@longtable/cli 0.1.59 → 0.1.61

package/dist/cli.js

@@ -10,7 +10,7 @@ import { homedir } from "node:os";
 import { fileURLToPath } from "node:url";
 import { collectHardStopBlockers } from "@longtable/core";
 import { classifyCheckpointTrigger } from "@longtable/checkpoints";
-import { assessSearchSourceCapabilities, buildResearchSearchIntent, parsePublisherTarget, probePublisherAccess, publisherConfigs, runResearchSearch, SEARCH_SOURCES, summarizeConfiguredPublisherAccess } from "./search/index.js";
+import { assessSearchSourceCapabilities, assessScholarResearchReadiness, buildResearchSearchIntent, buildScholarResearchSmokeFixture, parsePublisherTarget, probePublisherAccess, publisherConfigs, runResearchSearch, SEARCH_SOURCES, writeScholarResearchRunScaffold, summarizeConfiguredPublisherAccess } from "./search/index.js";
 import { buildProviderChoices, buildQuickSetupFlow, createPersistedSetupOutput, installRuntimeConfigFromStoredSetup, loadSetupOutput, renderInstallSummary, renderSetupSummary, resolveDefaultRuntimeConfigPath, resolveDefaultSetupPath, saveSetupOutput, saveSetupAndRuntimeConfig, serializeSetupOutput, writeRuntimeConfig } from "@longtable/setup";
 import { buildCodexSkillSpecs, buildCodexThinWrappedPrompt, installCodexSkills, listInstalledCodexSkills, renderQuestionRecordPrompt, removeCodexSkills, resolveCodexSkillsDir, runCodexThinWrapper } from "@longtable/provider-codex";
 import { buildClaudeSkillSpecs, installClaudeSkills, listInstalledClaudeSkills, renderQuestionRecordInput, removeClaudeSkills, resolveClaudeSkillsDir } from "@longtable/provider-claude";
@@ -153,7 +153,10 @@ function usage() {
         "  longtable access status [--json]",
         "  longtable access doctor [--doi <doi>] [--publisher auto|elsevier|springer_nature|wiley|taylor_francis|all] [--json]",
         "  longtable access probe --doi <doi> [--publisher auto|elsevier|springer_nature|wiley|taylor_francis] [--json]",
-        "  longtable search --query <text> [--intent literature|theory|measurement|citation|metadata|venue] [--field <text>] [--source all|crossref,arxiv,openalex,semantic_scholar,pubmed,eric,doaj,unpaywall] [--must <term[,term]>] [--exclude <term[,term]>] [--limit <n>] [--allow-partial] [--publisher-access] [--record] [--cwd <path>] [--json]",
+        "  longtable search --query <text> [--intent literature|theory|measurement|citation|metadata|venue] [--field <text>] [--source all|crossref,arxiv,openalex,semantic_scholar,pubmed,eric,doaj] [--must <term[,term]>] [--exclude <term[,term]>] [--limit <n>] [--allow-partial] [--publisher-access] [--record] [--cwd <path>] [--json]",
+        "  longtable scholar-research doctor [--json]",
+        "  longtable scholar-research scaffold [--cwd <path>] [--run-id <id>] [--json]",
+        "  longtable scholar-research smoke-fixture [--json]",
         "  longtable sentinel --prompt <text> [--cwd <path>] [--json] [--record]",
         "  longtable ask [--prompt <text>] [--print] [--json] [--setup <path>] [--cwd <path>]",
         "  longtable clarify --prompt <task-context> [--provider codex|claude] [--required|--advisory] [--print] [--cwd <path>] [--json] [--force]",
@@ -201,7 +204,7 @@ function parseArgs(argv) {
     const values = {};
     let subcommand = maybeSubcommand;
     const modeCommand = command && VALID_MODES.has(command);
-    const directCommand = command && ["init", "setup", "start", "resume", "doctor", "status", "audit", "roles", "show", "install", "mcp", "codex", "claude", "ask", "clarify", "question", "clear-question", "prune-questions", "panel", "handoff", "decide", "sentinel", "access", "search", "spec"].includes(command);
+    const directCommand = command && ["init", "setup", "start", "resume", "doctor", "status", "audit", "roles", "show", "install", "mcp", "codex", "claude", "ask", "clarify", "question", "clear-question", "prune-questions", "panel", "handoff", "decide", "sentinel", "access", "search", "scholar-research", "spec"].includes(command);
     let startIndex = 1;
     if (modeCommand) {
