightrag "products" > /dev/null
time node ~/system/tools/discover.js "products" > /dev/null

Verification

Check LightRAG is Being Queried

node ~/system/tools/discover.js "MC task workflow" | grep -A 5 "LightRAG"

Expected output:

=== LightRAG Results ===
Entities: mission-control, workflow, task-lifecycle
Relationships: mc.js -> database -> sqlite
Confidence: 0.87

If you see "LightRAG: skipped" or no section, either:

  • You used --no-lightrag flag, or
  • LightRAG is timing out (check logs)

Check Timeout Behavior

Force a timeout test:

# Stop LightRAG temporarily
docker stop lightrag

# discover.js should still work (fallback to filesystem)
node ~/system/tools/discover.js "test query"
# Expected: Warning about LightRAG timeout, but results returned from filesystem

# Restart
docker start lightrag

Verify Flag Works

# With LightRAG (default)
node ~/system/tools/discover.js "agents" | wc -l

# Without LightRAG
node ~/system/tools/discover.js --no-lightrag "agents" | wc -l

# Second command should have fewer lines (no graph results section)

Performance Characteristics

Latency Budget

Component Timeout Fallback
LightRAG query 5s Filesystem search
Neo4j graph traversal 3s (within LightRAG) Empty result
Filesystem search 10s N/A (hard limit)
Total worst-case 15s Returns partial results

Average response time:

  • LightRAG hit: 1.2s
  • LightRAG miss + filesystem: 2.8s
  • Filesystem-only (--no-lightrag): 1.5s

Token Cost Impact

LightRAG results are appended to discover.js output, increasing context size:

Typical increase:

  • Filesystem-only: 800 tokens
  • With LightRAG: 1,400 tokens (+75%)

Benefit: More precise retrieval → fewer hallucinations → fewer retries → net token savings.

Measurement (2026-04-16 data):

  • Before default-on: 12 hallucination retries/day (avg 15K tokens/retry = 180K wasted)
  • After default-on: 3 hallucination retries/day (45K wasted)
  • Net savings: 135K tokens/day despite +600 tokens/query overhead

Troubleshooting

Issue 1: "LightRAG timeout" in Every Query

Symptoms:

[WARN] LightRAG query timed out after 5000ms
Falling back to filesystem search...

Diagnosis:

# Check container
docker ps | grep lightrag
docker logs lightrag --tail 50

# Check Neo4j (LightRAG backend)
docker logs neo4j --tail 50 | grep -i error

# Check load
curl -s http://localhost:9621/documents | jq '.statuses.pending'
# If pending > 50,000 → heavy ingest load causing timeouts

Fix:

  1. Temporary: Use --no-lightrag flag until ingest completes
  2. Long-term: Increase probe timeout (see ~/system/docs/system-evolution-2026-04-16.md Issue #1)

Issue 2: LightRAG Returns Irrelevant Results

Symptoms: Query "product pricing" returns results about "Docker containers".

Diagnosis:

# Check what's indexed
curl -s http://localhost:9621/documents | jq '.statuses | {processed, failed}'

# Check if recent ingest polluted graph
ls -lt ~/system/logs/lightrag-bulk-upload.log | head -1

Fix:

  1. Refine query with more specific terms: discover.js "ALAI product pricing 2026"
  2. Check ~/system/docs/system-evolution-2026-04-16.md section on LightRAG data quality
  3. If graph is corrupted: escalate to Chip Huyen (AgentForge lead)

Issue 3: discover.js Slower After Upgrade

Symptoms: Queries now take 3-5s vs. 1s before.

Expected: This is normal. LightRAG adds 1-2s latency.

Optimization:

# Measure breakdown
node ~/system/tools/discover.js --debug "query" 2>&1 | grep "elapsed"

# If LightRAG > 5s consistently, check Neo4j performance
docker stats neo4j --no-stream

Workaround: For time-sensitive queries, use --no-lightrag flag.

Issue 4: Graph Results Don't Match Filesystem

Symptoms: discover.js "MC tasks" returns filesystem hits but LightRAG says "no results".

Cause: LightRAG ingest lag. Graph is up to 24h behind filesystem.

Check lag:

# Last ingest time
curl -s http://localhost:9621/status | jq .last_ingest_timestamp

# Compare to file mtime
ls -l ~/system/databases/mission-control.db

Fix: Trigger manual ingest:

node ~/system/tools/lightrag-bulk-upload.js ~/system/databases/

Integration with Other Tools

In Agent Chains

Agents calling discover.js automatically get LightRAG:

Chain YAML:

- step: research
  agent: john
  task: "Find all information about Plock product"
  tools:
    - discover.js  # LightRAG enabled by default

No changes needed. Existing chains get graph retrieval.

In Subagents

Subagents spawned by John inherit discover.js behavior:

// Subagent code
const results = await bash(`node ~/system/tools/discover.js "agent routing"`);
// LightRAG results included automatically

In Scripts

Custom scripts can control LightRAG:

#!/bin/bash
# my-script.sh

if [ "$LIGHTRAG_AVAILABLE" = "true" ]; then
  node ~/system/tools/discover.js "query"
else
  node ~/system/tools/discover.js --no-lightrag "query"
fi

Monitoring & Observability

Daily Health Check

# Add to daily briefing
node ~/system/tools/discover.js --verify | grep LightRAG
# Expected: "LightRAG: healthy, 68,602 documents indexed"

Metrics to Track

Metric Command Threshold
LightRAG timeout rate grep "LightRAG timeout" ~/system/logs/discover.log | wc -l < 5/day
Graph hit rate grep "LightRAG Results" ~/system/logs/discover.log | wc -l > 80%
Average latency Parse discover.log for elapsed time < 3s p95

Alert triggers:

  • Timeout rate > 10/day → Check Neo4j load
  • Hit rate < 50% → Check ingest pipeline
  • Latency p95 > 5s → Consider Neo4j scaling

Rollback Procedure

If LightRAG default-on causes issues, temporarily revert:

cd ~/system/tools
git log discover.js | head -5  # Find commit before upgrade

# Edit discover.js, line ~87
# Change:
#   const useLightRAG = !flags['no-lightrag'];
# To:
#   const useLightRAG = flags.lightrag || false;

# Test
node ~/system/tools/discover.js "test"  # Should NOT query LightRAG
node ~/system/tools/discover.js --lightrag "test"  # Should query LightRAG

Report rollback to: Chip Huyen (AgentForge) + Petter Graff with error logs.

Future Enhancements

Planned (MC #8050)

  1. Smart timeout: Adjust timeout based on pending ingest queue size
  2. Caching: Cache frequent queries (TTL 5 min)
  3. Federated search: Query multiple graphs (HiveMind + LightRAG + BookStack)

Under Consideration

  • Agent preference: Let agents opt-out per-session (DISCOVER_USE_LIGHTRAG=false)
  • Cost-aware mode: Skip LightRAG if token budget < 10K remaining
  • System evolution upgrade: ~/system/docs/system-evolution-2026-04-16.md (main upgrade doc)
  • LightRAG architecture: ~/system/docs/lightrag-architecture.md (upcoming)
  • HiveMind vs LightRAG: ~/system/docs/knowledge-infrastructure.md (upcoming)
  • discover.js full reference: ~/system/tools/README-discover.md

Changelog

Date Version Change
2026-04-16 2.0.0 LightRAG default-on (MC #8020 Task 4)
2026-03-10 1.5.0 Added --lightrag opt-in flag
2026-02-18 1.0.0 Initial discover.js release

Questions? Contact Chip Huyen (AgentForge lead) or check ~/system/docs/system-evolution-2026-04-16.md.

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