@inflexa-ai/harness 0.28.1 → 0.30.0

package/dist/contracts/target-dossier.d.ts

@@ -611,9 +611,9 @@ export declare const ClinicalTrialRowSchema: 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<{
@@ -821,9 +821,9 @@ export declare const ClinicalDevelopmentSchema: 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<{
@@ -878,9 +878,9 @@ export declare const ClinicalDevelopmentSchema: 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<{
@@ -1231,9 +1231,9 @@ export declare const OrganRiskRowSchema: 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<{
@@ -1759,9 +1759,9 @@ export declare const SafetyFlagSchema: 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">;
@@ -2008,9 +2008,9 @@ export declare const SafetyProfileSchema: 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<{
@@ -2562,9 +2562,9 @@ export declare const SafetyProfileSchema: 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">;
@@ -4112,11 +4112,11 @@ export declare const ExpressionHeatmapCellSchema: 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.$strip>;
@@ -4131,11 +4131,11 @@ export declare const ExpressionHeatmapSchema: z.ZodObject<{
             dog: "dog";
         }>;
         rank: z.ZodEnum<{
+            low: "low";
+            medium: "medium";
+            high: "high";
             no_data: "no_data";
             absent: "absent";
-            high: "high";
-            medium: "medium";
-            low: "low";
             not_loaded: "not_loaded";
         }>;
     }, z.core.$strip>>;
@@ -4267,11 +4267,11 @@ export declare const PreclinicalProfileSchema: 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>>;
@@ -4631,9 +4631,9 @@ export declare const DiscoveryTrialRowSchema: 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">;
@@ -4703,9 +4703,9 @@ export declare const DiscoveryTrialsSchema: z.ZodDiscriminatedUnion<[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">;
@@ -4772,9 +4772,9 @@ export declare const DiscoveryTrialsSchema: z.ZodDiscriminatedUnion<[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">;
@@ -4861,9 +4861,9 @@ export declare const ExecutiveRecommendationDataSchema: 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>>;
@@ -4899,9 +4899,9 @@ export declare const ExecutiveRecommendationSchema: z.ZodDiscriminatedUnion<[z.Z
             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>>;
@@ -5713,11 +5713,11 @@ export declare const ReferenceBiologyShape: 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>>;
@@ -6231,9 +6231,9 @@ export declare const DossierSchema: 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<{
@@ -6288,9 +6288,9 @@ export declare const DossierSchema: 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<{
@@ -6644,9 +6644,9 @@ export declare const DossierSchema: 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<{
@@ -7198,9 +7198,9 @@ export declare const DossierSchema: 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">;
@@ -8417,11 +8417,11 @@ export declare const DossierSchema: 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.$strip>>;
@@ -8755,9 +8755,9 @@ export declare const DossierSchema: z.ZodObject<{
                     start_date: z.ZodOptional<z.ZodString>;
                     completion_date: z.ZodOptional<z.ZodString>;
                     match_confidence: z.ZodEnum<{
-                        high: "high";
-                        medium: "medium";
                         low: "low";
+                        medium: "medium";
+                        high: "high";
                     }>;
                     relevance_basis: z.ZodDiscriminatedUnion<[z.ZodObject<{
                         kind: z.ZodLiteral<"drug_in_class_match">;
@@ -8824,9 +8824,9 @@ export declare const DossierSchema: z.ZodObject<{
                     start_date: z.ZodOptional<z.ZodString>;
                     completion_date: z.ZodOptional<z.ZodString>;
                     match_confidence: z.ZodEnum<{
-                        high: "high";
-                        medium: "medium";
                         low: "low";
+                        medium: "medium";
+                        high: "high";
                     }>;
                     relevance_basis: z.ZodDiscriminatedUnion<[z.ZodObject<{
                         kind: z.ZodLiteral<"drug_in_class_match">;
@@ -9077,9 +9077,9 @@ export declare const DossierSchema: z.ZodObject<{
                 insufficient_evidence: "insufficient_evidence";
             }>;
             confidence: z.ZodEnum<{
-                high: "high";
-                medium: "medium";
                 low: "low";
+                medium: "medium";
+                high: "high";
             }>;
             rationale: z.ZodString;
             key_strengths: z.ZodDefault<z.ZodArray<z.ZodString>>;
@@ -9342,6 +9342,27 @@ export declare const DossierBodySchema: z.ZodObject<{
         coverage: z.ZodLiteral<"not_loaded">;
         reason: z.ZodOptional<z.ZodString>;
     }, z.core.$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<{
@@ -9565,27 +9586,6 @@ export declare const DossierBodySchema: 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<{
@@ -9660,9 +9660,9 @@ export declare const DossierBodySchema: 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<{
@@ -9717,9 +9717,9 @@ export declare const DossierBodySchema: 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<{
@@ -10073,9 +10073,9 @@ export declare const DossierBodySchema: 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<{
@@ -10627,9 +10627,9 @@ export declare const DossierBodySchema: 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">;
@@ -11680,11 +11680,11 @@ export declare const DossierBodySchema: 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>>;
@@ -12018,9 +12018,9 @@ export declare const DossierBodySchema: 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">;
@@ -12087,9 +12087,9 @@ export declare const DossierBodySchema: 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">;
@@ -12340,9 +12340,9 @@ export declare const DossierBodySchema: 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/data/safety-panel-schema.d.ts

