@inflexa-ai/harness 0.28.1 → 0.30.0

package/dist/tools/workspace/workspace-search.js

@@ -29,25 +29,49 @@ function indexName(analysisId) {
     }
     return name;
 }
+/** Entry types that address a pattern spanning many files, never a single one. */
+const PATTERN_TYPES = new Set(["input-group", "input-dimension", "input-kind"]);
+/**
+ * The workspace path a hit addresses, or `undefined` for a pattern entry. Resolved here,
+ * once, across every index era — group/dimension/kind entries and previous-era entity
+ * entries (`entity` in metadata) are patterns; everything else is a file whose path is
+ * stamped in metadata or, on rows older than the stamp, is the id minus the resource
+ * segment. The consumer branches on presence, nothing else.
+ */
+export function fileTargetOf(id, metadata) {
+    const meta = metadata && typeof metadata === "object" ? metadata : {};
+    const type = typeof meta.type === "string" ? meta.type : undefined;
+    if (type !== undefined && PATTERN_TYPES.has(type))
+        return undefined;
+    if (type === "input" && meta.entity !== undefined)
+        return undefined;
+    if (typeof meta.path === "string")
+        return meta.path;
+    return id.replace(/^\/[^/]+\//, "");
+}
 export function createWorkspaceSearchTool(pool, embedding) {
     return defineTool({
         id: "workspace_search",
         description: "Semantic search over the analysis workspace. Returns ranked entries with descriptions " +
-            "and metadata; read a file separately to see its contents. Indexed entries are exactly " +
-            'five types, and `type` restricts results to one of them: "input-kind" (a KIND of input ' +
-            "data — a repeating set the data profiler named, carrying its count and a pathPattern " +
-            'matching its members), "input" (one entity the dataset is about — a subject, sample, or ' +
-            'other axis value — with the kinds of file it carries), "output" (files a step produced), ' +
-            '"summary" (a step\'s summary), "synthesis" (a run\'s literature-grounded synthesis). ' +
-            "For output/summary/synthesis the entry id IS the workspace path; for the two input types " +
-            "it is not, because a kind and an entity each span many files — search input-kind for a " +
-            "set's pathPattern, then list the tree for its members.",
+            "and metadata; read a file separately to see its contents. `type` restricts results to one " +
+            'entry type: "input-group" (a GROUP of input data the data profiler declared, carrying its ' +
+            'derived count, its display pattern, and its slots), "input-dimension" (something that VARIES ' +
+            "across the dataset — subject, timepoint, batch — with the observations evidencing it), " +
+            '"input" (one input file the profiler annotated individually, or, on a profile of the ' +
+            'previous era, one entity the dataset is about), "output" (files a step produced), ' +
+            '"summary" (a step\'s summary), "synthesis" (a run\'s literature-grounded synthesis), ' +
+            '"input-kind" (a repeating set, on a profile of the previous era). ' +
+            "A hit carrying `path` is a FILE — read that path to see its contents. A hit without " +
+            "`path` is a PATTERN spanning many files (a group, a dimension, an entity): use its " +
+            "metadata, e.g. search input-group for a group's display pattern, then list the tree for " +
+            "its members. Most input files carry no entry of their own — find them through their " +
+            "group and the listing tools.",
         inputSchema: z.object({
             query: z.string().min(1).describe("What to search for, in natural language"),
             type: z
-                .enum(["input-kind", "input", "output", "summary", "synthesis"])
+                .enum(["input-group", "input-dimension", "input", "input-kind", "output", "summary", "synthesis"])
                 .optional()
-                .describe('Restrict results to one entry type: "input-kind", "input", "output", "summary", or "synthesis"'),
+                .describe('Restrict results to one entry type: "input-group", "input-dimension", "input", "input-kind", "output", "summary", or "synthesis"'),
             limit: z.number().int().min(1).max(50).default(8).describe("Maximum number of results to return"),
         }),
         describeCall: ({ query, type }) => (type === undefined ? query : `${query} (${type})`),
@@ -77,11 +101,15 @@ export function createWorkspaceSearchTool(pool, embedding) {
             // exist. That is absence, not a failure: recover into ok([]).
             isUndefinedTable(e.cause) ? okAsync([]) : err(e)));
             return ok({
-                results: rows.map((r) => ({
-                    id: r.id,
-                    score: r.score,
-                    metadata: r.metadata,
-                })),
+                results: rows.map((r) => {
+                    const path = fileTargetOf(r.id, r.metadata);
+                    return {
+                        id: r.id,
+                        score: r.score,
+                        ...(path !== undefined ? { path } : {}),
+                        metadata: r.metadata,
+                    };
+                }),
             });
         },
     });

