v0.3.0b2 — Agent-friendly responses + hot-reload

Patch release — better multi-agent ergonomics

Focused on making the /context endpoint respond more usefully to programmatic agents (not just Continue), and letting operators refresh runtime state without restarting the process.

What's New

Agent-friendly /context response

The /context endpoint now returns an agent metadata field alongside the existing Continue-compatible fields. Backward compatible — existing integrations work unchanged.

New fields:
```json
{
"name": "Helix Genome Context",
"description": "...",
"content": "...",
"context_health": { ... },
"agent": {
"recommendation": "trust" | "verify" | "refresh" | "reread_raw",
"hint": "Context is well-grounded. Use directly.",
"citations": [
{ "gene_id": "a23ff24e...", "source": "...", "score": 108.71 },
...
],
"latency_ms": 1996.2,
"total_tokens_est": 3614,
"compression_ratio": 2.77,
"moe_mode": true
}
}
```

Pass verbose: true in the request body to include promoter tags (domains, entities) for each citation — useful when agents need to inspect why a gene was ranked.

Recommendation semantics

The recommendation field tells the agent what to do with the context based on delta-epsilon health:

Health status	Recommendation	Meaning
aligned	trust	Use the context directly
sparse	verify	Verify specific values before acting
stale	refresh	Expressed genes are outdated
denatured	reread_raw	Unreliable — read raw files instead

Hot-reload endpoints

Three admin endpoints for refreshing runtime state without killing the process:

• POST /admin/reload — full refresh (config + genome snapshot + ΣĒMA cache + clear stale per-query state)
• POST /admin/sema/rebuild — force rebuild the ΣĒMA vector cache
• POST /admin/checkpoint?mode=TRUNCATE — flush WAL to main DB (already existed, documented here)

What hot-reload refreshes:

• helix.toml config
• Genome WAL snapshot (sees external writes)
• ΣĒMA vector cache (rebuilt from current genome)
• last_query_scores cleared

What it does NOT refresh (these still need a process restart):

• Python code changes
• Ribosome backend swap (model stays loaded)

Use hot-reload when you want to tweak thresholds in helix.toml or pick up new genes from an external writer without dropping in-flight requests.

Replica schema resilience fix

_build_sema_cache now catches no such column: compression_tier errors from stale replicas and falls back to the legacy query. This was silently breaking the live server on replicated read paths where the replica hadn't been migrated to the current schema.

Benchmark validation (post-restart)

Needle-in-a-haystack benchmark against the 7,313-gene live genome after restarting on v0.3.0b2:

Metric	Pre-v0.3.0b2	v0.3.0b2
Context retrieval	8/10 (80%)	10/10 (100%)
Answer accuracy	7/10	8/10
Avg context latency	21-120s (ΣĒMA Mode B 7K JSON loads)	1.0s (numpy cache)

The 100x latency improvement comes from the v0.2.0b2 ΣĒMA vector cache fix, which was shipped in code but never active against the live server until this restart. The retrieval quality improvement comes from the v0.2.0b2 authority boosts combined with the fresh server picking up the new code.

All 179 tests passing.

🤖 Generated with Claude Code