agent-bober 0.18.0 → 0.19.0

package/dist/medical/research/online-research.d.ts

@@ -0,0 +1,65 @@
+/**
+ * runResearchJob — egress-gated online research job (schedulable entrypoint).
+ *
+ * When literature-retrieval is OFF: returns { disabled: true, notesWritten: 0, findingsWritten: 0 }
+ * IMMEDIATELY — NO retriever constructed, ZERO egress. This is the zero-egress proof (sc-5-2).
+ *
+ * When ON: retrieves MedlinePlus passages via LiteratureRetriever, grounds notes through
+ * synthesizeGrounded (fail-closed grounding critic), writes research notes and optional watch
+ * findings to the vault.
+ *
+ * PURE clock: `now` is injected — NEVER call Date.now()/new Date() here.
+ * NO network imports — ADR-6 restricts network to medline-source.ts only.
+ *
+ * Exported as the schedulable entrypoint for spec-20260628-research-scheduler.
+ * Signature: (projectRoot, config, {markers, now}, deps?) => Promise<ResearchSummary>
+ */
+import type { BoberConfig } from "../../config/schema.js";
+import { type ClientFactory } from "../inference.js";
+import { writeFinding } from "../analysis/finding-writer.js";
+import type { LLMClient } from "../../providers/types.js";
+import type { RetrievalOutcome } from "../retrieval/medline-source.js";
+/** Summary returned by runResearchJob. */
+export interface ResearchSummary {
+    notesWritten: number;
+    findingsWritten: number;
+    disabled: boolean;
+}
+/**
+ * Injectable dependencies for runResearchJob.
+ * Production callers pass no deps — all defaults are wired from real modules.
+ * Tests inject fakes for: retriever (avoids MedlineSource), clientFactory (spy), writeFindingFn.
+ */
+export interface ResearchDeps {
+    /** Injectable retriever — defaults to a real LiteratureRetriever when axis is ON. */
+    retriever?: {
+        retrieve(query: string): Promise<RetrievalOutcome>;
+    };
+    /** Injectable LLMClient for synthesis — use clientFactory instead when testing sc-5-5. */
+    llmClient?: LLMClient;
+    /** Injectable client factory so tests can spy on which provider/endpoint is requested (sc-5-5). */
+    clientFactory?: ClientFactory;
+    /** Injectable finding writer so tests avoid real fs writes. Defaults to writeFinding. */
+    writeFindingFn?: typeof writeFinding;
+}
+/**
+ * Run the online research job for the given markers.
+ *
+ * Gating order (load-bearing — mirrors runImportLabs pattern at medical.ts:165-178):
+ *   1. Build EgressGuard.
+ *   2. axis OFF -> return {disabled:true, notesWritten:0, findingsWritten:0} BEFORE any construction.
+ *   3. Build synthesis client via buildMedicalInferenceClient (fail-closed local unless cloud-inference ON).
+ *   4. Resolve vault dir.
+ *   5. For each marker: retrieve -> synthesizeGrounded -> abstained? skip : write note + finding.
+ *   6. Return { disabled: false, notesWritten, findingsWritten }.
+ *
+ * @param projectRoot  Absolute project root path
+ * @param config       Loaded BoberConfig
+ * @param opts         { markers: string[]; now: string } — clock injected NEVER read here
+ * @param deps         Optional injectable dependencies (tests only)
+ */
+export declare function runResearchJob(projectRoot: string, config: BoberConfig, opts: {
+    markers: string[];
+    now: string;
+}, deps?: ResearchDeps): Promise<ResearchSummary>;
+//# sourceMappingURL=online-research.d.ts.map

package/dist/medical/research/online-research.d.ts.map

@@ -0,0 +1 @@
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package/dist/medical/research/online-research.js