package/dist/workflows/sandbox-step.d.ts

@@ -106,6 +106,12 @@ export interface SandboxStepInput {
  * declare it explicitly.
  */
 export declare const DEFAULT_STEP_TIMEOUT_SECONDS = 3600;
+/**
+ * Deterministic `blocked_reason` for a loop that spent every iteration and
+ * persisted no output files (see the harness-sandbox-agents spec). Fixed prose,
+ * never model output — the summarizer does not run on this path.
+ */
+export declare const CAPPED_OUT_EMPTY_REASON = "The step hit its iteration cap with no output files persisted.";
 export type SandboxStepStatus = "complete" | "failed" | "canceled" | "blocked";
 /**
  * DBOS message topic the child uses to notify the parent that it is

package/dist/workflows/sandbox-step.js

@@ -46,6 +46,12 @@ import { createBlockerHolder } from "../tools/sandbox/report-blocker.js";
  * declare it explicitly.
  */
 export const DEFAULT_STEP_TIMEOUT_SECONDS = 3600;
+/**
+ * Deterministic `blocked_reason` for a loop that spent every iteration and
+ * persisted no output files (see the harness-sandbox-agents spec). Fixed prose,
+ * never model output — the summarizer does not run on this path.
+ */
+export const CAPPED_OUT_EMPTY_REASON = "The step hit its iteration cap with no output files persisted.";
 /**
  * DBOS message topic the child uses to notify the parent that it is
  * about to self-cancel because of a 402 budget-exceeded error. The
@@ -427,20 +433,36 @@ export async function runSandboxStepBody(input, deps) {
             usage: stepUsage,
         });
     }
+    // Manifest walk, hoisted above the blocked branch so the capped-out
+    // predicate can read it. The call is inline (not `DBOS.runStep`-wrapped),
+    // so the hoist shifts no function id (see the harness-durable-runtime spec).
+    const manifest = await safeRunValue(logger, () => walkStepArtifacts({
+        writePrefix,
+        stepId: input.stepId,
+        runId: input.runId,
+    }), "post-step.walk", []);
     // Blocker (see the harness-sandbox-agents spec): the agent declared it cannot fulfil the step. A
     // blocked step has no deliverables — skip the artifact post-step pipeline,
     // mark `blocked` (carrying the reason), emit the blocked part, and return a
     // terminal-failure status so the parent's fail-fast cascade fires.
+    //
+    // The capped-out empty case routes into the same branch: a loop that spent
+    // every iteration and persisted nothing has no deliverables, and a green
+    // status would attest an empty step. A blocker outcome keeps its own
+    // reason. A capped-out step WITH artifacts stays on the completed path,
+    // because partial output is real output.
     const blockerOutcome = blockerHolder.outcome;
-    if (blockerOutcome) {
+    const cappedOutEmpty = hitMaxSteps && manifest.length === 0;
+    if (blockerOutcome || cappedOutEmpty) {
+        const blockedReason = blockerOutcome?.reason ?? CAPPED_OUT_EMPTY_REASON;
         await tryTeardown(logger, deps, sandbox);
         const durationMs = (await DBOS.now()) - startedAt;
         await DBOS.runStep(async () => {
             unwrapOrThrow(await updateStepExecution(deps.pool, input.runId, input.stepId, {
                 status: "blocked",
                 durationMs,
-                error: blockerOutcome.reason,
-                blockedReason: blockerOutcome.reason,
+                error: blockedReason,
+                blockedReason,
                 attempts: 1,
                 lastErrorClass: "blocked",
                 finishReason,
@@ -453,21 +475,21 @@ export async function runSandboxStepBody(input, deps) {
             runId: input.runId,
             stepId: input.stepId,
             agentId: input.agentId,
-            reason: blockerOutcome.reason,
+            reason: blockedReason,
         });
         await emitActivity("failed", "Step blocked");
         return {
             status: "blocked",
             durationMs,
             finishReason,
-            error: blockerOutcome.reason,
+            error: blockedReason,
             ...(stepUsage ? { usage: stepUsage } : {}),
         };
     }
-    // (4-8) post-step — the body is the explicit composition: walk the artifact
-    // tree once, then thread each stage's typed output into the next. Helpers
-    // run inline (not `DBOS.runStep`-wrapped), so a replay re-executes this
-    // section. Each helper is best-effort (`safeRun*` logs + degrades) so a
+    // (4-8) post-step — the body is the explicit composition: the manifest from
+    // the single walk above threads each stage's typed output into the next.
+    // Helpers run inline (not `DBOS.runStep`-wrapped), so a replay re-executes
+    // this section. Each helper is best-effort (`safeRun*` logs + degrades) so a
     // single failure never fails the step.
     const postCtx = {
         input,
@@ -478,11 +500,6 @@ export async function runSandboxStepBody(input, deps) {
         lineageCollector,
     };
     await emitActivity("generating-metadata", "Describing output files");
-    const manifest = await safeRunValue(logger, () => walkStepArtifacts({
-        writePrefix,
-        stepId: input.stepId,
-        runId: input.runId,
-    }), "post-step.walk", []);
     // The two post-step LLM producers are wrapped in `DBOS.runStep` so their
     // outputs are checkpointed (see the harness-durable-runtime spec): the conditional terminal emits they
     // gate (`data-step-summary`, file-tree) stay replay-stable and the billed

