@longtable/cli 0.1.44 → 0.1.47

package/README.md

@@ -269,16 +269,17 @@ deduplicates, ranks, and labels results as evidence cards. Some sources work
 without keys, some require a contact email, and some need API keys for reliable
 use.
 
-Publisher access is configured separately through environment variables and
-DOI probes. `longtable search setup` checks Elsevier, Springer Nature, Wiley,
-and Taylor & Francis credentials or TDM tokens without storing secrets.
+Scholarly access is configured separately through `longtable access setup`.
+It records readiness for metadata, OA full text, institutional access,
+publisher API/TDM credentials, and manual PDFs without storing secrets.
+Publisher probes cover Elsevier, Springer Nature, Wiley, and Taylor & Francis.
 
 Citation support should be checked explicitly. A reference can be useful as
 background while still failing to support the specific claim attached to it.
 
 ```bash
-longtable search setup
-longtable search probe --doi "10.1016/example" --publisher elsevier
+longtable access setup
+longtable access probe --doi "10.1016/example" --publisher elsevier
 longtable search --query "trust calibration measurement" --intent measurement
 longtable search --query "trust calibration measurement" --publisher-access --json
 longtable search --query "trust calibration citation support" --intent citation --record

package/dist/cli.js

@@ -9,7 +9,7 @@ import { dirname, join, resolve } from "node:path";
 import { homedir } from "node:os";
 import { fileURLToPath } from "node:url";
 import { classifyCheckpointTrigger } from "@longtable/checkpoints";
-import { assessSearchSourceCapabilities, buildResearchSearchIntent, buildSearchCapabilitySnapshot, parsePublisherTarget, probePublisherAccess, publisherConfigs, runResearchSearch, searchCapabilitySnapshotPath, summarizeConfiguredPublisherAccess } from "./search/index.js";
+import { assessSearchSourceCapabilities, buildResearchSearchIntent, parsePublisherTarget, probePublisherAccess, publisherConfigs, runResearchSearch, SEARCH_SOURCES, 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";
@@ -49,8 +49,35 @@ const require = createRequire(import.meta.url);
 const LONGTABLE_PACKAGE_VERSION = String(require("../package.json").version ?? "0.0.0");
 const LONGTABLE_MCP_SERVER_NAME = "longtable-state";
 const LONGTABLE_MCP_PACKAGE_VERSION = LONGTABLE_PACKAGE_VERSION;
+const LONGTABLE_MCP_PACKAGE_SPEC = `@longtable/mcp@${LONGTABLE_MCP_PACKAGE_VERSION}`;
 const LONGTABLE_MCP_MARKER_START = "# LongTable state MCP START";
 const LONGTABLE_MCP_MARKER_END = "# LongTable state MCP END";
+const LONGTABLE_MCP_MANAGED_TOOLS = [
+    "read_project",
+    "read_session",
+    "inspect_workspace",
+    "create_workspace",
+    "begin_interview",
+    "append_interview_turn",
+    "summarize_interview",
+    "summarize_research_specification",
+    "read_research_specification",
+    "cancel_interview",
+    "confirm_first_research_shape",
+    "confirm_research_specification",
+    "pending_questions",
+    "evaluate_checkpoint",
+    "create_question",
+    "elicit_question",
+    "render_question",
+    "append_decision",
+    "regenerate_current"
+];
+const LONGTABLE_MCP_RESEARCH_SPECIFICATION_TOOLS = [
+    "summarize_research_specification",
+    "read_research_specification",
+    "confirm_research_specification"
+];
 function style(text, prefix) {
     return `${prefix}${text}${ANSI.reset}`;
 }
@@ -84,7 +111,7 @@ function renderInterviewLaunchSteps(provider) {
         `2. run \`${command}\``,
         "3. invoke `$longtable-interview`",
         "",
-        "The interview will create or resume `.longtable/`, build a First Research Shape, and use option UI only for the final confirmation."
+        "The interview will create or resume `.longtable/`, may store a short First Research Shape handle, and uses option UI for the final Research Specification confirmation."