@@ -0,0 +1,101 @@
+/**
+ * runResearchJob — egress-gated online research job (schedulable entrypoint).
+ *
+ * When literature-retrieval is OFF: returns { disabled: true, notesWritten: 0, findingsWritten: 0 }
+ * IMMEDIATELY — NO retriever constructed, ZERO egress. This is the zero-egress proof (sc-5-2).
+ *
+ * When ON: retrieves MedlinePlus passages via LiteratureRetriever, grounds notes through
+ * synthesizeGrounded (fail-closed grounding critic), writes research notes and optional watch
+ * findings to the vault.
+ *
+ * PURE clock: `now` is injected — NEVER call Date.now()/new Date() here.
+ * NO network imports — ADR-6 restricts network to medline-source.ts only.
+ *
+ * Exported as the schedulable entrypoint for spec-20260628-research-scheduler.
+ * Signature: (projectRoot, config, {markers, now}, deps?) => Promise<ResearchSummary>
+ */
+import { writeFile } from "node:fs/promises";
+import { join, dirname } from "node:path";
+import { EgressGuard } from "../egress.js";
+import { LiteratureRetriever } from "../retrieval/literature.js";
+import { synthesizeGrounded } from "../retrieval/literature.js";
+import { buildMedicalInferenceClient } from "../inference.js";
+import { DisclaimerComposer } from "../disclaimer.js";
+import { writeFinding } from "../analysis/finding-writer.js";
+import { findingId } from "../analysis/finding.js";
+import { ensureDir } from "../../utils/fs.js";
+import { serializeResearchNote, researchNotePath } from "./research-note.js";
+// ── runResearchJob ─────────────────────────────────────────────────────
+/**
+ * Run the online research job for the given markers.
+ *
+ * Gating order (load-bearing — mirrors runImportLabs pattern at medical.ts:165-178):
+ *   1. Build EgressGuard.
+ *   2. axis OFF -> return {disabled:true, notesWritten:0, findingsWritten:0} BEFORE any construction.
+ *   3. Build synthesis client via buildMedicalInferenceClient (fail-closed local unless cloud-inference ON).
+ *   4. Resolve vault dir.
+ *   5. For each marker: retrieve -> synthesizeGrounded -> abstained? skip : write note + finding.
+ *   6. Return { disabled: false, notesWritten, findingsWritten }.
+ *
+ * @param projectRoot  Absolute project root path
+ * @param config       Loaded BoberConfig
+ * @param opts         { markers: string[]; now: string } — clock injected NEVER read here
+ * @param deps         Optional injectable dependencies (tests only)
+ */
+export async function runResearchJob(projectRoot, config, opts, deps = {}) {
+    // ── 1. Egress guard ─────────────────────────────────────────────────
+    const egress = EgressGuard.fromConfig(config);
+    // ── 2. Zero-egress short-circuit (sc-5-2) ────────────────────────────
+    // Return BEFORE constructing any LiteratureRetriever / MedlineSource (zero-egress proof).
+    if (!egress.isAllowed("literature-retrieval")) {
+        return { disabled: true, notesWritten: 0, findingsWritten: 0 };
+    }
+    // ── 3. Synthesis client (fail-closed local unless cloud-inference ON) (sc-5-5) ─
+    const { client, model } = buildMedicalInferenceClient(config, egress, deps.clientFactory);
+    const llm = deps.llmClient ?? client;
+    // ── 4. Vault dir resolution (mirrors review-pass.ts:78-79) ─────────
+    const vaultDir = config.medical?.vaultDir ?? join(projectRoot, ".bober", "medical", "vault");
+    // ── 5. Retriever (constructed ONLY here — axis-on branch) ───────────
+    // Injecting deps.retriever keeps tests free of real MedlineSource construction.
+    const retriever = deps.retriever ?? new LiteratureRetriever(egress);
+    const footer = new DisclaimerComposer().footer();
+    const writeFindingFn = deps.writeFindingFn ?? writeFinding;
+    let notesWritten = 0;
+    let findingsWritten = 0;
+    // ── 6. Per-marker retrieval + grounded synthesis ─────────────────────
+    for (const marker of opts.markers) {
+        const query = `Latest evidence on ${marker}`;
+        // Retrieve passages from MedlinePlus
+        const outcome = await retriever.retrieve(query);
+        // Grounded synthesis with fail-closed critic gate
+        const result = await synthesizeGrounded(query, outcome, llm, footer, model);
+        // sc-5-4: if critic rejected / abstained -> write NO clinical note for this topic
+        if (result.answer.abstained) {
+            // Count as abstained — do not persist uncited synthesis
+            continue;
+        }
+        // Non-abstained: write research note under <vault>/research/<date>-<marker>.md
+        const notePath = researchNotePath(vaultDir, marker, opts.now);
+        const noteContent = serializeResearchNote(marker, result.answer, opts.now);
+        await ensureDir(dirname(notePath));
+        await writeFile(notePath, noteContent, "utf-8");
+        notesWritten++;
+        // Optional watch finding (Pattern G)
+        const finding = {
+            id: findingId("medical", marker, "new-evidence"),
+            domain: "medical",
+            title: `New evidence on ${marker}`,
+            kind: "watch",
+            urgency: 2,
+            severity: 2,
+            evidence: result.answer.citations.map((c) => c.url),
+            surfacedAt: opts.now, // injected — never wall-clock
+            tags: ["research", marker],
+            status: "open",
+        };
+        await writeFindingFn(vaultDir, finding);
+        findingsWritten++;
+    }
+    return { disabled: false, notesWritten, findingsWritten };
+}
+//# sourceMappingURL=online-research.js.map

package/dist/medical/research/online-research.js.map

@@ -0,0 +1 @@
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package/dist/medical/research/research-note.d.ts

