agent-bober 0.18.0 → 0.19.0

package/dist/cli/commands/hub.js

@@ -0,0 +1,233 @@
+/**
+ * `bober hub list` — print findings held in the project's own FactStore.
+ * `bober hub priority` — rank findings across siblings and write priority.md.
+ * `bober hub decide <expr>` — rank findings under decision scope ("X vs Y").
+ *
+ * Error handling: handlers MUST NOT throw. Set process.exitCode=1 and return.
+ * Pattern mirrors src/cli/commands/facts.ts and src/cli/commands/blackboard.ts.
+ */
+import { writeFile } from "node:fs/promises";
+import { join, dirname } from "node:path";
+import chalk from "chalk";
+import { findProjectRoot, readJson, fileExists, ensureDir } from "../../utils/fs.js";
+import { loadConfig } from "../../config/loader.js";
+import { resolveRoleProviders } from "../../config/role-providers.js";
+import { createClient } from "../../providers/factory.js";
+import { loadTeam } from "../../teams/registry.js";
+import { FactStore, factsDbPath, ensureFactsDir } from "../../state/facts.js";
+import { FactStoreFindingSource, HUB_SCOPE } from "../../hub/finding-source.js";
+import { resolveSiblingRepos } from "../../hub/repo-resolver.js";
+import { collectFindings } from "../../hub/collector.js";
+import { parseScope } from "../../hub/scope.js";
+import { rankFindings } from "../../hub/judge.js";
+import { renderPriorityMd } from "../../hub/priority-md.js";
+import { resolveOutVault, priorityMdPath } from "../../hub/hub-config.js";
+// ── Config candidates ─────────────────────────────────────────────────
+const CONFIG_CANDIDATES = ["bober.config.json", ".bober/config.json"];
+// ── Root resolver ─────────────────────────────────────────────────────
+async function resolveRoot() {
+    const root = await findProjectRoot();
+    return root ?? process.cwd();
+}
+// ── Namespace resolver ────────────────────────────────────────────────
+/**
+ * Resolve the active memory namespace from the default team.
+ * Falls back to undefined (current .bober/memory/ path) if config is missing.
+ * Never throws — config absence is not fatal for hub commands.
+ */
+async function resolveDefaultNamespace(projectRoot) {
+    try {
+        const config = await loadConfig(projectRoot);
+        return loadTeam(config, undefined).memoryNamespace || undefined;
+    }
+    catch {
+        return undefined;
+    }
+}
+// ── Configured repos resolver ─────────────────────────────────────────
+/**
+ * Read the raw config file (bypassing Zod which strips unknown keys) and
+ * extract hub.repos if present. Falls back to undefined so the resolver
+ * can discover kb-* siblings instead. Never throws.
+ * schema.ts is NOT edited in this sprint — hub is not yet a typed field.
+ */
+async function resolveConfiguredRepos(projectRoot) {
+    for (const candidate of CONFIG_CANDIDATES) {
+        try {
+            const raw = await readJson(join(projectRoot, candidate));
+            const repos = raw.hub?.repos;
+            if (Array.isArray(repos)) {
+                return repos.filter((r) => typeof r === "string");
+            }
+            return undefined;
+        }
+        catch {
+            // file not found, not valid JSON, or no hub section — try next
+        }
+    }
+    return undefined;
+}
+// ── Scope label helper ────────────────────────────────────────────────
+function buildScopeLabel(scope) {
+    if (scope.mode === "general")
+        return "general";
+    if (scope.mode === "decision")
+        return `decide: ${scope.optionA} vs ${scope.optionB}`;
+    // filtered
+    const parts = ["filtered"];
+    if (scope.domain !== undefined)
+        parts.push(`domain=${scope.domain}`);
+    if (scope.tag !== undefined)
+        parts.push(`tag=${scope.tag}`);
+    if (scope.dueWithinDays !== undefined)
+        parts.push(`due<=${scope.dueWithinDays}d`);
+    return parts.join(", ");
+}
+// ── runHubList ────────────────────────────────────────────────────────
+/**
+ * DI core for `hub list` — accepts an injected FindingSource so tests can
+ * drive it against an in-memory store without spawning the CLI.
+ * Prints one line per finding with title, kind, urgency, and severity.