@@ -29,9 +29,9 @@ export declare const SafetyTargetSchema: z.ZodObject<{
     }>;
     clinical_consequence: z.ZodString;
     severity: z.ZodEnum<{
-        high: "high";
-        medium: "medium";
         low: "low";
+        medium: "medium";
+        high: "high";
     }>;
     references: z.ZodArray<z.ZodString>;
 }, z.core.$strip>;
@@ -68,9 +68,9 @@ export declare const SafetyPanelFileSchema: z.ZodObject<{
         }>;
         clinical_consequence: z.ZodString;
         severity: z.ZodEnum<{
-            high: "high";
-            medium: "medium";
             low: "low";
+            medium: "medium";
+            high: "high";
         }>;
         references: z.ZodArray<z.ZodString>;
     }, z.core.$strip>>;

package/dist/execution/input-signature.d.ts

@@ -2,14 +2,21 @@
  * The input signature — the fixed-width comparand a completed profile persists in
  * place of a per-file identity list.
  *
- * `inputFileIds` had exactly one consumer, the staleness comparison, so a set of
- * several thousand identifiers was persisted, detoasted on every read of the row, and
+ * A per-file identity list would have exactly one consumer, the staleness comparison —
+ * several thousand identifiers persisted, detoasted on every read of the row, and
  * compared element-wise to answer a question 40 bytes answer. The signature covers
  * `size` and `mtimeMs` as well, so it also notices that the bytes behind a path
  * changed — a `fileId` is a path identity and survives an in-place edit unchanged.
  *
  * Order independence is a property of the digest, not of the caller: entries are
  * sorted canonically before hashing, so two enumerations of the same set agree.
+ *
+ * It digests KEPT files only — quarantine runs before the digest, on both sides of the
+ * comparison. A partial-download twin or an OS droppings file was never part of what was
+ * profiled, so its appearance, edit, or removal is not drift, and a profile that
+ * re-triggered on it would re-run on churn nobody caused. A change to the quarantine rules
+ * themselves recomputes every signature once on the next scan, which is the correct
+ * consequence: the definition of "kept" changed.
  */
 import type { DataProfileInputSignature } from "../state/data-profile.js";
 import type { StagedInput } from "./staged-input.js";
@@ -18,9 +25,15 @@ export interface SignableInput {
     readonly fileId: string;
     readonly size: number;
     readonly mtimeMs?: number;
+    /**
+     * Path relative to the data dir — what quarantine reads. An entry carrying none is
+     * always kept: a caller that cannot name a path cannot be asked to prove its file is
+     * not junk, and dropping it would be the one outcome worse than including it.
+     */
+    readonly relativePath?: string;
 }
 /**
- * Digest a staged input set.
+ * Digest a staged input set, quarantine first.
  *
  * A workflow input persisted before `StagedInput.mtimeMs` existed deserializes without
  * it despite the compile-time type; such an entry contributes `-` in the mtime field