         subcommand = undefined;
@@ -210,7 +213,7 @@ function parseArgs(argv) {
     else if (command === "codex" || command === "claude" || command === "mcp") {
         startIndex = 2;
     }
-    else if ((command === "access" || command === "search" || command === "spec" || command === "panel") && maybeSubcommand && !maybeSubcommand.startsWith("--")) {
+    else if ((command === "access" || command === "search" || command === "scholar-research" || command === "spec" || command === "panel") && maybeSubcommand && !maybeSubcommand.startsWith("--")) {
         subcommand = maybeSubcommand;
         startIndex = 2;
     }
@@ -991,15 +994,25 @@ async function collectProjectInterview(setup, args) {
         ]));
         console.log("");
     }
-    const projectName = (typeof args.name === "string" && args.name.trim()) ||
+    const projectNameInput = (typeof args.name === "string" && args.name.trim()) ||
         (await promptText(renderQuestionHeader(1, 2, "Workspace", "What should this project be called?"), true));
+    if (!projectNameInput) {
+        throw new Error("LongTable start needs a project name.");
+    }
+    const projectName = projectNameInput;
     const suggestedParentDir = typeof args.path === "string" && args.path.trim()
         ? normalizeUserPath(args.path.trim())
         : homedir();
     const suggestedPath = resolveInteractiveProjectPath(suggestedParentDir, projectName);
-    const projectPath = (typeof args.path === "string" && args.path.trim()
+    const projectPathInput = typeof args.path === "string" && args.path.trim()
         ? normalizeUserPath(args.path.trim())
-        : resolveInteractiveProjectPath((await promptText(renderQuestionHeader(2, 2, "Workspace", `Which parent directory should contain this project?\nLongTable will create this folder:\n${suggestedPath}`), true)), projectName));
+        : await promptText(renderQuestionHeader(2, 2, "Workspace", `Which parent directory should contain this project?\nLongTable will create this folder:\n${suggestedPath}`), true);
+    if (!projectPathInput) {
+        throw new Error("LongTable start needs a project path.");
+    }
+    const projectPath = typeof args.path === "string" && args.path.trim()
+        ? projectPathInput
+        : resolveInteractiveProjectPath(projectPathInput, projectName);
     const adaptive = skipResearchInterview
         ? {}
         : await collectAdaptiveStartInterview({
@@ -1637,6 +1650,7 @@ async function collectDoctorStatus(args) {
     return {
         setupPath,
         setupExists: existsSync(setupPath),
+        scholarResearch: assessScholarResearchReadiness(env),
         providers: {
             codex: {
                 command: "codex",
@@ -1700,6 +1714,8 @@ function renderDoctorStatus(status) {
     const lines = [
         "LongTable doctor",
         `- setup: ${status.setupExists ? "present" : "missing"} (${status.setupPath})`,
+        `- scholar-research connectors: ${status.scholarResearch.connectors.filter((connector) => connector.status === "ready").length}/${status.scholarResearch.connectors.length} ready`,
+        `- scholar-research safety: paywall bypass ${status.scholarResearch.safety.paywallBypassAllowed ? "allowed" : "disabled"}, institution login automation ${status.scholarResearch.safety.institutionLoginAutomationAllowed ? "allowed" : "disabled"}`,
         "",
         ...renderProviderDoctorBlock("Codex", status.providers.codex),
         `- legacy prompt files: ${status.providers.codex.legacyPromptFilesInstalled.length}`,
@@ -2083,12 +2099,14 @@ function buildRoleAuditEntry(provider, spec) {
 }
 function runRoleAudit() {
     const baseSkillNames = new Set([
+        "critical-interview",
         "longtable",
         "longtable-start",
         "longtable-interview",
         "longtable-panel",
         "longtable-explore",
-        "longtable-review"
+        "longtable-review",
+        "scholar-research"
     ]);
     const roles = [
         ...buildCodexSkillSpecs(listRoleDefinitions(), "full")
@@ -2829,6 +2847,9 @@ async function runPanelCommand(args) {