@@ -0,0 +1,32 @@
+/**
+ * Research note serializer — PURE citation-frontmatter markdown note for MedlinePlus findings.
+ *
+ * PURE / NO network / NO LLM / NO Date.now()
+ * All timestamps are injected parameters; the wall clock is read ONLY at the CLI boundary.
+ *
+ * Produces a vault research note with flattened citation frontmatter (title/url/source
+ * as parallel arrays) so serializeFrontmatter (scalar/array-of-scalar only) renders correctly.
+ * See: Pattern E / briefing §2 (the nested-object pitfall with Citation[]).
+ */
+import type { MedicalAnswer } from "../types.js";
+/**
+ * Derive the canonical path for a research note under the vault.
+ * Output: <vaultDir>/research/<YYYY-MM-DD>-<marker>.md
+ * Date is sliced from the injected ISO string — never wall-clock.
+ */
+export declare function researchNotePath(vaultDir: string, marker: string, now: string): string;
+/**
+ * Serialize a grounded MedicalAnswer into a vault research note string.
+ *
+ * Frontmatter:
+ *   title, domain, type, marker, source (scalar "medlineplus"),
+ *   citationTitles[] (strings), citationUrls[] (strings), surfacedAt, status.
+ *
+ * PITFALL: Citation is an object {title, url, source}. Passing citations straight into
+ * serializeFrontmatter would render "  - [object Object]". This function FLATTENS them
+ * into parallel arrays-of-strings (citationTitles, citationUrls) + a scalar `source`.
+ *
+ * Body: answer.body + disclaimerFooter.
+ */
+export declare function serializeResearchNote(marker: string, answer: MedicalAnswer, now: string): string;
+//# sourceMappingURL=research-note.d.ts.map

package/dist/medical/research/research-note.d.ts.map

@@ -0,0 +1 @@
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package/dist/medical/research/research-note.js

@@ -0,0 +1,55 @@
+/**
+ * Research note serializer — PURE citation-frontmatter markdown note for MedlinePlus findings.
+ *
+ * PURE / NO network / NO LLM / NO Date.now()
+ * All timestamps are injected parameters; the wall clock is read ONLY at the CLI boundary.
+ *
+ * Produces a vault research note with flattened citation frontmatter (title/url/source
+ * as parallel arrays) so serializeFrontmatter (scalar/array-of-scalar only) renders correctly.
+ * See: Pattern E / briefing §2 (the nested-object pitfall with Citation[]).
+ */
+import { serializeFrontmatter } from "../../vault/frontmatter.js";
+import { join } from "node:path";
+// ── Path helper ──────────────────────────────────────────────────────
+/**
+ * Derive the canonical path for a research note under the vault.
+ * Output: <vaultDir>/research/<YYYY-MM-DD>-<marker>.md
+ * Date is sliced from the injected ISO string — never wall-clock.
+ */
+export function researchNotePath(vaultDir, marker, now) {
+    const date = now.slice(0, 10); // YYYY-MM-DD
+    return join(vaultDir, "research", `${date}-${marker}.md`);
+}
+// ── Serializer ───────────────────────────────────────────────────────
+/**
+ * Serialize a grounded MedicalAnswer into a vault research note string.
+ *
+ * Frontmatter:
+ *   title, domain, type, marker, source (scalar "medlineplus"),
+ *   citationTitles[] (strings), citationUrls[] (strings), surfacedAt, status.
+ *
+ * PITFALL: Citation is an object {title, url, source}. Passing citations straight into
+ * serializeFrontmatter would render "  - [object Object]". This function FLATTENS them
+ * into parallel arrays-of-strings (citationTitles, citationUrls) + a scalar `source`.
+ *
+ * Body: answer.body + disclaimerFooter.
+ */
+export function serializeResearchNote(marker, answer, now) {
+    // Flatten Citation[] into scalar/array-of-string fields (Pattern E)
+    const citationTitles = answer.citations.map((c) => c.title);
+    const citationUrls = answer.citations.map((c) => c.url);
+    const frontmatter = {
+        title: `Latest evidence — ${marker}`,
+        domain: "medical",
+        type: "research",
+        marker,
+        source: "medlineplus", // scalar — satisfies sc-5-3 "source 'medlineplus'"
+        citationTitles, // array of strings — serializeFrontmatter safe
+        citationUrls, // array of strings — serializeFrontmatter safe
+        surfacedAt: now, // injected ISO string — never wall-clock
+        status: "open",
+    };
+    const body = `\n## Latest evidence on ${marker}\n\n${answer.body}\n\n${answer.disclaimerFooter}\n`;
+    return serializeFrontmatter(frontmatter, body);
+}
+//# sourceMappingURL=research-note.js.map