package/dist/workflows/target-assessment/assemblers/safety.d.ts

@@ -319,7 +319,7 @@ export declare function aggregateClassPrecedent(phase2: Phase2Bundle, fanout: Fa
 } | null;
 export declare function buildOrganRollup(faers: ReturnType<typeof aggregateFaersAcrossModulators>, trialAes: ReturnType<typeof aggregateTrialAes>, offTarget: OffTargetPanelRows | null, classP: ReturnType<typeof aggregateClassPrecedent>, regulatoryActions?: RegulatoryActionRow[] | null): {
     organ: "hematologic" | "metabolic" | "immune" | "hepatic" | "musculoskeletal" | "cns" | "renal" | "reproductive" | "respiratory" | "cardiac" | "vascular" | "pns" | "gi" | "pancreas" | "endocrine_thyroid" | "dermatologic" | "ocular" | "oncology";
-    risk_level: "high" | "medium" | "low";
+    risk_level: "low" | "medium" | "high";
     signal_type_count: number;
     signals: {
         chembl_polypharm_count: number;

package/dist/workflows/target-assessment/phase4-assemble.d.ts

@@ -124,6 +124,27 @@ export declare const Phase4OutputSchema: z.ZodObject<{
             coverage: z.ZodLiteral<"not_loaded">;
             reason: z.ZodOptional<z.ZodString>;
         }, z.core.$strip>], "coverage">;
+        entity: z.ZodObject<{
+            canonicalId: z.ZodString;
+            symbol: z.ZodString;
+            displayName: z.ZodString;
+            entityType: z.ZodEnum<{
+                gene: "gene";
+                rna: "rna";
+                protein: "protein";
+                complex: "complex";
+            }>;
+            ontology: z.ZodString;
+            identifiers: z.ZodObject<{
+                hgnc: z.ZodOptional<z.ZodString>;
+                ensembl: z.ZodOptional<z.ZodString>;
+                uniprot: z.ZodOptional<z.ZodString>;
+                chembl: z.ZodOptional<z.ZodString>;
+                ncbiGene: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>;
+            synonyms: z.ZodDefault<z.ZodArray<z.ZodString>>;
+            proteinFamily: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>;
         off_target_panel: z.ZodDiscriminatedUnion<[z.ZodObject<{
             coverage: z.ZodLiteral<"available">;
             data: z.ZodObject<{
@@ -347,27 +368,6 @@ export declare const Phase4OutputSchema: z.ZodObject<{
             inferred_therapeutic_area: z.ZodNullable<z.ZodString>;
             no_liabilities_disclosure: z.ZodOptional<z.ZodString>;
         }, z.core.$strict>;
-        entity: z.ZodObject<{
-            canonicalId: z.ZodString;
-            symbol: z.ZodString;
-            displayName: z.ZodString;
-            entityType: z.ZodEnum<{
-                gene: "gene";
-                rna: "rna";
-                protein: "protein";
-                complex: "complex";
-            }>;
-            ontology: z.ZodString;
-            identifiers: z.ZodObject<{
-                hgnc: z.ZodOptional<z.ZodString>;
-                ensembl: z.ZodOptional<z.ZodString>;
-                uniprot: z.ZodOptional<z.ZodString>;
-                chembl: z.ZodOptional<z.ZodString>;
-                ncbiGene: z.ZodOptional<z.ZodString>;
-            }, z.core.$strip>;
-            synonyms: z.ZodDefault<z.ZodArray<z.ZodString>>;
-            proteinFamily: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>;
         indications: z.ZodDiscriminatedUnion<[z.ZodObject<{
             coverage: z.ZodLiteral<"available">;
             data: z.ZodObject<{
@@ -442,9 +442,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                         start_date: z.ZodNullable<z.ZodString>;
                         completion_date: z.ZodNullable<z.ZodString>;