     ]);
 }
 function renderProgressBar(current, total) {
@@ -109,10 +136,11 @@ function usage() {
         "  longtable show [--json] [--path <file>]",
         "  longtable install [--json] [--path <file>] [--runtime-path <file>]",
         "  longtable mcp install [--provider codex|claude|all] [--write] [--checkpoint-ui off|interactive|strong] [--json] [--codex-config <path>] [--claude-settings <path>] [--package <spec>]",
+        "  longtable access setup [--doi <doi>] [--json]",
+        "  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 setup [--doi <doi>] [--json]",
-        "  longtable search doctor [--doi <doi>] [--publisher auto|elsevier|springer_nature|wiley|taylor_francis|all] [--json]",
-        "  longtable search probe --doi <doi> [--publisher auto|elsevier|springer_nature|wiley|taylor_francis] [--json]",
         "  longtable sentinel --prompt <text> [--cwd <path>] [--json] [--record]",
         "  longtable team --prompt <text> [--role <role[,role]>] [--debate] [--rounds 3|5] [--cwd <path>] [--json]",
         "  longtable ask [--prompt <text>] [--print] [--json] [--setup <path>] [--cwd <path>]",
@@ -154,7 +182,7 @@ 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", "decide", "sentinel", "team", "search"].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", "decide", "sentinel", "team", "access", "search"].includes(command);
     let startIndex = 1;
     if (modeCommand) {
         subcommand = undefined;
@@ -163,7 +191,7 @@ function parseArgs(argv) {
     else if (command === "codex" || command === "claude" || command === "mcp") {
         startIndex = 2;
     }
-    else if (command === "search" && maybeSubcommand && !maybeSubcommand.startsWith("--")) {
+    else if ((command === "access" || command === "search") && maybeSubcommand && !maybeSubcommand.startsWith("--")) {
         subcommand = maybeSubcommand;
         startIndex = 2;
     }
@@ -1130,7 +1158,7 @@ function resolveMcpProviders(value) {
 function resolveMcpPackageSpec(args) {
     return typeof args.package === "string" && args.package.trim()
         ? args.package.trim()
-        : `@longtable/mcp@${LONGTABLE_MCP_PACKAGE_VERSION}`;
+        : LONGTABLE_MCP_PACKAGE_SPEC;
 }
 function resolveCodexMcpConfigPath(args) {
     return resolve(normalizeUserPath(typeof args["codex-config"] === "string" && args["codex-config"].trim()
@@ -1161,6 +1189,12 @@ function renderCodexMcpBlock(serverName, command, mcpArgs) {
         `[mcp_servers.${serverName}]`,
         `command = ${escapeTomlString(command)}`,
         `args = [${mcpArgs.map((arg) => escapeTomlString(arg)).join(", ")}]`,
+        "",
+        ...LONGTABLE_MCP_MANAGED_TOOLS.flatMap((tool) => [
+            `[mcp_servers.${serverName}.tools.${tool}]`,
+            "approval_mode = \"approve\"",
+            ""
+        ]),
         LONGTABLE_MCP_MARKER_END
     ].join("\n");
 }
@@ -1184,10 +1218,55 @@ function codexMcpElicitationsAllowed(config) {
 function codexLongTableMcpConfigured(config) {
     return new RegExp(`\\[mcp_servers\\.${LONGTABLE_MCP_SERVER_NAME.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}\\]`).test(config);
 }
+function codexLongTableMcpPackageSpec(config) {
+    const serverName = LONGTABLE_MCP_SERVER_NAME.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+    const match = new RegExp(`\\[mcp_servers\\.${serverName}\\][\\s\\S]*?(?=\\n\\[|$)`).exec(config);
+    if (!match) {
+        return undefined;
+    }
+    const packageMatch = /@longtable\/mcp@[A-Za-z0-9._~+:-]+/.exec(match[0]);
+    return packageMatch?.[0];
+}
+function codexLongTableMcpToolConfigured(config, tool) {