package/dist/execution/post-step-pipeline.js

@@ -212,7 +212,7 @@ export async function vectorIndexStepOutputs(deps, postCtx, artifacts) {
     let indexed = 0;
     let failed = 0;
     for (const entry of liveMetadata) {
-        const ok = await indexOne(`/${input.analysisId}/${entry.dbPath}`, entry.description, { text: entry.description, type: "output", ...entry.metadata });
+        const ok = await indexOne(`/${input.analysisId}/${entry.dbPath}`, entry.description, { text: entry.description, type: "output", ...entry.metadata, path: entry.dbPath });
         if (ok)
             indexed++;
         else

package/dist/execution/staged-input.d.ts

@@ -26,10 +26,10 @@ export interface StagedInput {
     readonly hash: string;
     readonly size: number;
     /**
-     * Last-modification time in epoch milliseconds. With `size` and `fileId` it forms
-     * the file's drift signature — the value a consumer compares against a completed
-     * profile's `inputFiles` to decide whether the same bytes were profiled, since a
-     * `fileId` is a path identity and survives an in-place content edit unchanged.
+     * Last-modification time in epoch milliseconds. With `size` and `fileId` it feeds
+     * the kept-files `inputSignature` a completed profile persists — what lets a
+     * consumer notice the bytes behind a path changed, since a `fileId` is a path
+     * identity and survives an in-place content edit unchanged.
      *
      * Embedder-supplied and opaque: the CLI reads it from the same `stat` that yields
      * `size`; a managed service supplies its object store's last-modified epoch. The