                         match_confidence: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                             off_target: "off_target";
                         }>;
                         attribution: z.ZodObject<{
@@ -499,9 +499,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                         start_date: z.ZodNullable<z.ZodString>;
                         completion_date: z.ZodNullable<z.ZodString>;
                         match_confidence: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                             off_target: "off_target";
                         }>;
                         attribution: z.ZodObject<{
@@ -855,9 +855,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                             oncology: "oncology";
                         }>;
                         risk_level: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                         }>;
                         signal_type_count: z.ZodNumber;
                         signals: z.ZodObject<{
@@ -1409,9 +1409,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                         trail: z.ZodString;
                         mechanism_hypothesis: z.ZodOptional<z.ZodNullable<z.ZodString>>;
                         severity: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                         }>;
                         support: z.ZodDiscriminatedUnion<[z.ZodObject<{
                             state: z.ZodLiteral<"scored">;
@@ -2462,11 +2462,11 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                                 dog: "dog";
                             }>;
                             rank: z.ZodEnum<{
+                                low: "low";
+                                medium: "medium";
+                                high: "high";
                                 no_data: "no_data";
                                 absent: "absent";
-                                high: "high";
-                                medium: "medium";
-                                low: "low";
                                 not_loaded: "not_loaded";
                             }>;
                         }, z.core.$strip>>;
@@ -2800,9 +2800,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                         start_date: z.ZodOptional<z.ZodString>;
                         completion_date: z.ZodOptional<z.ZodString>;
                         match_confidence: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                         }>;
                         relevance_basis: z.ZodDiscriminatedUnion<[z.ZodObject<{
                             kind: z.ZodLiteral<"drug_in_class_match">;
@@ -2869,9 +2869,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                         start_date: z.ZodOptional<z.ZodString>;
                         completion_date: z.ZodOptional<z.ZodString>;
                         match_confidence: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                         }>;
                         relevance_basis: z.ZodDiscriminatedUnion<[z.ZodObject<{
                             kind: z.ZodLiteral<"drug_in_class_match">;
@@ -3122,9 +3122,9 @@ export declare const Phase4OutputSchema: z.ZodObject<{
                     insufficient_evidence: "insufficient_evidence";
                 }>;
                 confidence: z.ZodEnum<{
-                    high: "high";
-                    medium: "medium";
                     low: "low";
+                    medium: "medium";
+                    high: "high";
                 }>;
                 rationale: z.ZodString;
                 key_strengths: z.ZodDefault<z.ZodArray<z.ZodString>>;

