@inflexa-ai/harness 0.16.0 → 0.18.0

package/dist/tools/report/submit-report.js

@@ -42,6 +42,7 @@ export function createSubmitReportTool(state) {
                 "samples — the rest had no QC row'. " +
                 "Leave empty when the report shipped cleanly."),
         }),
+        describeCall: "none",
         execute: async (input) => {
             const problems = [];
             // 1. report.html.j2 exists — the report itself, as opposed to the

package/dist/tools/report/version-fs.js

@@ -44,6 +44,7 @@ export function createVersionFsTools(state) {
             path: z.string().min(1),
             content: z.string(),
         }),
+        describeCall: "none",
         execute: async ({ path, content }) => {
             const resolved = resolveAgentPath(path, state.versionDir);
             if (resolved.kind === "out_of_scope") {
@@ -73,6 +74,7 @@ export function createVersionFsTools(state) {
             oldText: z.string().min(1),
             newText: z.string(),
         }),
+        describeCall: "none",
         execute: async ({ path, oldText, newText }) => {
             const resolved = resolveAgentPath(path, state.versionDir);
             if (resolved.kind === "out_of_scope") {
@@ -112,6 +114,7 @@ export function createVersionFsTools(state) {
         inputSchema: z.object({
             path: z.string().min(1),
         }),
+        describeCall: "none",
         execute: async ({ path }) => {
             const resolved = resolveAgentPath(path, state.versionDir);
             if (resolved.kind === "out_of_scope") {
@@ -148,6 +151,7 @@ export function createVersionFsTools(state) {
         inputSchema: z.object({
             path: z.string().min(1),
         }),
+        describeCall: "none",
         execute: async ({ path }) => {
             const resolved = resolveAgentPath(path, state.versionDir);
             if (resolved.kind === "out_of_scope") {