+ */
+export function runHubList(source) {
+    const findings = source.read();
+    if (findings.length === 0) {
+        process.stdout.write(chalk.gray("No findings found.\n"));
+        return;
+    }
+    for (const f of findings) {
+        process.stdout.write(`${f.title}  [${f.kind}]  urgency=${f.urgency}  severity=${f.severity}\n`);
+    }
+}
+// ── runHubPriority ────────────────────────────────────────────────────
+/**
+ * DI core for `hub priority` / `hub decide`. Injected llm + resolved outVault
+ * keep tests offline. Ranks (judge order), renders, writes <outVault>/priority.md,
+ * prints ranked summary to stdout.
+ *
+ * Missing outVault dir → clear stderr + process.exitCode=1, NEVER throws.
+ */
+export async function runHubPriority(findings, scope, llm, outVault, now) {
+    if (!(await fileExists(outVault))) {
+        process.stderr.write(chalk.red(`kb-hub vault not found at ${outVault} — create it or set hub.outVault in bober.config.json\n`));
+        process.exitCode = 1;
+        return;
+    }
+    const ranked = await rankFindings(findings, scope, llm, now);
+    const label = buildScopeLabel(scope);
+    const md = renderPriorityMd(ranked, label, now);
+    const target = priorityMdPath(outVault);
+    // dirname(target) === outVault (already exists) — ensureDir is a harmless no-op
+    // kept for symmetry with writeLabNote (lab-note.ts:232) and defensive safety.
+    await ensureDir(dirname(target));
+    await writeFile(target, md, "utf-8");
+    for (let i = 0; i < ranked.length; i++) {
+        process.stdout.write(`${i + 1}. ${ranked[i].title}\n`);
+    }
+}
+// ── registerHubCommand ────────────────────────────────────────────────
+export function registerHubCommand(program) {
+    const hubCmd = program
+        .command("hub")
+        .description("Unified cross-domain priority hub");
+    // ── list ────────────────────────────────────────────────────────
+    hubCmd
+        .command("list")
+        .description("Print findings held in the project's own FactStore")
+        .action(async () => {
+        const projectRoot = await resolveRoot();
+        try {
+            const ns = await resolveDefaultNamespace(projectRoot);
+            await ensureFactsDir(projectRoot, ns);
+            const store = new FactStore(factsDbPath(projectRoot, ns));
+            try {
+                // own findings come first (own store takes priority in dedup)
+                const own = new FactStoreFindingSource(store, HUB_SCOPE).read();
+                const configuredRepos = await resolveConfiguredRepos(projectRoot);
+                const siblings = await resolveSiblingRepos(projectRoot, configuredRepos);
+                const sibFindings = collectFindings(siblings, HUB_SCOPE);
+                // merge: own first, then sibling findings not already seen
+                const seen = new Set(own.map((f) => f.id));
+                const merged = [...own];
+                for (const f of sibFindings) {
+                    if (!seen.has(f.id)) {
+                        seen.add(f.id);
+                        merged.push(f);
+                    }
+                }
+                runHubList({ read: () => merged });
+            }
+            finally {
+                store.close();
+            }
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`Failed to list findings: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1;
+        }
+    });
+    // ── priority ─────────────────────────────────────────────────────
+    hubCmd
+        .command("priority")
+        .description("Rank findings across siblings and write priority.md to the kb-hub vault")
+        .option("--domain <domain>", "filter to one domain")
+        .option("--due <days>", "filter to findings due within N days")
+        .option("--tag <tag>", "filter to a tag")
+        .action(async (opts) => {
+        const projectRoot = await resolveRoot();
+        try {
+            const config = await loadConfig(projectRoot);
+            const providers = resolveRoleProviders(config);
+            const client = createClient(providers.chat, config.chat?.endpoint ?? null, config.chat?.providerConfig, config.chat?.model, "chat");
+            const configuredRepos = await resolveConfiguredRepos(projectRoot);
+            const siblings = await resolveSiblingRepos(projectRoot, configuredRepos);