package/dist/workflows/target-assessment/schemas.d.ts

@@ -17,8 +17,8 @@ export declare const ResolvedTargetSchema: z.ZodObject<{
     goal: z.ZodNullable<z.ZodString>;
     canonicalId: z.ZodString;
     canonicalOntology: z.ZodEnum<{
-        ensembl: "ensembl";
         hgnc: "hgnc";
+        ensembl: "ensembl";
     }>;
     geneSymbol: z.ZodString;
     approvedName: z.ZodString;
@@ -249,10 +249,10 @@ export declare const ExpressionMultiSpeciesBundleSchema: z.ZodObject<{
         tissues: z.ZodArray<z.ZodObject<{
             tissue: z.ZodString;
             rank: z.ZodEnum<{
-                absent: "absent";
-                high: "high";
-                medium: "medium";
                 low: "low";
+                medium: "medium";
+                high: "high";
+                absent: "absent";
             }>;
             expressionScore: z.ZodNullable<z.ZodNumber>;
         }, z.core.$strip>>;
@@ -400,9 +400,9 @@ export declare const TherapeuticProgramsBundleSchema: z.ZodObject<{
             }, z.core.$strip>>;
         }, z.core.$strip>>;
         confidence: z.ZodEnum<{
-            high: "high";
-            medium: "medium";
             low: "low";
+            medium: "medium";
+            high: "high";
         }>;
     }, z.core.$strip>>;
 }, z.core.$strip>;
@@ -432,8 +432,8 @@ export declare const Phase1BundleSchema: z.ZodObject<{
         goal: z.ZodNullable<z.ZodString>;
         canonicalId: z.ZodString;
         canonicalOntology: z.ZodEnum<{
-            ensembl: "ensembl";
             hgnc: "hgnc";
+            ensembl: "ensembl";
         }>;
         geneSymbol: z.ZodString;
         approvedName: z.ZodString;
@@ -688,10 +688,10 @@ export declare const Phase1BundleSchema: z.ZodObject<{
                     tissues: z.ZodArray<z.ZodObject<{
                         tissue: z.ZodString;
                         rank: z.ZodEnum<{
-                            absent: "absent";
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
+                            absent: "absent";
                         }>;
                         expressionScore: z.ZodNullable<z.ZodNumber>;
                     }, z.core.$strip>>;
@@ -954,9 +954,9 @@ export declare const Phase1BundleSchema: z.ZodObject<{
                         }, z.core.$strip>>;
                     }, z.core.$strip>>;
                     confidence: z.ZodEnum<{
-                        high: "high";
-                        medium: "medium";
                         low: "low";
+                        medium: "medium";
+                        high: "high";
                     }>;
                 }, z.core.$strip>>;
             }, z.core.$strip>;