package/dist/tools/report-authoring/authoring-tools.d.ts

@@ -0,0 +1,134 @@
+/**
+ * The authoring tool surface over the draft operations.
+ *
+ * The factory closes over a private draft holder and the pinned snapshot. It gives eight tools and a
+ * read of the current draft. The tools read no ambient state, thus two factories hold two independent
+ * drafts.
+ *
+ * Each tool maps its flat input onto a core operation, and it applies the pure operation. The holder
+ * swaps only on a landed operation. A refused operation returns typed data in the ok channel, and the
+ * error channel stays for an unexpected failure.
+ *
+ * The primitive admits a flat object input only. Thus a destination is four optional fields, and not a
+ * nested union. A conflict between the flat fields refuses before the core runs.
+ */
+import { z } from "zod";
+import { type DraftRefusal } from "../../report-model/draft-operations.js";
+import { type OutlineEntry, type ReadableBlock } from "../../report-model/draft-read.js";
+import { type FinishResult } from "../../report-model/draft-finish.js";
+import { type DraftDocument } from "../../report-model/draft.js";
+import type { ReportSnapshot } from "../../report-model/reference-resolver.js";
+import { type Tool } from "../define-tool.js";
+/** The flat destination fields. An anchor is `before` or `after`, and a place is `start` or `end`. */
+declare const addBlockInput: z.ZodObject<{
+    block: z.ZodUnion<readonly [z.ZodType<import("../../report-model/draft.js").DraftBlock, unknown, z.core.$ZodTypeInternals<import("../../report-model/draft.js").DraftBlock, unknown>>, z.ZodUnknown]>;
+    parentId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    place: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
+        end: "end";
+        start: "start";
+    }>>>;
+    before: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    after: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+}, z.core.$strip>;
+/**
+ * The change payload is a title for a section target, or a block for an atom target, and exactly one of
+ * the two. Both fields are absentable, because a section retitle names no block. Zod 4 treats a bare
+ * `z.unknown()` as a required key, thus an optional marker is what makes the retitle call representable.
+ */
+declare const changeBlockInput: z.ZodObject<{
+    targetId: z.ZodString;
+    title: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    block: z.ZodOptional<z.ZodUnion<readonly [z.ZodType<import("../../report-model/draft.js").DraftBlock, unknown, z.core.$ZodTypeInternals<import("../../report-model/draft.js").DraftBlock, unknown>>, z.ZodUnknown]>>;
+}, z.core.$strip>;
+declare const removeBlockInput: z.ZodObject<{
+    targetId: z.ZodString;
+}, z.core.$strip>;
+declare const moveBlockInput: z.ZodObject<{
+    targetId: z.ZodString;
+    parentId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    place: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
+        end: "end";
+        start: "start";
+    }>>>;
+    before: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    after: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+}, z.core.$strip>;
+declare const readOutlineInput: z.ZodObject<{}, z.core.$strip>;
+/** The read names its target with the same field name as each mutation, thus one id key serves them all. */
+declare const readBlockInput: z.ZodObject<{
+    targetId: z.ZodString;
+}, z.core.$strip>;
+declare const setTitleInput: z.ZodObject<{
+    title: z.ZodString;
+}, z.core.$strip>;
+declare const finishDraftInput: z.ZodObject<{}, z.core.$strip>;
+export type AddBlockInput = z.infer<typeof addBlockInput>;
+export type ChangeBlockInput = z.infer<typeof changeBlockInput>;
+export type RemoveBlockInput = z.infer<typeof removeBlockInput>;
+export type MoveBlockInput = z.infer<typeof moveBlockInput>;
+export type ReadOutlineInput = z.infer<typeof readOutlineInput>;
+export type ReadBlockInput = z.infer<typeof readBlockInput>;
+export type SetTitleInput = z.infer<typeof setTitleInput>;
+export type FinishDraftInput = z.infer<typeof finishDraftInput>;
+/** One container that an operation changed, and the child order inside it after the operation. */
+export interface ChangedContainer {
+    /** The section that holds the children. It is absent when the container is the root. */
+    parentId?: string;
+    children: OutlineEntry[];
+}
+/**
+ * The result of a mutation tool. A refusal carries the typed reason.
+ *
+ * A landing carries the child order of each container that it changed, and not the whole outline. A whole
+ * outline costs the size of the draft on every landing, thus composing a report of n blocks would spend
+ * n-squared outline entries of agent context to author it. Only the container that the operation touched
+ * can surprise the agent: it chose the id, and the rest of the tree did not move. `read_outline` stays
+ * the way to read the whole draft, and it costs one call when the agent wants one.
+ *
+ * A move across two containers reports both. An operation that changes no child order reports none.
+ */
+export type MutationResult = {
+    applied: true;
+    changed: ChangedContainer[];
+} | {
+    applied: false;
+    refusal: DraftRefusal;
+};
+/** The result of `read_outline`. */
+export interface OutlineResult {
+    outline: OutlineEntry[];
+}
+/** The result of `read_block`. An absent block is an expected outcome, thus it stays in the ok channel. */
+export type ReadBlockResult = {
+    found: true;
+    block: ReadableBlock;
+} | {
+    found: false;
+};
+/** The state that the factory closes over. */
+export interface ReportAuthoringState {
+    readonly snapshot: ReportSnapshot;
+    /** The draft to start from. The default is an empty draft. */
+    readonly initialDraft?: DraftDocument;
+}
+/** The eight authoring tools, plus a read of the current draft. */
+export interface ReportAuthoringTools {
+    readonly add_block: Tool<AddBlockInput, MutationResult>;
+    readonly change_block: Tool<ChangeBlockInput, MutationResult>;
+    readonly remove_block: Tool<RemoveBlockInput, MutationResult>;
+    readonly move_block: Tool<MoveBlockInput, MutationResult>;
+    readonly set_title: Tool<SetTitleInput, MutationResult>;
+    readonly read_outline: Tool<ReadOutlineInput, OutlineResult>;
+    readonly read_block: Tool<ReadBlockInput, ReadBlockResult>;
+    readonly finish_draft: Tool<FinishDraftInput, FinishResult>;
+    currentDraft(): DraftDocument;
+}
+/**
+ * Make the eight authoring tools over one draft.
+ *
+ * The holder is a private `let`. Each tool reads the holder at call time, thus a landing through one tool
+ * shows in the next call of every tool. The holder swaps only inside `land`, thus a refused operation
+ * leaves the draft as it was.
+ */
+export declare function createReportAuthoringTools(state: ReportAuthoringState): ReportAuthoringTools;
+export {};