+            const findings = collectFindings(siblings, HUB_SCOPE);
+            const scope = opts.domain !== undefined || opts.due !== undefined || opts.tag !== undefined
+                ? parseScope({
+                    mode: "filtered",
+                    domain: opts.domain,
+                    tag: opts.tag,
+                    dueWithinDays: opts.due !== undefined ? Number(opts.due) : undefined,
+                })
+                : parseScope({ mode: "general" });
+            const outVault = await resolveOutVault(projectRoot);
+            await runHubPriority(findings, scope, client, outVault, new Date());
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`hub priority failed: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1;
+        }
+    });
+    // ── decide <expr> ─────────────────────────────────────────────────
+    hubCmd
+        .command("decide <expr>")
+        .description("Rank findings under decision scope (e.g. 'X vs Y') and write priority.md")
+        .action(async (expr) => {
+        const projectRoot = await resolveRoot();
+        try {
+            const parts = expr.split(/\s+vs\s+/i);
+            if (parts.length !== 2 || !parts[0].trim() || !parts[1].trim()) {
+                process.stderr.write(chalk.red(`hub decide: expected 'X vs Y' expression, got: ${expr}\n` +
+                    `Usage: bober hub decide "option A vs option B"\n`));
+                process.exitCode = 1;
+                return;
+            }
+            const optionA = parts[0].trim();
+            const optionB = parts[1].trim();
+            const config = await loadConfig(projectRoot);
+            const providers = resolveRoleProviders(config);
+            const client = createClient(providers.chat, config.chat?.endpoint ?? null, config.chat?.providerConfig, config.chat?.model, "chat");
+            const configuredRepos = await resolveConfiguredRepos(projectRoot);
+            const siblings = await resolveSiblingRepos(projectRoot, configuredRepos);
+            const findings = collectFindings(siblings, HUB_SCOPE);
+            const scope = parseScope({ mode: "decision", optionA, optionB });
+            const outVault = await resolveOutVault(projectRoot);
+            await runHubPriority(findings, scope, client, outVault, new Date());
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`hub decide failed: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1;
+        }
+    });
+}
+//# sourceMappingURL=hub.js.map

package/dist/cli/commands/hub.js.map

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

@@ -1,5 +1,6 @@
 import type { Command } from "commander";
 import { WhoopClient } from "../../medical/whoop/whoop-client.js";
+import { parseLabPdf } from "../../medical/lab-pdf-parser.js";
 /** Injectable dependencies for runWhoopSync — production callers pass undefined. */
 export interface WhoopSyncDeps {
     /** Override the WhoopClient (e.g. fixture client in tests). */
@@ -15,6 +16,30 @@ export interface WhoopSyncDeps {
 export declare function runWhoopSync(projectRoot: string, opts: {
     since?: string;
 }, deps?: WhoopSyncDeps): Promise<void>;
+/** Injectable dependencies for runImportLabs — production callers pass undefined. */
+export interface ImportLabsDeps {
+    /** Override the PDF parser (e.g. fixture parser in tests). */
+    parse?: typeof parseLabPdf;
+    /** Override the current time ISO string (default: new Date().toISOString()). */
+    nowIso?: string;
+}
+/**
+ * Core logic for `bober medical import-labs <pdf>`.
+ * Extracted so tests can inject fixture deps without module-level mocking.
+ * The CLI .action() calls this with no deps (production).
+ *
+ * LOAD-BEARING ORDER (ADR-6 / sc-3-3):
+ *   1. loadConfig + EgressGuard.fromConfig
+ *   2. cloud-inference axis check — exits 1 BEFORE any readFile or client build
+ *   3. buildMedicalInferenceClient
+ *   4. readFile(pdfPath) + parse(pdfBytes)
+ *   5. writeLabNote per marker + reindexLabNotes into HealthDataStore (dedup)
+ *   6. AuditLog.append (IDs/enums only — PHI rule)
+ *   7. finally: store?.close()
+ */
+export declare function runImportLabs(projectRoot: string, pdfPath: string, deps?: ImportLabsDeps, opts?: {
+    vault?: string;
+}): Promise<void>;
 /**
  * Register the `bober medical` command tree.
  * Provides `medical import <file>` and `medical whoop sync [--since <iso>]`.