package/dist/index.d.ts

@@ -67,8 +67,9 @@ export { createConfiguredAiSdkProvider, DEFAULT_MAX_OUTPUT_TOKENS } from "./prov
 export type { AiSdkProviderConfig, ConfiguredAiSdkProviderDeps } from "./providers/ai-sdk.js";
 export { createEmbeddingProvider } from "./providers/embedding.js";
 export type { EmbeddingProviderDeps } from "./providers/embedding.js";
-export type { AgentChat, ChatProvider, EmbeddingProvider, ChatRequest, ChatResponse, ChatStreamEvent, ChatUsage, ModelMessage, PromptCachePolicy, } from "./providers/types.js";
+export type { AgentChat, ChatProvider, EmbeddingProvider, ChatRequest, ChatResponse, ChatStreamEvent, ChatUsage, ModelMessage, PromptCachePolicy, ReasoningEffort, ReasoningPolicy, } from "./providers/types.js";
 export { DEFAULT_PROMPT_CACHE, promptCacheProviderOptions } from "./providers/prompt-cache.js";
+export { DEFAULT_REASONING, reasoningProviderOptions } from "./providers/reasoning.js";
 export { toProviderError, isProviderError } from "./providers/errors.js";
 export type { ProviderError } from "./providers/errors.js";
 export { createStreamingChat } from "./providers/streaming-chat.js";
@@ -115,8 +116,12 @@ export { DATA_PROFILE_RUN_LITERAL } from "./contracts/data-profile.js";
 export { initCortexState } from "./state/init.js";
 export { upsertAnalysis } from "./state/analyses.js";
 export { clearDataProfile, loadDataProfileStatus, tryRetryDataProfile, reconcileOrphanedDataProfile } from "./state/data-profile.js";
-export type { DataProfileAxis, DataProfileCoverage, DataProfileFile, DataProfileInputFile, DataProfileInputSignature, DataProfileKind, DataProfileLifecycleStatus, DataProfileOrganism, DataProfileQualityAssessment, DataProfileResult, DataProfileSubjectSource, } from "./contracts/data-profile.js";
+export type { DataProfileAxis, DataProfileChecked, DataProfileCompanionCompleteness, DataProfileCoverage, DataProfileDimension, DataProfileFile, DataProfileGroup, DataProfileGroupSlot, DataProfileInputSignature, DataProfileKind, DataProfileLifecycleStatus, DataProfileMemberAnnotation, DataProfileObservation, DataProfileOrganism, DataProfilePartition, DataProfileProbeReport, DataProfileQualityAssessment, DataProfileQuarantine, DataProfileRecipeStep, DataProfileResult, DataProfileSubjectSource, } from "./contracts/data-profile.js";
 export type { DataProfileStatus } from "./state/data-profile.js";
+export { DIMENSION_CATEGORIES, DIMENSION_CATEGORY_IDS, DIMENSION_PROBES, DIMENSION_PROBE_IDS, GROUP_CATEGORIES, GROUP_CATEGORY_IDS, GROUP_ROLES, GROUP_ROLE_IDS, PROBE_OUTCOME_IDS, dimensionCategoryEntry, dimensionScope, groupCategoryEntry, } from "./contracts/profile-vocabulary.js";
+export type { DimensionCategory, DimensionCategoryEntry, DimensionProbe, DimensionProbeEntry, DimensionScope, DimensionTreatment, GroupCategory, GroupCategoryEntry, GroupRole, GroupRoleEntry, ProbeOutcome, } from "./contracts/profile-vocabulary.js";
+export { dimensionCardinalities, profileCaveats, profileDatasetFileCount, profileDimensions, profileFileRecords, profileGroups, } from "./app/data-profile-view.js";
+export type { ProfileDimensionView, ProfileGroupView } from "./app/data-profile-view.js";
 export { createAnalysisPurge } from "./state/purge-analysis.js";
 export type { AnalysisPurge, AnalysisPurgeDeps, AnalysisPurgeOutcome } from "./state/purge-analysis.js";
 export type { StagedInput } from "./execution/staged-input.js";

package/dist/index.js

@@ -104,6 +104,13 @@ export { createEmbeddingProvider } from "./providers/embedding.js";
 // `"off"`; the `cortex.harness.agent.cache_*_tokens` metrics show which case a
 // deployment is actually in.
 export { DEFAULT_PROMPT_CACHE, promptCacheProviderOptions } from "./providers/prompt-cache.js";
+// Reasoning depth. `ReasoningPolicy` is the vendor-neutral directive for how
+// deep a model reasons; a composition root sets it per run through
+// `RunAgentOptions.reasoning`. It defaults to `DEFAULT_REASONING` — adaptive
+// thinking at the `xhigh` effort — because an agent loop drives tools over many
+// iterations, and a shallow turn there wastes more calls than the deeper turn
+// costs in tokens. A host on a model with no reasoning support passes `"off"`.
+export { DEFAULT_REASONING, reasoningProviderOptions } from "./providers/reasoning.js";
 // Provider error channel. `ProviderError` is the value `chat`/`embed` fail
 // with; `toProviderError` is its sole constructor. Exposed so an embedder
 // realizing its own `ChatProvider`/`EmbeddingProvider` fails with the exact
@@ -204,6 +211,13 @@ export { upsertAnalysis } from "./state/analyses.js";
 // analysis's input set empties (deferring on a running workflow), so the UI
 // stops advertising a profile that describes files the analysis no longer has.
 export { clearDataProfile, loadDataProfileStatus, tryRetryDataProfile, reconcileOrphanedDataProfile } from "./state/data-profile.js";
+// The controlled vocabulary the profiler draws from, as data. A consumer rendering a
+// stored group needs the category's meaning, and the package owns the catalogue — a host
+// does not extend it.
+export { DIMENSION_CATEGORIES, DIMENSION_CATEGORY_IDS, DIMENSION_PROBES, DIMENSION_PROBE_IDS, GROUP_CATEGORIES, GROUP_CATEGORY_IDS, GROUP_ROLES, GROUP_ROLE_IDS, PROBE_OUTCOME_IDS, dimensionCategoryEntry, dimensionScope, groupCategoryEntry, } from "./contracts/profile-vocabulary.js";
+// Reading a persisted profile of either era through one shape — the projection every
+// consumer uses so that a row written before groups existed still renders.
+export { dimensionCardinalities, profileCaveats, profileDatasetFileCount, profileDimensions, profileFileRecords, profileGroups, } from "./app/data-profile-view.js";
 // Analysis reclamation — `purgeAnalysis` reclaims an analysis's whole Postgres
 // footprint from its id alone; workspace files stay the embedder's to dispose of.
 export { createAnalysisPurge } from "./state/purge-analysis.js";