package/dist/tools/report-authoring/authoring-tools.js

@@ -0,0 +1,352 @@
+/**
+ * The authoring tool surface over the draft operations.
+ *
+ * The factory closes over a private draft holder and the pinned snapshot. It gives eight tools and a
+ * read of the current draft. The tools read no ambient state, thus two factories hold two independent
+ * drafts.
+ *
+ * Each tool maps its flat input onto a core operation, and it applies the pure operation. The holder
+ * swaps only on a landed operation. A refused operation returns typed data in the ok channel, and the
+ * error channel stays for an unexpected failure.
+ *
+ * The primitive admits a flat object input only. Thus a destination is four optional fields, and not a
+ * nested union. A conflict between the flat fields refuses before the core runs.
+ */
+import { err, ok } from "neverthrow";
+import { z } from "zod";
+import { addBlock, changeBlock, locate, moveBlock, removeBlock, setTitle, } from "../../report-model/draft-operations.js";
+import { buildOutline, childOutline, readBlock } from "../../report-model/draft-read.js";
+import { finishDraft } from "../../report-model/draft-finish.js";
+import { DraftBlockSchema } from "../../report-model/draft.js";
+import { defineTool } from "../define-tool.js";
+/**
+ * The block payload.
+ *
+ * The published JSON Schema carries the whole draft grammar, because a tool is self-describing at attach
+ * time and the schema is the only place where the model learns the shape of the eight block kinds. A bare
+ * `z.unknown()` emits the empty schema, which tells the model nothing and leaves it to discover each
+ * required field through one refusal at a time.
+ *
+ * The `z.unknown()` member keeps the runtime parse permissive. Thus a malformed payload still reaches the
+ * core, which parses it with the same grammar and refuses `malformed-block` as typed data in the ok
+ * channel. A strict input schema would turn that designed refusal into a hard input-validation error from
+ * the loop.
+ */
+const blockPayload = z.union([DraftBlockSchema, z.unknown()]);
+/**
+ * A flat field that the model can leave out.
+ *
+ * Nullish, and not optional. A model that must choose one of four destination fields routinely sends
+ * `null` for the three it does not use, and strict function calling requires every declared key to be
+ * present. Under `.optional()` each of those nulls fails the input parse, and the block never lands.
+ */
+const absentable = (schema) => schema.nullish();
+/** The flat destination fields. An anchor is `before` or `after`, and a place is `start` or `end`. */
+const addBlockInput = z.object({
+    block: blockPayload,
+    parentId: absentable(z.string()),
+    place: absentable(z.enum(["start", "end"])),
+    before: absentable(z.string()),
+    after: absentable(z.string()),
+});
+/**
+ * The change payload is a title for a section target, or a block for an atom target, and exactly one of
+ * the two. Both fields are absentable, because a section retitle names no block. Zod 4 treats a bare
+ * `z.unknown()` as a required key, thus an optional marker is what makes the retitle call representable.
+ */
+const changeBlockInput = z.object({
+    targetId: z.string(),
+    title: absentable(z.string()),
+    block: blockPayload.optional(),
+});
+const removeBlockInput = z.object({
+    targetId: z.string(),
+});
+const moveBlockInput = z.object({
+    targetId: z.string(),
+    parentId: absentable(z.string()),
+    place: absentable(z.enum(["start", "end"])),
+    before: absentable(z.string()),
+    after: absentable(z.string()),
+});
+const readOutlineInput = z.object({});
+/** The read names its target with the same field name as each mutation, thus one id key serves them all. */
+const readBlockInput = z.object({
+    targetId: z.string(),
+});
+const setTitleInput = z.object({
+    title: z.string().min(1),
+});
+const finishDraftInput = z.object({});
+/** Read an absentable field. An explicit `null` and an omitted key both mean that the model gave no value. */
+function given(value) {
+    return value ?? undefined;
+}
+/**
+ * Map the flat destination fields onto the core destination.
+ *
+ * Two anchors, or an anchor beside a place, name two places at one time. Thus the map refuses with