package/dist/medical/research/research-note.js.map

@@ -0,0 +1 @@
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package/dist/medical/supplements.d.ts

@@ -0,0 +1,82 @@
+/**
+ * Supplements list -> FactStore. PURE deterministic reconcile.
+ * NO LLM, NO network, NO Date.now() — `now` is injected.
+ * Hand-rolled frontmatter parse mirrors lab-note.ts:120-148.
+ * NEVER import src/vault.
+ */
+import { FactStore } from "../state/facts.js";
+/** A single supplement entry parsed from the markdown-frontmatter list. */
+export interface SupplementEntry {
+    name: string;
+    dose: string | undefined;
+}
+/** Placeholder value when --dose is omitted (FactSchema requires value.min(1)). */
+export declare const DEFAULT_DOSE = "unspecified";
+/**
+ * Parse a supplements markdown-frontmatter file into a list of entries.
+ *
+ * Expected format:
+ * ```
+ * ---
+ * supplements:
+ *   - Vitamin D | 1000 IU
+ *   - Magnesium | 200 mg
+ * ---
+ * ```
+ *
+ * Replicates the hand-rolled fence-find loop from lab-note.ts:121-136.
+ * NEVER imports src/vault/frontmatter.ts (lab-note.ts:9-12 precedent).
+ * NEVER imports parseLabNote — it returns the lab flat-scalar shape and is list-unaware.
+ */
+export declare function parseSupplementsFile(raw: string): SupplementEntry[];
+/**
+ * Build a FactInput from a supplement name + optional dose.
+ *
+ * scope = "medical", subject = supplement name, predicate = "dose", value = dose ?? DEFAULT_DOSE.
+ * `now` is injected (never reads the clock).
+ *
+ * bober: predicate "dose" makes each supplement its own subject row in FactStore;
+ *        contrast with medications which use subject "patient", predicate "takes-medication".
+ */
+export declare function supplementToFact(name: string, dose: string | undefined, now: string): {
+    scope: string;
+    subject: string;
+    predicate: string;
+    value: string;
+    confidence: number;
+    sourceRunId: null;
+    tValid: string;
+    tCreated: string;
+};
+/** Injectable dependencies for runSupplementAdd — production callers pass undefined. */
+export interface SupplementAddDeps {
+    /** Override the FactStore (e.g. in-memory store in tests). */
+    store?: FactStore;
+    /** Override the current time ISO string (default: new Date().toISOString()). */
+    now?: string;
+}
+/**
+ * Core logic for `bober medical supplements add <name> [--dose <d>]`.
+ *
+ * Reconciles one supplement into FactStore (scope "medical") via writeFact.
+ * NO judge — deterministic ADD/UPDATE/NOOP path only.
+ * `now` is stamped at this boundary; the pure reconcile path never reads the clock.
+ *
+ * .action() MUST NOT throw — errors are caught, process.exitCode is set to 1, and the
+ * function returns. Pattern mirrors runImportLabs in medical.ts:203-212.
+ */
+export declare function runSupplementAdd(projectRoot: string, name: string, opts: {
+    dose?: string;
+}, deps?: SupplementAddDeps): Promise<void>;
+/**
+ * Core logic for `bober medical supplements list [--file <path>]`.
+ *
+ * Reads the supplements markdown-frontmatter file and prints each entry to stdout.
+ * Default file path: <projectRoot>/.bober/medical/supplements.md
+ *
+ * .action() MUST NOT throw — errors are caught and process.exitCode is set to 1.
+ */
+export declare function runSupplementList(projectRoot: string, opts: {
+    file?: string;
+}): Promise<void>;
+//# sourceMappingURL=supplements.d.ts.map