package/dist/workflows/target-assessment/steps/phase2-aggregate.d.ts

@@ -18,8 +18,8 @@ export declare const Phase2BundleSchema: z.ZodObject<{
             goal: z.ZodNullable<z.ZodString>;
             canonicalId: z.ZodString;
             canonicalOntology: z.ZodEnum<{
-                ensembl: "ensembl";
                 hgnc: "hgnc";
+                ensembl: "ensembl";
             }>;
             geneSymbol: z.ZodString;
             approvedName: z.ZodString;
@@ -274,10 +274,10 @@ export declare const Phase2BundleSchema: z.ZodObject<{
                         tissues: z.ZodArray<z.ZodObject<{
                             tissue: z.ZodString;
                             rank: z.ZodEnum<{
-                                absent: "absent";
-                                high: "high";
-                                medium: "medium";
                                 low: "low";
+                                medium: "medium";
+                                high: "high";
+                                absent: "absent";
                             }>;
                             expressionScore: z.ZodNullable<z.ZodNumber>;
                         }, z.core.$strip>>;
@@ -540,9 +540,9 @@ export declare const Phase2BundleSchema: z.ZodObject<{
                             }, z.core.$strip>>;
                         }, z.core.$strip>>;
                         confidence: z.ZodEnum<{
-                            high: "high";
-                            medium: "medium";
                             low: "low";
+                            medium: "medium";
+                            high: "high";
                         }>;
                     }, z.core.$strip>>;
                 }, z.core.$strip>;

package/dist/workflows/target-assessment/steps/phase3-aggregate.d.ts

@@ -11,8 +11,8 @@ export declare const Phase3BundleSchema: z.ZodObject<{
                 goal: z.ZodNullable<z.ZodString>;
                 canonicalId: z.ZodString;
                 canonicalOntology: z.ZodEnum<{
-                    ensembl: "ensembl";
                     hgnc: "hgnc";
+                    ensembl: "ensembl";
                 }>;
                 geneSymbol: z.ZodString;
                 approvedName: z.ZodString;
@@ -267,10 +267,10 @@ export declare const Phase3BundleSchema: z.ZodObject<{
                             tissues: z.ZodArray<z.ZodObject<{
                                 tissue: z.ZodString;
                                 rank: z.ZodEnum<{
-                                    absent: "absent";
-                                    high: "high";
-                                    medium: "medium";
                                     low: "low";
+                                    medium: "medium";
+                                    high: "high";
+                                    absent: "absent";
                                 }>;
                                 expressionScore: z.ZodNullable<z.ZodNumber>;
                             }, z.core.$strip>>;
@@ -533,9 +533,9 @@ export declare const Phase3BundleSchema: z.ZodObject<{
                                 }, z.core.$strip>>;
                             }, z.core.$strip>>;
                             confidence: z.ZodEnum<{
-                                high: "high";
-                                medium: "medium";
                                 low: "low";
+                                medium: "medium";
+                                high: "high";
                             }>;
                         }, z.core.$strip>>;
                     }, z.core.$strip>;