+ * `conflicting-destination`, and the detail names the conflict. An anchor implies its own parent, thus a
+ * place beside an anchor is a contradiction and not a refinement.
+ *
+ * The reason is not `unknown-target`, which means that no block holds a named id. A conflict is a fault in
+ * the shape of the call, and the repair is to drop one field. An agent that reads `unknown-target` instead
+ * goes back to the outline for a better id, finds the ids were already correct, and sends the same
+ * conflicting pair again.
+ */
+function toDestination(input) {
+    const parentId = given(input.parentId);
+    const place = given(input.place);
+    const before = given(input.before);
+    const after = given(input.after);
+    if (before !== undefined && after !== undefined) {
+        return err({ reason: "conflicting-destination", detail: "a destination names `before` or `after`, not both" });
+    }
+    const hasAnchor = before !== undefined || after !== undefined;
+    if (hasAnchor && place !== undefined) {
+        return err({ reason: "conflicting-destination", detail: "a destination names an anchor or a `place`, not both" });
+    }
+    let resolvedPlace;
+    if (before !== undefined) {
+        resolvedPlace = { before };
+    }
+    else if (after !== undefined) {
+        resolvedPlace = { after };
+    }
+    else {
+        resolvedPlace = place;
+    }
+    return ok({ parentId, place: resolvedPlace });
+}
+/**
+ * Map the flat change fields onto the core change operation.
+ *
+ * A change names a title or a block, and exactly one of the two. Neither field and both fields each name
+ * an ambiguous change. Thus the map refuses with `payload-kind-mismatch`.
+ */
+function toChangeOperation(input) {
+    const title = given(input.title);
+    const block = given(input.block);
+    if (title !== undefined && block !== undefined) {
+        return err({ reason: "payload-kind-mismatch", detail: "a change names a `title` or a `block`, not both" });
+    }
+    if (title !== undefined) {
+        return ok({ targetId: input.targetId, title });
+    }
+    if (block !== undefined) {
+        return ok({ targetId: input.targetId, block: decodeBlockPayload(block) });
+    }
+    return err({ reason: "payload-kind-mismatch", detail: "a change names a `title` or a `block`" });
+}
+/**
+ * Give the block payload as the core expects it, and decode a double-encoded one.
+ *
+ * A model routinely sends a nested object as a `JSON.stringify` string. The loop repairs that at its own
+ * input boundary, but only for a schema that rejects the string, and this payload accepts any value so
+ * that a malformed block can come back as a typed refusal. Thus the decode happens here. A string that is
+ * not JSON passes through as it is, and the core refuses it as a malformed block.
+ */
+function decodeBlockPayload(block) {
+    if (typeof block !== "string") {
+        return block;
+    }
+    try {
+        return JSON.parse(block);
+    }
+    catch {
+        return block;
+    }
+}
+/** Read the `kind` of an untyped block payload, or `undefined` when the payload names none. */
+function readKind(block) {
+    return readStringField(block, "kind");
+}
+/** Read the `id` of an untyped block payload, or `undefined` when the payload names none. */
+function readId(block) {
+    return readStringField(block, "id");
+}
+function readStringField(block, field) {
+    if (block !== null && typeof block === "object") {
+        const value = block[field];
+        if (typeof value === "string") {
+            return value;
+        }
+    }
+    return undefined;
+}
+/**
+ * The id of the section that holds a block, or `undefined` when the block sits at the root.
+ *
+ * The two cases are not distinguishable from the value alone, thus a caller that needs to tell "the root"
+ * from "no such block" tests the block itself first.
+ */
+function holderIdOf(document, blockId) {
+    return locate(document, blockId)?.parent?.id;
+}
+/** Read the child order of one container out of a document. */
+function containerIn(document, parentId) {
+    if (parentId === undefined) {
+        return { children: childOutline(document.sections, 0) };
+    }
+    const located = locate(document, parentId);
+    // A parent id reaches here only from a landed operation, which already resolved it to a section. The
