Cymatix Context
Hosting Wiki Discord GitHub Issues Contribute
Pages

Cymatix Context

Start

Concepts

Reference

Project

Agent Contract

  • Every /context and /context/packet response carries exactly one of two top-level blocks: know (the retrieved bytes are grounded — you may answer from them) or miss (retrieval did not find it — do not answer from the knowledge store, legacy: genome, which is why the wire field below is spelled do_not_answer_from_genome).
  • There is no third "maybe" branch. The discriminator collapses every retrieval outcome onto one of the two blocks, and a response with both keys set — or neither — is a server bug, not a fall-through case for you to handle.
  • The contract exists so a downstream agent can calibrate trust without guessing. Branch on the structured block; do not parse prose out of the assembled window.
  • The contract shape is stable and load-bearing. The confidence scalar is not — see The confidence honesty block below. Rely on found and reason.
  • Honoring the contract is the agent's job, and a capable model will not do it by accident. The prompt fragment that makes it stick ships in the package: cymatix_context.agent_prompt.full_fragment().

The two blocks

know — you may answer

{
  "found": true,
  "confidence": 0.83,
  "top_score": 0.92,
  "score_gap": 0.41,
  "lexical_dense_agree": true,
  "gene_id_match": "config.py",
  "coordinate_confidence": 0.78,
  "soft_stale": false
}
Field Meaning
found Always true on this branch — the discriminator's verdict
confidence [0, 1] from a 5-feature logistic. Provisional — see below
top_score Rank-1 fused retrieval score
score_gap top1 − top2, a raw subtraction (the miss block's ratio is the division)
lexical_dense_agree true when the lexical and dense top-3 clusters share a document. Structurally false on the neural-free default path
gene_id_match Beacon: a query token that matches a top-1 filename or path token exactly and case-insensitively. null when there is no match
coordinate_confidence Folder-grain and file-grain agreement between query and source
soft_stale Stage 7. true when top-1 is fresh enough to act on but lower-ranked supporting documents are stale — answer, and plan a refresh
  • The beacon is deliberately strict: filename match beats path match, a path token must be at least four characters and must not be src / lib / app / bin / var / tmp / out, and there is no prefix, substring, edit-distance or synonym matching. The asymmetry is intentional — a wrong beacon makes a frontier model lock in a wrong answer, while a missing beacon only lowers confidence.

miss — do not answer from the store

{
  "miss": true,
  "reason": "stale",
  "top_score": 0.83,
  "ratio": 1.42,
  "escalate_to": [],
  "refresh_targets": ["F:/Projects/cymatix-context/cymatix_context/config.py"],
  "do_not_answer_from_genome": true
}
  • do_not_answer_from_genome is always true and is the load-bearing bit. An agent that ignores it and answers from its training prior is the exact failure the contract exists to prevent.
  • escalate_to and refresh_targets are mutually exclusive by class, and a Pydantic model validator raises on a construction that violates it. Escalate-class reasons must carry at least one escalation tool and an empty refresh list; refresh-class reasons the reverse.

Reason vocabulary

The full tuple, in wire order (clients that index into it depend on the order):

reason Class Fires when What the agent does
abstain escalate The store is healthy; the query just does not touch any document The web or an external RAG tier may know. Reading raw files will not help
denatured escalate The store's shape is bad — corrupt or empty Trust no answer from the store right now. Ask a human or search locally
sparse escalate The top hit fell below the confidence floor Retrieval saw something but does not trust its own match. Escalate or reframe
no_promoter_match escalate Zero candidate documents came back at all Tag vocabulary mismatch between query and corpus. See the [synonyms] note on Troubleshooting
stale refresh Top-1's source mtime is newer than its last verification Re-read the paths in refresh_targets, then retry the same query
cold refresh A sparse fall-through, but a cold-tier peek surfaced hits Same loop — the answer is probably there, just demoted
superseded refresh Top-1 has a successor row Re-read the successor source and retry
  • Escalate means the answer is not here; refresh means the answer is here but out of date. The two branches are distinct and must not be conflated — that distinction is exactly what the shipped refresh fragment codifies.
  • escalate_to is drawn from ("grep", "rag", "web", "ask_human") and is ordered by expected information yield for the query's shape. Pick the first tool in the list. The ordering rules, first match wins:
# Query shape escalate_to
1 Code-shaped (dotted identifier, a def/class/import/function/fn/let/var/const keyword, or a filename extension token) ["grep", "rag"]
2 Entity-shaped with no_promoter_match and no code shape ["rag", "web"]
3 denatured store ["grep", "ask_human"]
4 abstain on a query of three tokens or fewer ["ask_human", "rag"]
5 Everything else ["rag"]

The confidence honesty block

  • At shipped 0.9.x defaults the know block effectively never fires. The measured maximum confidence is ≈ 0.28 against a shipped [know] emit_floor of 0.45, so the discriminator falls through to miss(reason="sparse") instead of emitting a KnowBlock.
  • The mechanism is structural, not a tuning miss: lexical_dense_agree is one of the five logistic features, and it can only be true when a dense cluster exists. On the neural-free default retrieval path there is no dense cluster, so that feature is dead by construction and its coefficient never contributes.
  • The 2026-08-19 know/abstain sanity replay measured it directly on the 141-needle 100k carve: 0 of 141 know emissions at shipped defaults versus 23 of 141 with the pre-flip encoders re-enabled. The empty-window class did not grow (2/141 in both arms) and the abstain difference (5/141 vs 2/141) was not significant — the set rotates with the pool.
  • This fails in the safe direction: 0% false-KNOW. The system under-claims rather than over-claims. It is still a defect, tracked as #287 (with #239) in the 0.9.x backlog, and disclosed in the 0.9.0 release notes rather than left for a user to discover.
  • What to do about it today: branch on found (presence of the know key) and on miss.reason. Do not gate behavior on confidence > X. Treat the scalar as provisional until the recalibration lands.
  • The agent block on every response carries ann_threshold_mode and abstain_mode, so you can see which calibration set produced a response without a second /health round trip.