package/dist/cli/commands/medical.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"medical.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/medical.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAYzC,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAC;AAalE,oFAAoF;AACpF,MAAM,WAAW,aAAa;IAC5B,+DAA+D;IAC/D,MAAM,CAAC,EAAE,WAAW,CAAC;IACrB,gFAAgF;IAChF,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED;;;;GAIG;AACH,wBAAsB,YAAY,CAChC,WAAW,EAAE,MAAM,EACnB,IAAI,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,EACxB,IAAI,GAAE,aAAkB,GACvB,OAAO,CAAC,IAAI,CAAC,CA0Ef;AAID;;;;GAIG;AACH,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CA2D7D"}
+{"version":3,"file":"medical.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/medical.ts"],"names":[],"mappings":"AAQA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAYzC,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAC;AAGlE,OAAO,EAAE,WAAW,EAAE,MAAM,iCAAiC,CAAC;AAmB9D,oFAAoF;AACpF,MAAM,WAAW,aAAa;IAC5B,+DAA+D;IAC/D,MAAM,CAAC,EAAE,WAAW,CAAC;IACrB,gFAAgF;IAChF,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED;;;;GAIG;AACH,wBAAsB,YAAY,CAChC,WAAW,EAAE,MAAM,EACnB,IAAI,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,EACxB,IAAI,GAAE,aAAkB,GACvB,OAAO,CAAC,IAAI,CAAC,CA0Ef;AAID,qFAAqF;AACrF,MAAM,WAAW,cAAc;IAC7B,8DAA8D;IAC9D,KAAK,CAAC,EAAE,OAAO,WAAW,CAAC;IAC3B,gFAAgF;IAChF,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAsB,aAAa,CACjC,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,MAAM,EACf,IAAI,GAAE,cAAmB,EACzB,IAAI,GAAE;IAAE,KAAK,CAAC,EAAE,MAAM,CAAA;CAAO,GAC5B,OAAO,CAAC,IAAI,CAAC,CAuDf;AAID;;;;GAIG;AACH,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAqQ7D"}

package/dist/cli/commands/medical.js

@@ -1,5 +1,9 @@
 /** `bober medical import <file>` — stream-ingest a health export (Phase 6, Sprint 5). */
 /** `bober medical whoop sync` — WHOOP device-connection sync (Phase 6, Sprint 3). */
+/** `bober medical import-labs <pdf>` — lab PDF ingest: fail-closed cloud-inference gate + vault + audit (Sprint 3). */
+/** `bober medical review` — deterministic proactive trend review pass (spec-20260628-medical-analysis Sprint 1). */
+/** `bober medical research` — egress-gated online research job (spec-20260628-medical-analysis Sprint 5). */
+import { readFile } from "node:fs/promises";
 import { join } from "node:path";
 import chalk from "chalk";
 import { findProjectRoot, ensureDir } from "../../utils/fs.js";
@@ -12,6 +16,15 @@ import { WhoopTokenStore } from "../../medical/whoop/whoop-token.js";
 import { WhoopClient } from "../../medical/whoop/whoop-client.js";
 import { WhoopSyncAdapter } from "../../medical/whoop/whoop-sync.js";
 import { AuditLog } from "../../medical/audit.js";
+import { parseLabPdf } from "../../medical/lab-pdf-parser.js";
+import { writeLabNote } from "../../medical/lab-note.js";
+import { reindexLabNotes } from "../../medical/lab-reindex.js";
+import { buildMedicalInferenceClient } from "../../medical/inference.js";
+import { runSupplementAdd, runSupplementList } from "../../medical/supplements.js";
+import { runProfileShow, runProfileSet } from "../../medical/profile.js";
+import { runProactiveReview, digDeeper } from "../../medical/analysis/review-pass.js";
+import { generateRecommendation } from "../../medical/recommend/recommend.js";
+import { runResearchJob } from "../../medical/research/online-research.js";
 // ── Root resolver ─────────────────────────────────────────────────────
 async function resolveRoot() {
     const root = await findProjectRoot();
@@ -75,6 +88,62 @@ export async function runWhoopSync(projectRoot, opts, deps = {}) {
         store?.close(); // always close — even if sync threw mid-pagination (sc-3-8)
     }
 }
+/**
+ * Core logic for `bober medical import-labs <pdf>`.
+ * Extracted so tests can inject fixture deps without module-level mocking.
+ * The CLI .action() calls this with no deps (production).