+    // empty fall-back keeps the read total rather than asserting that.
+    const children = located !== undefined && located.block.kind === "section" ? located.block.blocks : [];
+    return { parentId, children: childOutline(children, located?.path.length ?? 0) };
+}
+/**
+ * Every tool of this surface runs inline.
+ *
+ * The draft is closure memory with no durable backing. A step-mode tool goes through `DBOS.runStep`, which
+ * caches the result of a step and replays it without running the body. A replay after a host restart would
+ * hand the agent the cached `applied: true` outline of each landed operation while the rebuilt closure
+ * holds an empty draft, and the finish would then report an empty document for a report that the
+ * transcript shows as complete. Inline mode keeps the tool result and the draft in one lifetime.
+ */
+const AUTHORING_EXECUTION_MODE = "inline";
+/**
+ * Make the eight authoring tools over one draft.
+ *
+ * The holder is a private `let`. Each tool reads the holder at call time, thus a landing through one tool
+ * shows in the next call of every tool. The holder swaps only inside `land`, thus a refused operation
+ * leaves the draft as it was.
+ */
+export function createReportAuthoringTools(state) {
+    const snapshot = state.snapshot;
+    let draft = state.initialDraft ?? { title: "", sections: [] };
+    /**
+     * Swap the holder on a landing, and report the containers that the operation changed.
+     *
+     * `holders` names them by id, and it reads the draft as it was and the draft as it becomes, because a
+     * removed block has a holder only in the first and an added block has one only in the second. The
+     * child order comes out of `next` in either case.
+     */
+    const land = (result, holders) => result.match((next) => {
+        const previous = draft;
+        draft = next;
+        // A move inside one container names the same holder two times.
+        const unique = [...new Set(holders(previous, next))];
+        return { applied: true, changed: unique.map((parentId) => containerIn(next, parentId)) };
+    }, (refusal) => ({ applied: false, refusal }));
+    const refuse = (refusal) => ({ applied: false, refusal });
+    const add_block = defineTool({
+        id: "add_block",
+        description: "Add one block to the draft. The `block` schema gives the eight kinds and the fields of each one. " +
+            "You choose the `id` of the block, and it must be unique in the draft. " +
+            "Name the destination with `parentId` and one of `place`, `before`, or `after`. " +
+            "The root admits a section only, and an atom needs a section as its parent.",
+        inputSchema: addBlockInput,
+        executionMode: AUTHORING_EXECUTION_MODE,
+        describeCall: (input) => {
+            const kind = readKind(decodeBlockPayload(input.block));
+            return kind !== undefined ? `add ${kind}` : "add a block";
+        },
+        execute: async (input) => {
+            const destination = toDestination(input);
+            if (destination.isErr()) {
+                return ok(refuse(destination.error));
+            }
+            const block = decodeBlockPayload(input.block);
+            const addedId = readId(block);
+            return ok(land(addBlock(draft, { block, destination: destination.value }, snapshot), (_previous, next) => [
+                addedId === undefined ? undefined : holderIdOf(next, addedId),
+            ]));
+        },
+    });
+    const change_block = defineTool({
+        id: "change_block",
+        description: "Change one block by its id. Give a `title` to retitle a section, or a `block` to replace an atom, and never both. " +
+            "The change keeps the id of the target, thus the `id` of the payload does not matter. A kind change is permitted.",
+        inputSchema: changeBlockInput,
+        executionMode: AUTHORING_EXECUTION_MODE,
+        describeCall: (input) => `change ${input.targetId}`,
+        execute: async (input) => {
+            const operation = toChangeOperation(input);
+            if (operation.isErr()) {
+                return ok(refuse(operation.error));
+            }
+            return ok(land(changeBlock(draft, operation.value, snapshot), (_previous, next) => [holderIdOf(next, input.targetId)]));