     console.log(renderPanelSummary(fallback.plan));
     console.log("");
     if (finalNativeRun) {
+        if (!nativeRunContext) {
+            throw new Error("Native panel worker run finished without a run context.");
+        }
         console.log("LongTable native panel worker run created");
         console.log(`- run: ${finalNativeRun.id}`);
         console.log(`- status: ${finalNativeRun.status}`);
@@ -3315,7 +3336,7 @@ async function runInteractiveAccessSetup(args) {
         return buildAccessReadinessProfile({ readiness, routes: [] });
     }
     const routeSelections = await promptMultiChoice("Select every scholarly access route that is available or intended. Secrets are never stored.", [
-        { id: "metadata", label: "Open metadata", description: "Crossref, OpenAlex, Semantic Scholar, PubMed, ERIC, DOAJ, Unpaywall." },
+        { id: "metadata", label: "Open metadata", description: "Crossref, OpenAlex, Semantic Scholar, PubMed, ERIC, DOAJ." },
         { id: "oa_full_text", label: "OA full text", description: "Use open-access PDF/full-text when legally available." },
         { id: "institutional", label: "Institutional access", description: "VPN, library proxy, or browser SSO handled by the researcher." },
         { id: "publisher_tdm", label: "Publisher API/TDM", description: "Use configured publisher API/TDM environment variables." },
@@ -3455,6 +3476,52 @@ async function runSearch(subcommand, args) {
     }
     console.log(renderEvidenceRunSummary(run, recordedPath));
 }
+async function runScholarResearch(subcommand, args) {
+    const json = args.json === true;
+    if (subcommand === "doctor" || subcommand === "status" || !subcommand) {
+        const readiness = assessScholarResearchReadiness(env);
+        if (json) {
+            console.log(JSON.stringify(readiness, null, 2));
+            return;
+        }
+        console.log("LongTable scholar-research doctor");
+        for (const connector of readiness.connectors) {
+            const missing = connector.missingEnv.length > 0 ? ` (missing ${connector.missingEnv.join(", ")})` : "";
+            console.log(`- ${connector.name}: ${connector.status}${missing}`);
+        }
+        console.log("- safety: paywall bypass disabled; institution-login automation disabled");
+        return;
+    }
+    if (subcommand === "scaffold") {
+        const workingDirectory = typeof args.cwd === "string" ? args.cwd : cwd();
+        const runId = typeof args["run-id"] === "string" ? args["run-id"] : undefined;
+        const scaffold = await writeScholarResearchRunScaffold({
+            cwd: workingDirectory,
+            ...(runId ? { runId } : {})
+        });
+        if (json) {
+            console.log(JSON.stringify(scaffold, null, 2));
+            return;
+        }
+        console.log("LongTable scholar-research scaffold");
+        console.log(`- run: ${scaffold.runId}`);
+        console.log(`- dir: ${scaffold.runDir}`);
+        return;
+    }
+    if (subcommand === "smoke-fixture") {
+        const fixture = buildScholarResearchSmokeFixture();
+        if (json) {
+            console.log(JSON.stringify({ fixture }, null, 2));
+            return;
+        }
+        console.log("LongTable scholar-research smoke fixture");
+        for (const item of fixture) {
+            console.log(`- ${item.id}: ${item.category} - ${item.label}`);
+        }
+        return;
+    }
+    throw new Error(`Unknown scholar-research subcommand: ${subcommand}`);
+}
 async function requireWorkspaceContext(args) {
     const workingDirectory = typeof args.cwd === "string" ? args.cwd : cwd();
     const context = await loadProjectContextFromDirectory(workingDirectory);
@@ -4588,6 +4655,10 @@ async function main() {
         await runSearch(subcommand, values);
         return;
     }
+    if (command === "scholar-research") {
+        await runScholarResearch(subcommand, values);
+        return;
+    }
     if (command === "spec") {
         await runSpec(subcommand, values);
         return;