package/dist/workflows/target-assessment/synthesis/index.d.ts

@@ -24,9 +24,9 @@ export declare const LiabilityBulletsOutputSchema: z.ZodObject<{
     bullets: z.ZodArray<z.ZodObject<{
         organ_or_axis: z.ZodString;
         severity: z.ZodEnum<{
-            high: "high";
-            medium: "medium";
             low: "low";
+            medium: "medium";
+            high: "high";
         }>;
         text: z.ZodString;
         evidence_pointer: z.ZodString;
@@ -66,9 +66,9 @@ export declare const SafetyFlagsTrailOutputSchema: z.ZodObject<{
             oncology: "oncology";
         }>;
         severity: z.ZodEnum<{
-            high: "high";
-            medium: "medium";
             low: "low";
+            medium: "medium";
+            high: "high";
         }>;
         trail: z.ZodString;
         mechanism_hypothesis: z.ZodNullable<z.ZodString>;
@@ -109,9 +109,9 @@ export declare const DossierRecommendationOutputSchema: z.ZodObject<{
         insufficient_evidence: "insufficient_evidence";
     }>;
     confidence: z.ZodEnum<{
-        high: "high";
-        medium: "medium";
         low: "low";
+        medium: "medium";
+        high: "high";
     }>;
     rationale: z.ZodString;
     key_strengths: z.ZodArray<z.ZodString>;
@@ -146,9 +146,9 @@ export declare const LiabilityBulletsStepOutputSchema: z.ZodDiscriminatedUnion<[
         bullets: z.ZodArray<z.ZodObject<{
             organ_or_axis: z.ZodString;
             severity: z.ZodEnum<{
-                high: "high";
-                medium: "medium";
                 low: "low";
+                medium: "medium";
+                high: "high";
             }>;
             text: z.ZodString;
             evidence_pointer: z.ZodString;
@@ -269,9 +269,9 @@ export declare const SafetyFlagsTrailStepOutputSchema: z.ZodDiscriminatedUnion<[
                 oncology: "oncology";
             }>;
             severity: z.ZodEnum<{
-                high: "high";
-                medium: "medium";
                 low: "low";
+                medium: "medium";
+                high: "high";
             }>;
             trail: z.ZodString;
             mechanism_hypothesis: z.ZodNullable<z.ZodString>;
@@ -461,9 +461,9 @@ export declare const DossierRecommendationStepOutputSchema: z.ZodDiscriminatedUn
             insufficient_evidence: "insufficient_evidence";
         }>;
         confidence: z.ZodEnum<{
-            high: "high";
-            medium: "medium";
             low: "low";
+            medium: "medium";
+            high: "high";
         }>;
         rationale: z.ZodString;
         key_strengths: z.ZodArray<z.ZodString>;

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@inflexa-ai/harness",
-    "version": "0.28.1",
+    "version": "0.30.0",
     "description": "Host-agnostic bioinformatics agent harness — hand-rolled agent loop, DBOS-durable workflows, sandboxed compute.",
     "license": "Apache-2.0",
     "type": "module",
@@ -33,15 +33,17 @@
         "directory": "harness"
     },
     "scripts": {
-        "build": "tsc -p tsconfig.json",
+        "build": "tsc -p tsconfig.json && node scripts/copy-assets.mjs",
         "design:fixture": "bun scripts/render-fixture.ts",
         "format": "prettier --write src/",
         "format:file": "prettier --write",
         "lint": "eslint .",
-        "prepare": "tsc -p tsconfig.json",
+        "lint:python": "ruff check src/input-scan/decoder && ruff format --check src/input-scan/decoder",
+        "prepare": "tsc -p tsconfig.json && node scripts/copy-assets.mjs",
         "prepublishOnly": "bun run build && bun run smoke",
         "smoke": "node scripts/smoke.mjs",
         "test:full": "bash scripts/test-full.sh",
+        "test:python": "python3 -m pytest src/input-scan/decoder -q",
         "typecheck": "tsc --noEmit"
     },
     "dependencies": {

package/dist/input-scan/coverage.d.ts

@@ -1,22 +0,0 @@
-/**
- * Profile coverage — how much of the scanned tree the agent's kinds actually describe.
- *
- * Measured against the SUBMITTED kinds, never against the scan's own shapes. Computed
- * from the shapes it would report only whether the scan grouped its own observations,
- * which is always yes; measured against the kinds it is a real check, and it is the
- * check that was missing when a profile covering 49 of 3513 files read as complete and
- * fresh.
- *
- * Deterministic by construction: matching declared patterns against a known file set
- * requires no judgement, and a coverage figure a model self-reported would not be a
- * check at all.
- */
-export interface ProfileCoverage {
-    /** Files matching at least one declared kind pattern. */
-    readonly matched: number;
-    readonly unmatched: number;
-    readonly total: number;
-    readonly unmatchedSample: string[];
-}
-/** Coverage of a scanned file set by a set of declared kind patterns. */
-export declare function computeCoverage(paths: readonly string[], patterns: readonly string[]): ProfileCoverage;