+        },
+    });
+    const remove_block = defineTool({
+        id: "remove_block",
+        description: "Remove one block by its id. A removed section takes its whole subtree with it, and the id is free for a later add.",
+        inputSchema: removeBlockInput,
+        executionMode: AUTHORING_EXECUTION_MODE,
+        describeCall: (input) => `remove ${input.targetId}`,
+        execute: async (input) => ok(land(removeBlock(draft, { targetId: input.targetId }, snapshot), (previous) => [holderIdOf(previous, input.targetId)])),
+    });
+    const move_block = defineTool({
+        id: "move_block",
+        description: "Move one block by its id to a new destination. Name the destination with `parentId` and one of `place`, `before`, or `after`. " +
+            "A section cannot move into its own subtree.",
+        inputSchema: moveBlockInput,
+        executionMode: AUTHORING_EXECUTION_MODE,
+        describeCall: (input) => `move ${input.targetId}`,
+        execute: async (input) => {
+            const destination = toDestination(input);
+            if (destination.isErr()) {
+                return ok(refuse(destination.error));
+            }
+            return ok(land(moveBlock(draft, { targetId: input.targetId, destination: destination.value }, snapshot), (previous, next) => [
+                holderIdOf(previous, input.targetId),
+                holderIdOf(next, input.targetId),
+            ]));
+        },
+    });
+    const set_title = defineTool({
+        id: "set_title",
+        description: "Set the title of the report document. A draft starts with no title, and a document needs one. " +
+            "The title names the whole report, and it is not the title of a section.",
+        inputSchema: setTitleInput,
+        executionMode: AUTHORING_EXECUTION_MODE,
+        describeCall: (input) => `title the report ${input.title}`,
+        // The title sits on the document, thus no container changes its child order.
+        execute: async (input) => ok(land(ok(setTitle(draft, input.title)), () => [])),
+    });
+    const read_outline = defineTool({
+        id: "read_outline",
+        description: "Read the outline of the draft. Each entry gives the id, the kind, the nesting depth, and a short label. " +
+            "A label that ends with the character … is clipped. Use the outline as the primary view of the draft, " +
+            "and read one block when the label is not enough.",
+        inputSchema: readOutlineInput,
+        executionMode: AUTHORING_EXECUTION_MODE,
+        // The input carries no field, thus a hook can only restate the name of the tool.
+        describeCall: "none",
+        execute: async () => ok({ outline: buildOutline(draft) }),
+    });
+    const read_block = defineTool({
+        id: "read_block",
+        description: "Read one block by its id. An atom gives the full block with its bindings. A section gives its title and the id of each child, " +
+            "because the outline already names every block under it. Use it when the outline label is not enough.",
+        inputSchema: readBlockInput,
+        executionMode: AUTHORING_EXECUTION_MODE,
+        describeCall: (input) => `read ${input.targetId}`,
+        execute: async (input) => {
+            const block = readBlock(draft, input.targetId);
+            const result = block !== undefined ? { found: true, block } : { found: false };
+            return ok(result);
+        },
+    });
+    const finish_draft = defineTool({
+        id: "finish_draft",
+        description: "Finish the draft. The result gives each completeness gap, or the valid report document, and each advisory warning. " +
+            "Use it to make sure that the draft passes the whole document schema, the id rule, and the structural tier.",
+        inputSchema: finishDraftInput,
+        executionMode: AUTHORING_EXECUTION_MODE,
+        // The input carries no field, thus a hook can only restate the name of the tool.
+        describeCall: "none",
+        execute: async () => ok(finishDraft(draft, snapshot)),
+    });
+    return {
+        add_block,
+        change_block,
+        remove_block,
+        move_block,
+        set_title,
+        read_outline,
+        read_block,
+        finish_draft,
+        currentDraft: () => draft,
+    };
+}