package/dist/medical/supplements.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"supplements.d.ts","sourceRoot":"","sources":["../../src/medical/supplements.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAAE,SAAS,EAA0C,MAAM,mBAAmB,CAAC;AAItF,2EAA2E;AAC3E,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,GAAG,SAAS,CAAC;CAC1B;AAED,mFAAmF;AACnF,eAAO,MAAM,YAAY,gBAAgB,CAAC;AAI1C;;;;;;;;;;;;;;;GAeG;AACH,wBAAgB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,eAAe,EAAE,CAmDnE;AAID;;;;;;;;GAQG;AACH,wBAAgB,gBAAgB,CAC9B,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,MAAM,GAAG,SAAS,EACxB,GAAG,EAAE,MAAM;;;;;;;;;EAYZ;AAID,wFAAwF;AACxF,MAAM,WAAW,iBAAiB;IAChC,8DAA8D;IAC9D,KAAK,CAAC,EAAE,SAAS,CAAC;IAClB,gFAAgF;IAChF,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAID;;;;;;;;;GASG;AACH,wBAAsB,gBAAgB,CACpC,WAAW,EAAE,MAAM,EACnB,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE;IAAE,IAAI,CAAC,EAAE,MAAM,CAAA;CAAE,EACvB,IAAI,GAAE,iBAAsB,GAC3B,OAAO,CAAC,IAAI,CAAC,CAuCf;AAED;;;;;;;GAOG;AACH,wBAAsB,iBAAiB,CACrC,WAAW,EAAE,MAAM,EACnB,IAAI,EAAE;IAAE,IAAI,CAAC,EAAE,MAAM,CAAA;CAAE,GACtB,OAAO,CAAC,IAAI,CAAC,CAqBf"}