+ *
+ * LOAD-BEARING ORDER (ADR-6 / sc-3-3):
+ *   1. loadConfig + EgressGuard.fromConfig
+ *   2. cloud-inference axis check — exits 1 BEFORE any readFile or client build
+ *   3. buildMedicalInferenceClient
+ *   4. readFile(pdfPath) + parse(pdfBytes)
+ *   5. writeLabNote per marker + reindexLabNotes into HealthDataStore (dedup)
+ *   6. AuditLog.append (IDs/enums only — PHI rule)
+ *   7. finally: store?.close()
+ */
+export async function runImportLabs(projectRoot, pdfPath, deps = {}, opts = {}) {
+    let store;
+    try {
+        const config = await loadConfig(projectRoot);
+        const egress = EgressGuard.fromConfig(config);
+        // axis-off branch: clear message, exit 1, NEVER read the PDF or build any client (FAIL CLOSED — sc-3-3)
+        if (!egress.isAllowed("cloud-inference")) {
+            process.stderr.write(chalk.red("cloud-inference egress not enabled — set medical.egress.cloudInference: true in bober.config.json\n"));
+            process.exitCode = 1;
+            return;
+        }
+        const { client, model } = buildMedicalInferenceClient(config, egress);
+        const pdfBytes = await readFile(pdfPath);
+        const parse = deps.parse ?? parseLabPdf;
+        const report = await parse(pdfBytes, { client, model });
+        const nowIso = deps.nowIso ?? new Date().toISOString();
+        const medicalDir = join(projectRoot, ".bober", "medical");
+        await ensureDir(medicalDir);
+        const vaultDir = opts.vault ?? medicalDir;
+        store = new HealthDataStore(join(medicalDir, "health.db"));
+        for (const marker of report.markers) {
+            await writeLabNote(vaultDir, marker, {
+                panel: report.panel,
+                collectedAtIso: report.collectedAtIso,
+                source: "lab-pdf",
+            });
+        }
+        const newRows = await reindexLabNotes(vaultDir, store);
+        // Audit entry — IDs/enums only (no values, panel names, counts, or PHI — audit.ts:1)
+        await new AuditLog(projectRoot).append({ tIso: nowIso, event: "ingest" });
+        process.stdout.write(chalk.green("Lab import complete\n"));
+        process.stdout.write(`  records parsed: ${report.markers.length}\n`);
+        process.stdout.write(`  new rows:       ${newRows}\n`);
+    }
+    catch (err) {
+        process.stderr.write(chalk.red(`Failed to import labs: ${err instanceof Error ? err.message : String(err)}\n`));
+        process.exitCode = 1;
+    }
+    finally {
+        store?.close();
+    }
+}
 // ── registerMedicalCommand ────────────────────────────────────────────
 /**
  * Register the `bober medical` command tree.
@@ -116,6 +185,15 @@ export function registerMedicalCommand(program) {
             process.exitCode = 1;
         }
     });
+    // ── medical import-labs ──────────────────────────────────────────
+    medicalCmd
+        .command("import-labs <pdf>")
+        .description("Parse a lab PDF and ingest results into the medical health store")
+        .option("--vault <dir>", "vault dir (default: under .bober/medical)")
+        .action(async (pdf, opts) => {
+        const projectRoot = await resolveRoot();
+        await runImportLabs(projectRoot, pdf, {}, opts);
+    });
     // ── medical whoop sync ────────────────────────────────────────────
     const whoopCmd = medicalCmd
         .command("whoop")
@@ -128,5 +206,160 @@ export function registerMedicalCommand(program) {
         const projectRoot = await resolveRoot();
         await runWhoopSync(projectRoot, opts);
     });
+    // ── medical supplements ───────────────────────────────────────────────
+    const suppCmd = medicalCmd
+        .command("supplements")
+        .description("Manage supplements list in FactStore (scope: medical)");
+    suppCmd
+        .command("add <name>")
+        .description("Reconcile a supplement into FactStore (creates or noops on duplicate)")
+        .option("--dose <d>", "dose string (default: unspecified)")
+        .action(async (name, opts) => {
+        const projectRoot = await resolveRoot();
+        await runSupplementAdd(projectRoot, name, opts);
+    });
+    suppCmd
+        .command("list")
+        .description("Print supplements from the markdown-frontmatter file")
+        .option("--file <path>", "supplements markdown file (default: .bober/medical/supplements.md)")
+        .action(async (opts) => {
+        const projectRoot = await resolveRoot();
+        await runSupplementList(projectRoot, opts);
+    });
+    // ── medical profile ───────────────────────────────────────────────────
+    const profileCmd = medicalCmd