package/dist/tools/research/context7-docs.js

@@ -25,6 +25,7 @@ export const resolveLibraryIdTool = defineTool({
         libraryName: z.string().describe("Package or library name to search for (e.g., 'scanpy', 'pysam', 'lifelines')."),
         query: z.string().describe("What you need help with — used to rank results by relevance (e.g., 'how to run differential expression')."),
     }),
+    describeCall: "none",
     execute: async ({ libraryName, query }) => {
         const result = await apiFetchValidated(`${CONTEXT7_BASE}/search?query=${encodeURIComponent(libraryName)}&topic=${encodeURIComponent(query)}`, Context7SearchResponseSchema, { maxRetries: 1 });
         if (result.isErr())
@@ -48,6 +49,7 @@ export const queryDocsTool = defineTool({
         libraryId: z.string().describe("Context7 library ID from resolve-library-id (e.g., '/scverse/scanpy')."),
         query: z.string().describe("Specific question about the library (e.g., 'rank_genes_groups function parameters and usage')."),
     }),
+    describeCall: "none",
     execute: async ({ libraryId, query }) => {
         const result = await apiFetchValidated(`${CONTEXT7_BASE}/docs?libraryId=${encodeURIComponent(libraryId)}&query=${encodeURIComponent(query)}`, Context7DocsResponseSchema, { maxRetries: 1 });
         if (result.isErr())

package/dist/tools/research/generate-analogy-report.js

@@ -23,7 +23,7 @@ import { finalText, runAgent } from "../../loop/run-agent.js";
 import { passthroughStep } from "../../loop/run-step.js";
 import { defineTool } from "../define-tool.js";
 // Cross-domain search tools the analogical-reasoner uses.
-import { searchSemanticScholarTool } from "./search-semantic-scholar.js";
+import { createSearchSemanticScholarTool } from "./search-semantic-scholar.js";
 import { searchArxivTool } from "./search-arxiv.js";
 import { createSearchGithubReposTool } from "./search-github-repos.js";
 // Biology literature — reused for analogies that land back in biology.
@@ -156,7 +156,7 @@ function buildConversionPrompt(rawOutput) {
 export function createGenerateAnalogyReportTool(deps) {
     const ncbi = createNcbiTools(deps.bioKeys);
     const reasonerTools = [
-        searchSemanticScholarTool,
+        createSearchSemanticScholarTool({ ...(deps.bioKeys.semanticScholar === undefined ? {} : { apiKey: deps.bioKeys.semanticScholar }) }),
         searchArxivTool,
         createSearchGithubReposTool({ githubToken: deps.bioKeys.github }),
         ncbi.pubmed,
@@ -193,6 +193,7 @@ export function createGenerateAnalogyReportTool(deps) {
             "latency on the same failure). Surface the message and ask the user to " +
             "narrow the problem.",
         inputSchema: generateAnalogyReportInputSchema,
+        describeCall: "none",
         execute: async (input, ctx) => {
             const childSession = forSubAgent(ctx.session, AGENT_ID);
             // Phase 1+2: drive the research agent over the cross-domain toolset.