package/dist/medical/supplements.js

@@ -0,0 +1,173 @@
+/**
+ * Supplements list -> FactStore. PURE deterministic reconcile.
+ * NO LLM, NO network, NO Date.now() — `now` is injected.
+ * Hand-rolled frontmatter parse mirrors lab-note.ts:120-148.
+ * NEVER import src/vault.
+ */
+import { readFile } from "node:fs/promises";
+import { join } from "node:path";
+import { FactStore, writeFact, factsDbPath, ensureFactsDir } from "../state/facts.js";
+/** Placeholder value when --dose is omitted (FactSchema requires value.min(1)). */
+export const DEFAULT_DOSE = "unspecified";
+// -- Pure parser ---------------------------------------------------------
+/**
+ * Parse a supplements markdown-frontmatter file into a list of entries.
+ *
+ * Expected format:
+ * ```
+ * ---
+ * supplements:
+ *   - Vitamin D | 1000 IU
+ *   - Magnesium | 200 mg
+ * ---
+ * ```
+ *
+ * Replicates the hand-rolled fence-find loop from lab-note.ts:121-136.
+ * NEVER imports src/vault/frontmatter.ts (lab-note.ts:9-12 precedent).
+ * NEVER imports parseLabNote — it returns the lab flat-scalar shape and is list-unaware.
+ */
+export function parseSupplementsFile(raw) {
+    const lines = raw.split("\n");
+    if (lines[0]?.trim() !== "---") {
+        throw new Error("parseSupplementsFile: missing opening '---' fence");
+    }
+    let closingIdx = -1;
+    for (let i = 1; i < lines.length; i++) {
+        if (lines[i]?.trim() === "---") {
+            closingIdx = i;
+            break;
+        }
+    }
+    if (closingIdx === -1) {
+        throw new Error("parseSupplementsFile: missing closing '---' fence");
+    }
+    const yamlLines = lines.slice(1, closingIdx);
+    const entries = [];
+    let inSupplements = false;
+    for (const line of yamlLines) {
+        if (line.trim() === "supplements:") {
+            inSupplements = true;
+            continue;
+        }
+        if (!inSupplements)
+            continue;
+        // Detect list items: lines starting with optional whitespace, then `- `
+        const listMatch = /^\s+-\s+(.+)$/.exec(line);
+        if (listMatch === null) {
+            // Non-indented non-empty line signals the end of the supplements list
+            if (line.trim().length > 0 && !/^\s/.test(line)) {
+                inSupplements = false;
+            }
+            continue;
+        }
+        const itemText = (listMatch[1] ?? "").trim();
+        const pipeIdx = itemText.indexOf("|");
+        if (pipeIdx >= 0) {
+            const name = itemText.slice(0, pipeIdx).trim();
+            const dose = itemText.slice(pipeIdx + 1).trim() || undefined;
+            if (name.length > 0)
+                entries.push({ name, dose });
+        }
+        else {
+            if (itemText.length > 0)
+                entries.push({ name: itemText, dose: undefined });
+        }
+    }
+    return entries;
+}
+// -- FactInput builder ---------------------------------------------------
+/**
+ * Build a FactInput from a supplement name + optional dose.
+ *
+ * scope = "medical", subject = supplement name, predicate = "dose", value = dose ?? DEFAULT_DOSE.
+ * `now` is injected (never reads the clock).
+ *
+ * bober: predicate "dose" makes each supplement its own subject row in FactStore;
+ *        contrast with medications which use subject "patient", predicate "takes-medication".
+ */
+export function supplementToFact(name, dose, now) {
+    return {
+        scope: "medical",
+        subject: name,
+        predicate: "dose",
+        value: dose ?? DEFAULT_DOSE,
+        confidence: 1,
+        sourceRunId: null,
+        tValid: now,
+        tCreated: now,
+    };
+}
+// -- Cores ---------------------------------------------------------------
+/**
+ * Core logic for `bober medical supplements add <name> [--dose <d>]`.
+ *
+ * Reconciles one supplement into FactStore (scope "medical") via writeFact.
+ * NO judge — deterministic ADD/UPDATE/NOOP path only.
+ * `now` is stamped at this boundary; the pure reconcile path never reads the clock.
+ *
+ * .action() MUST NOT throw — errors are caught, process.exitCode is set to 1, and the
+ * function returns. Pattern mirrors runImportLabs in medical.ts:203-212.
+ */
+export async function runSupplementAdd(projectRoot, name, opts, deps = {}) {
+    // Stamp wall-clock ONCE at the CLI boundary (injected `now` used in tests).
+    const now = deps.now ?? new Date().toISOString();
+    // Track the store we own so we can close it in finally without closing injected stores.
+    let ownedStore;
+    try {
+        let store;
+        if (deps.store !== undefined) {
+            store = deps.store;
+        }
+        else {
+            await ensureFactsDir(projectRoot, "medical");
+            ownedStore = new FactStore(factsDbPath(projectRoot, "medical"));
+            store = ownedStore;
+        }
+        const input = supplementToFact(name, opts.dose, now);
+        const action = await writeFact(store, input, { now });
+        if (action === "add") {
+            process.stdout.write(`Added supplement: ${name} (${opts.dose ?? DEFAULT_DOSE})\n`);
+        }
+        else if (action === "update") {
+            process.stdout.write(`Updated supplement: ${name} -> ${opts.dose ?? DEFAULT_DOSE}\n`);
+        }
+        else {
+            // "noop" (or "delete", which only occurs with a judge — never here)
+            process.stdout.write(`Supplement unchanged: ${name}\n`);
+        }
+    }
+    catch (err) {
+        process.stderr.write(`Failed to add supplement: ${err instanceof Error ? err.message : String(err)}\n`);
+        process.exitCode = 1;
+    }
+    finally {
+        ownedStore?.close();
+    }
+}
+/**
+ * Core logic for `bober medical supplements list [--file <path>]`.
+ *
+ * Reads the supplements markdown-frontmatter file and prints each entry to stdout.
+ * Default file path: <projectRoot>/.bober/medical/supplements.md
+ *
+ * .action() MUST NOT throw — errors are caught and process.exitCode is set to 1.
+ */
+export async function runSupplementList(projectRoot, opts) {
+    try {
+        const filePath = opts.file ?? join(projectRoot, ".bober", "medical", "supplements.md");
+        const raw = await readFile(filePath, "utf-8");
+        const entries = parseSupplementsFile(raw);
+        if (entries.length === 0) {
+            process.stdout.write("No supplements found.\n");
+            return;
+        }
+        for (const entry of entries) {
+            process.stdout.write(`${entry.name}: ${entry.dose ?? DEFAULT_DOSE}\n`);
+        }
+    }
+    catch (err) {
+        process.stderr.write(`Failed to list supplements: ${err instanceof Error ? err.message : String(err)}\n`);
+        process.exitCode = 1;
+    }
+}
+//# sourceMappingURL=supplements.js.map

package/dist/medical/supplements.js.map

@@ -0,0 +1 @@
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