+        .command("profile")
+        .description("Manage personalization profile (SOPS-encrypted profile.yaml)");
+    profileCmd
+        .command("show")
+        .description("Decrypt and display the current personalization profile")
+        .option("--vault <dir>", "vault dir (default: .bober/medical under project root)")
+        .action(async (opts) => {
+        const projectRoot = await resolveRoot();
+        await runProfileShow(projectRoot, opts);
+    });
+    profileCmd
+        .command("set <key> <value>")
+        .description("Update one profile field after Zod validation")
+        .option("--vault <dir>", "vault dir (default: .bober/medical under project root)")
+        .action(async (key, value, opts) => {
+        const projectRoot = await resolveRoot();
+        await runProfileSet(projectRoot, key, value, opts);
+    });
+    // ── medical review ────────────────────────────────────────────────────
+    medicalCmd
+        .command("review")
+        .description("Run the deterministic proactive trend review pass and write Finding notes + dashboard")
+        .option("--dig-deeper <id>", "run deeper cross-marker analysis for the given offer finding id (gated LLM path)")
+        .action(async (opts) => {
+        const projectRoot = await resolveRoot();
+        try {
+            const config = await loadConfig(projectRoot);
+            // Clock read ONLY here at the CLI boundary (mirrors medical.ts:97)
+            const now = new Date().toISOString();
+            if (opts.digDeeper !== undefined) {
+                // -- dig-deeper path (gated LLM) --
+                const result = await digDeeper(projectRoot, config, opts.digDeeper, { now });
+                if (result.kind === "accepted") {
+                    process.stdout.write(chalk.green(`Deep analysis accepted\n`));
+                    if (result.findingPath !== undefined) {
+                        process.stdout.write(`  finding: ${result.findingPath}\n`);
+                    }
+                }
+                else if (result.kind === "question") {
+                    process.stdout.write(chalk.yellow(`Deep analysis flagged for review\n`));
+                    if (result.findingPath !== undefined) {
+                        process.stdout.write(`  finding: ${result.findingPath}\n`);
+                    }
+                }
+                else if (result.kind === "escalated") {
+                    process.stdout.write(chalk.red(`Escalated: ${result.cannedResponse ?? ""}\n`));
+                }
+                else {
+                    // refused
+                    process.stdout.write(chalk.yellow(`Deep analysis refused: ${result.reason ?? ""}\n`));
+                }
+                return;
+            }
+            // -- standard review path (offline, deterministic) --
+            // counts now include gap + offer findings from sprint-4 analyzers (sc-4-7)
+            const result = await runProactiveReview(projectRoot, config, { now });
+            process.stdout.write(chalk.green(`Proactive review complete\n`));
+            process.stdout.write(`  findings written: ${result.findingsWritten}\n`);
+            process.stdout.write(`  dashboard:        ${result.dashboardPath}\n`);
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`Failed to run review: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1; // MUST NOT throw (mirrors import action pattern at line 257-265)
+        }
+    });
+    // ── medical recommend ─────────────────────────────────────────────────
+    medicalCmd
+        .command("recommend <question>")
+        .description("Generate a medical recommendation through the 4-lens judge panel and write a Finding note")
+        .option("--goal <g>", "optional health goal to include in the recommendation context")
+        .action(async (question, opts) => {
+        const projectRoot = await resolveRoot();
+        try {
+            const config = await loadConfig(projectRoot);
+            // Clock read ONLY here at the CLI boundary (sc-3-7)
+            const now = new Date().toISOString();
+            const result = await generateRecommendation(projectRoot, config, {
+                question,
+                goal: opts.goal,
+                now,
+            });
+            if (result.kind === "accepted") {
+                process.stdout.write(chalk.green(`Recommendation accepted\n`));
+                if (result.findingPath !== undefined) {
+                    process.stdout.write(`  finding: ${result.findingPath}\n`);
+                }
+            }
+            else if (result.kind === "question") {