package/dist/tools/research/generate-plan.js

@@ -344,6 +344,7 @@ function buildInnerTools(holder, trace, persistCtx, pool, resourcePolicy, logger
             // structured issue reporting.
             plan: z.union([PlannerPlanSchema, z.unknown()]).describe("Candidate plan; malformed values are reported in issues."),
         }),
+        describeCall: "none",
         execute: async (input) => {
             if (holder.outcome !== null) {
                 trace.duplicateTerminalCalls++;
@@ -416,6 +417,7 @@ function buildInnerTools(holder, trace, persistCtx, pool, resourcePolicy, logger
             question: z.string().min(1),
             questionContext: z.string().optional(),
         }),
+        describeCall: "none",
         execute: async (input) => {
             if (holder.outcome !== null) {
                 trace.duplicateTerminalCalls++;
@@ -670,6 +672,7 @@ export function createGeneratePlanTool(deps) {
                 .optional()
                 .describe("The planId of the prior plan being iterated on. Set only when " + "the user is asking for modifications to an existing plan."),
         }),
+        describeCall: ({ researchQuestion }) => researchQuestion,
         execute: async (input, ctx) => {
             const analysisId = scopeResource(ctx.session.scope).resourceId;
             // Bound per invocation: `analysisId` comes from the call-time session, not from

package/dist/tools/research/index.d.ts

@@ -14,3 +14,4 @@ export * from "./context7-docs.js";
 export * from "./search-semantic-scholar.js";
 export * from "./search-arxiv.js";
 export * from "./search-github-repos.js";
+export * from "./resolve-citation.js";

package/dist/tools/research/index.js

@@ -14,3 +14,4 @@ export * from "./context7-docs.js";
 export * from "./search-semantic-scholar.js";
 export * from "./search-arxiv.js";
 export * from "./search-github-repos.js";
+export * from "./resolve-citation.js";

package/dist/tools/research/inspect-data-profile.js

@@ -98,6 +98,10 @@ export function createInspectDataProfileTool(pool) {
                 .optional()
                 .describe(`Per-file records per page. Only used when scope is 'files'. Default ${DEFAULT_PAGE_SIZE}, max ${MAX_PAGE_SIZE}.`),
         }),
+        // `execute` defaults both fields internally, and the hook applies the same
+        // defaults. Without them the ordinary call, which names no field at all,
+        // gives no detail. `page` acts only on the `files` scope, as in `execute`.
+        describeCall: ({ scope, page }) => ((scope ?? "overview") === "files" ? `files (page ${page ?? 1})` : "overview"),
         execute: async (input, ctx) => {
             const resourceId = scopeResource(ctx.session.scope).resourceId;
             const status = unwrapOrThrow(await loadDataProfileStatus(pool, resourceId));

package/dist/tools/research/inspect-run.d.ts

@@ -53,7 +53,7 @@ declare function formatRun(r: CortexRunRow, verbose: boolean, exposePaths?: bool
     synthesisReason?: string | undefined;
     runId: string;
     workflowName: string;
-    status: "running" | "completed" | "failed" | "partial" | "canceled" | "suspended_insufficient_funds";
+    status: "partial" | "running" | "completed" | "failed" | "canceled" | "suspended_insufficient_funds";
     startedAt: string;
     completedAt: string | null;
     planId: string | null;

package/dist/tools/research/literature-reviewer.d.ts

@@ -19,6 +19,7 @@ import { type Tool } from "../define-tool.js";
 import { type BioToolKeys } from "../bio/keys.js";
 import type { Logger } from "../../lib/logger.js";
 import type { UsageRecorder } from "../../billing/usage-recorder.js";
+import type { CitationResolver } from "../../citations/types.js";
 export interface LiteratureReviewerDeps {
     /** Operational logging seam; omitted falls back to no-op. */
     readonly logger?: Logger;
@@ -30,6 +31,8 @@ export interface LiteratureReviewerDeps {
     readonly bioKeys: BioToolKeys;
     /** LLM usage-accounting seam for the child loop; omitted falls back to the no-op recorder. */
     readonly usageRecorder?: UsageRecorder;
+    /** Shared bibliographic verification service; all agent surfaces share its pacing/cache. */
+    readonly citationResolver: CitationResolver;
 }
 /** Build the `literature_reviewer` delegation tool bound to its provider. */
 export declare function createLiteratureReviewerTool(deps: LiteratureReviewerDeps): Tool;