The prompt fragment

  • Without the fragment in the system prompt, a capable model papers over do_not_answer_from_genome: true and answers from its training prior anyway. The fragment's highest-leverage sentence is the one telling the model that doing so is scored as a hard failure.
  • Two fragments ship, and they concatenate cleanly — nothing in the Stage-6 text contradicts the Stage-7 addendum:
from cymatix_context.agent_prompt import full_fragment

SYSTEM_PROMPT = full_fragment() + "\n\nYou are a coding assistant ..."
Export Teaches
CYMATIX_NO_MATCH_FRAGMENT The know/miss split, the four Stage-6 reasons, and the escalate-tool discipline
CYMATIX_REFRESH_FRAGMENT The Stage-7 addendum: refresh-versus-escalate, and the re-read-then-retry loop
full_fragment() Both, in order — the one call to make
  • The same text is published as prose in docs/agent-sdk-fragment.md if you would rather paste it than import it.
  • Assembly-time forgery is closed separately. [budget] neutralize_control_tags (default on since 2026-08-19) escapes a literal <cymatix: found in retrieved content so an ingested document cannot forge the genuine control tags this fragment trains the agent to trust. See Configuration.

Freshness: how a hit becomes a downgrade

  • Three freshness signals are computed per retrieval, replacing the single pre-Stage-7 mean: freshness_min (minimum decay across candidates), freshness_top1 (decay of the score leader), and freshness_weighted (the score-weighted sum, also aliased to the back-compat freshness field).
  • A retrieval with documents expressed but freshness_top1 < 0.4 or freshness_weighted < 0.5 is classified stale — regardless of how many fresh padding documents accompany the stale needle.
  • freshness_min also enters the confidence logistic as its fifth feature, and is treated as neutral when there are no candidates.
  • Soft-stale is not a miss. When the discriminator emits know but freshness_min < 0.5, know.soft_stale = true and the response's agent.recommendation becomes "refresh". You may answer from the store and should schedule a refresh of the lower-ranked supporting documents.
  • The refresh loop the contract expects:
1. Receive `miss` with recommendation="refresh"  (or `know` with soft_stale=true)
2. For each entry in refresh_targets: re-read the file, or fetch the URL
3. Re-POST /ingest the refreshed content
4. Re-call /context with the same query
  • Each refresh_targets entry is an absolute file path or a fully-qualified URL. MissBlock.to_refresh_targets() widens the flat list into RefreshTarget rows (target_kind, source_id, reason, priority) for callers that want the richer shape. POST /context/refresh-plan returns just that plan when you already hold the content and only need to know what to re-read.
  • Targeted per-document server-side re-consolidation is deliberately not implemented — POST /consolidate is session-scoped and ignores a request body by design. The supported per-document path is the four-step loop above.

The inline tag is legacy, the envelope is canonical

  • An empty window may carry a self-closing marker inside the assembled bytes:
<cymatix:no_match reason="abstain" do_not_answer="true"/>
  • It only ever carries the four Stage-6 reasons (abstain, denatured, sparse, no_promoter_match), and an unknown reason falls back to the abstain form. The Stage-7 freshness reasons (stale, cold, superseded) are never emitted as inline tags, because their semantics are the opposite: non-empty content that is shown but flagged, rather than an empty do-not-answer window.
  • The tag is a compatibility surface for regex-based clients written before Stage 6. New clients branch on the structured know / miss fields. The design decision is recorded in ADR 2026-05-14.

Packet semantics

POST /context/packet is the agent-safe surface: model-free end to end, and it returns what to re-read rather than a bundle to trust. It lifts know / miss to the top of the response and adds:

Field What it is
verified Evidence rows whose sources still check out against disk
stale_risk Evidence rows that are shown but flagged — the data is there, its verification is not current
contradictions Rows the packet builder found in conflict with each other
refresh_targets RefreshTarget rows: what to re-read, in priority order
coordinate_confidence Folder- and file-grain agreement between query and delivered sources
file_coverage Fraction of the query's implied file set that the packet actually covers
notes Builder-emitted caveats about this particular packet
  • Request knobs: query (required), task_type (default "explain"), max_genes (the wire spelling of the per-turn document cap; default 8, clamped to [1, 32]), clean, read_only, include_raw (full document bodies instead of the 280-character thumbnail) and max_item_chars.
  • Branch on miss versus know before you read stale_risk or verified. The packet's evidence lists are meaningful only once you know which branch you are on.
  • The full request and response shapes, with a worked packet example: HTTP API.

Caller class changes the render, not the contract

  • caller_model_class ("generic" default, "small_moe", "frontier") selects a render branch — ordering, assembly cap, decoder mode, whether legibility headers and the answer slate are emitted. It does not change retrieval and it does not change the know/miss contract.
  • frontier gets rank-1-first ordering and a widened assembly cap; small_moe gets a JSON answer slate and suppressed headers; generic is regression-locked byte-identical to pre-Stage-5 output. The full matrix is on HTTP API.

Wire field names are legacy. gene_id_match, do_not_answer_from_genome, and the refresh_targets path strings above are reproduced verbatim — the JSON contract still speaks the biology lexicon even though the prose and the config surface use software terms. Renaming them is a tracked Tier-3 change, deliberately not taken in 0.9.1 because it breaks every existing consumer. See Lexicon.

Go deeper