package/dist/index.d.ts

@@ -6,3 +6,4 @@ export * from "./panel.js";
 export * from "./project-session.js";
 export * from "./question-obligations.js";
 export * from "./hard-stop.js";
+export * from "./search/index.js";

package/dist/index.js

@@ -6,3 +6,4 @@ export * from "./panel.js";
 export * from "./project-session.js";
 export * from "./question-obligations.js";
 export * from "./hard-stop.js";
+export * from "./search/index.js";

package/dist/search/index.d.ts

@@ -1,6 +1 @@
-export * from "./types.js";
-export * from "./query.js";
-export * from "./sources.js";
-export * from "./rank.js";
-export * from "./run.js";
-export * from "./publisher-access.js";
+export * from "@longtable/scholar-research";

package/dist/search/index.js

@@ -1,6 +1 @@
-export * from "./types.js";
-export * from "./query.js";
-export * from "./sources.js";
-export * from "./rank.js";
-export * from "./run.js";
-export * from "./publisher-access.js";
+export * from "@longtable/scholar-research";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@longtable/cli",
-  "version": "0.1.59",
+  "version": "0.1.61",
   "private": false,
   "description": "Researcher-facing LongTable CLI",
   "type": "module",
@@ -29,12 +29,13 @@
   },
   "dependencies": {
     "@clack/prompts": "^1.2.0",
-    "@longtable/checkpoints": "0.1.59",
-    "@longtable/core": "0.1.59",
-    "@longtable/memory": "0.1.59",
-    "@longtable/provider-claude": "0.1.59",
-    "@longtable/provider-codex": "0.1.59",
-    "@longtable/setup": "0.1.59"
+    "@longtable/checkpoints": "0.1.61",
+    "@longtable/core": "0.1.61",
+    "@longtable/memory": "0.1.61",
+    "@longtable/provider-claude": "0.1.61",
+    "@longtable/provider-codex": "0.1.61",
+    "@longtable/scholar-research": "0.1.61",
+    "@longtable/setup": "0.1.61"
   },
   "devDependencies": {
     "@types/node": "^22.10.1",

package/dist/search/publisher-access.d.ts

@@ -1,21 +0,0 @@
-import { type CrossrefTdmDiscovery, type EvidenceCard, type Publisher, type PublisherAccessRecord, type PublisherProbeInput, type PublisherProbeTarget, type SearchFetch } from "./types.js";
-interface PublisherConfig {
-    publisher: Publisher;
-    label: string;
-    requiredEnv: string[];
-    optionalEnv: string[];
-    setupHint: string;
-}
-export declare function normalizeDoi(value: string): string;
-export declare function parsePublisherTarget(value?: string | boolean): PublisherProbeTarget;
-export declare function discoverCrossrefTdm(doi: string, env?: Record<string, string | undefined>, httpFetch?: SearchFetch): Promise<CrossrefTdmDiscovery>;
-export declare function publisherConfigs(): PublisherConfig[];
-export declare function probePublisherAccess(input: PublisherProbeInput): Promise<PublisherAccessRecord>;
-export declare function summarizeConfiguredPublisherAccess(env?: Record<string, string | undefined>): PublisherAccessRecord[];
-export declare function enrichCardsWithPublisherAccess(input: {
-    cards: EvidenceCard[];
-    env?: Record<string, string | undefined>;
-    fetch?: SearchFetch;
-    limit?: number;
-}): Promise<EvidenceCard[]>;
-export {};