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

@@ -0,0 +1,63 @@
+/**
+ * Stage 2 — sibling directories that agree become one template.
+ *
+ * A tree whose per-entity variation is expressed as one directory per entity is
+ * structure, not the absence of it: grouping within a directory sees one entity at a
+ * time and reports thousands of unrelated observations. Sibling directories whose
+ * contents agree on name template and format census cluster into instances of one
+ * template, and the directory segment becomes a slot like any other.
+ *
+ * Agreement is judged on three channels, strongest first: the masked name templates
+ * beneath each directory, the format census when the directory names are already
+ * skeleton-kin, and the immediate subdirectory layout. Content-schema agreement is a
+ * fourth channel this pipeline cannot read, so it is injected — see
+ * {@link ContentSimilarity}.
+ */
+import type { MemberFile } from "./set-types.js";
+export interface DirectoryNode {
+    readonly name: string;
+    readonly children: Map<string, DirectoryNode>;
+    readonly files: MemberFile[];
+    readonly fineSignature: Set<string>;
+    readonly coarseSignature: Set<string>;
+    readonly childNames: Set<string>;
+}
+/** One concrete directory, carrying the values of the template positions above it. */
+export interface DirectoryEntry {
+    readonly node: DirectoryNode;
+    readonly varValues: readonly string[];
+}
+/** What a content-schema comparison would be given to judge two candidate clusters by. */
+export interface ClusterEvidence {
+    readonly names: readonly string[];
+    readonly files: readonly MemberFile[];
+}
+/**
+ * Similarity from file contents — header fields, delimiters, column names.
+ *
+ * The extension point for read-based evidence: this pipeline is pure over paths and
+ * sizes, so a host that has header readouts injects the comparison rather than the
+ * pipeline reaching for a decoder. Returning `undefined` means "no opinion".
+ */
+export type ContentSimilarity = (a: ClusterEvidence, b: ClusterEvidence) => number | undefined;
+export declare function buildTree(files: readonly MemberFile[]): DirectoryNode;
+/**
+ * Postorder masked-template signatures: the fine one keys on name skeletons, the
+ * coarse one only on extensions. Both are capped — a wide directory needs no more
+ * keys than the cap to be compared by.
+ */
+export declare function computeSignatures(node: DirectoryNode): DirectoryNode;
+/**
+ * Cluster the child directories of a set of template-equivalent parents.
+ *
+ * Same-named children are one candidate by construction — they already occupy the same
+ * template position. Candidates then merge by agreement, majority first: the largest
+ * seeds a cluster, which is the rule that keeps a lone odd directory outside rather
+ * than dragging the cluster toward it. A second agglomerative pass merges whole
+ * clusters to a fixpoint, because the largest candidate can fail against each sibling
+ * individually while the siblings agree with each other.
+ */
+export declare function clusterChildren(entries: readonly DirectoryEntry[], contentSimilarity?: ContentSimilarity): {
+    names: string[];
+    entries: DirectoryEntry[];
+}[];