+                process.stdout.write(chalk.yellow(`Recommendation flagged for review\n`));
+                if (result.findingPath !== undefined) {
+                    process.stdout.write(`  finding: ${result.findingPath}\n`);
+                }
+            }
+            else if (result.kind === "escalated") {
+                process.stdout.write(chalk.red(`Escalated: ${result.cannedResponse ?? ""}\n`));
+            }
+            else {
+                // refused
+                process.stdout.write(chalk.yellow(`Recommendation refused: ${result.reason ?? ""}\n`));
+            }
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`Failed to generate recommendation: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1; // MUST NOT throw — sc-3-7 exit 0 on normal outcomes
+        }
+    });
+    // ── medical research ──────────────────────────────────────────────────
+    medicalCmd
+        .command("research")
+        .description("Retrieve latest MedlinePlus evidence for markers and write vault research notes (egress-gated)")
+        .option("--marker <m>", "marker to research (default: ldl, hdl, a1c)")
+        .action(async (opts) => {
+        const projectRoot = await resolveRoot();
+        try {
+            const config = await loadConfig(projectRoot);
+            // Clock read ONLY here at the CLI boundary (sc-5-7)
+            const now = new Date().toISOString();
+            const markers = opts.marker !== undefined ? [opts.marker] : ["ldl", "hdl", "a1c"];
+            const summary = await runResearchJob(projectRoot, config, { markers, now });
+            if (summary.disabled) {
+                process.stdout.write(chalk.yellow("literature-retrieval egress not enabled — research skipped (zero egress)\n"));
+            }
+            else {
+                process.stdout.write(chalk.green("Research complete\n"));
+                process.stdout.write(`  notes written:    ${summary.notesWritten}\n`);
+                process.stdout.write(`  findings written: ${summary.findingsWritten}\n`);
+            }
+        }
+        catch (err) {
+            process.stderr.write(chalk.red(`Failed to run research: ${err instanceof Error ? err.message : String(err)}\n`));
+            process.exitCode = 1; // MUST NOT throw (sc-5-7: exit 0 on both ran and disabled)
+        }
+    });
 }
 //# sourceMappingURL=medical.js.map

package/dist/cli/commands/medical.js.map

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package/dist/cli/commands/research.d.ts

@@ -0,0 +1,41 @@
+/**
+ * `agent-bober research job add|list|remove` — manage recurring multi-model research jobs.
+ * `agent-bober research run <jobId>`         — execute a stored research job.
+ * `agent-bober research tick [--watch]`      — run every due job (idempotent).
+ *
+ * Subcommands:
+ *   research job add --question "..." [--cadence daily|weekly|monthly] [--tier <t>]
+ *                    [--domain <d>] [--target-repo <r>] [--online-research]
+ *   research job list
+ *   research job remove <jobId>
+ *   research run <jobId>
+ *   research tick [--watch] [--interval <ms>]
+ *
+ * Error handling: CLI handlers MUST NOT throw. They set process.exitCode=1 and
+ * return on all errors. Pattern mirrors src/cli/commands/task.ts:360-367.
+ *
+ * Clock discipline: new Date().toISOString() is called ONLY at the .action()
+ * boundary — never inside the store (mirrors task.ts:352 "stamp wall-clock time
+ * at handler boundary").
+ *
+ * fs boundary: ALL direct fs work (ensureDir, writeFile) happens inside runner.ts
+ * and note-writer.ts. This file only calls readJob (JSON read) and opens FactStore.
+ * This keeps the utils/fs.js import surface minimal (only findProjectRoot) so that
+ * the research.test.ts whole-module vi.mock of utils/fs.js stays stable.
+ */
+import type { Command } from "commander";
+import type { DigestRun } from "../../research/digest.js";
+import type { QueryModel, FindingSink } from "../../research/runner.js";
+/**
+ * Optional overrides injected at registration time.
+ * Allows tests to bypass the real LLM provider and hub store without
+ * mocking additional modules beyond utils/fs.js.
+ */
+export interface ResearchRunOverrides {
+    queryModel?: QueryModel;
+    findingSink?: FindingSink;
+    /** Injected collector for `research digest` — skips real vault I/O in tests. */
+    digestCollectRuns?: (since: string, now: string) => Promise<DigestRun[]>;
+}
+export declare function registerResearchCommand(program: Command, overrides?: ResearchRunOverrides): void;
+//# sourceMappingURL=research.d.ts.map