+    const serverName = LONGTABLE_MCP_SERVER_NAME.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+    const escapedTool = tool.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
+    return new RegExp(`\\[mcp_servers\\.${serverName}\\.tools\\.${escapedTool}\\]`).test(config);
+}
+function missingCodexLongTableMcpTools(config) {
+    if (!codexLongTableMcpConfigured(config)) {
+        return [...LONGTABLE_MCP_MANAGED_TOOLS];
+    }
+    return LONGTABLE_MCP_MANAGED_TOOLS.filter((tool) => !codexLongTableMcpToolConfigured(config, tool));
+}
+function preserveNonLongTableSectionsFromMarkedBlock(block, serverName) {
+    const body = block
+        .replace(LONGTABLE_MCP_MARKER_START, "")
+        .replace(LONGTABLE_MCP_MARKER_END, "")
+        .trim();
+    if (!body) {
+        return "";
+    }
+    const sections = body.split(/(?=^\[[^\]]+\])/m);
+    const serverHeader = `[mcp_servers.${serverName}]`;
+    const toolPrefix = `[mcp_servers.${serverName}.tools.`;
+    return sections
+        .map((section) => section.trim())
+        .filter(Boolean)
+        .filter((section) => {
+        const header = section.split(/\r?\n/, 1)[0]?.trim() ?? "";
+        return header !== serverHeader && !header.startsWith(toolPrefix);
+    })
+        .join("\n\n");
+}
 function replaceMarkedCodexMcpBlock(existing, block, serverName) {
-    const markerPattern = new RegExp(`${LONGTABLE_MCP_MARKER_START.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}[\\s\\S]*?${LONGTABLE_MCP_MARKER_END.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}\\n?`, "m");
-    const serverPattern = new RegExp(`\\n?\\[mcp_servers\\.${serverName.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}\\][\\s\\S]*?(?=\\n\\[|$)`, "m");
-    const trimmed = existing.replace(markerPattern, "").replace(serverPattern, "").trimEnd();
+    const markerPattern = new RegExp(`${LONGTABLE_MCP_MARKER_START.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}[\\s\\S]*?${LONGTABLE_MCP_MARKER_END.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}\\n?`);
+    const serverPattern = new RegExp(`\\n?\\[mcp_servers\\.${serverName.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}\\][\\s\\S]*?(?=\\n\\[|$)`);
+    const toolPattern = new RegExp(`\\n?\\[mcp_servers\\.${serverName.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}\\.tools\\.[^\\]]+\\][\\s\\S]*?(?=\\n\\[|$)`, "g");
+    const withoutMarked = existing.replace(markerPattern, (matched) => {
+        const preserved = preserveNonLongTableSectionsFromMarkedBlock(matched, serverName);
+        return preserved ? `${preserved}\n\n` : "";
+    });
+    const trimmed = withoutMarked.replace(toolPattern, "").replace(serverPattern, "").trimEnd();
     return trimmed ? `${trimmed}\n\n${block}\n` : `${block}\n`;
 }
 async function writeCodexMcpConfig(path, block, serverName, options = {}) {
@@ -1466,6 +1545,8 @@ async function collectDoctorStatus(args) {
     const codexMcpConfig = existsSync(codexMcpConfigPath)
         ? await readFile(codexMcpConfigPath, "utf8")
         : "";
+    const codexMcpPackageSpec = codexLongTableMcpPackageSpec(codexMcpConfig);
+    const missingMcpTools = missingCodexLongTableMcpTools(codexMcpConfig);
     const codexHooksPath = resolveCodexHooksPath(args);
     const codexHooksContent = existsSync(codexHooksPath)
         ? await readFile(codexHooksPath, "utf8")
@@ -1501,6 +1582,10 @@ async function collectDoctorStatus(args) {
                 mcpConfigPath: codexMcpConfigPath,
                 mcpConfigExists: existsSync(codexMcpConfigPath),
                 longtableMcpConfigured: codexLongTableMcpConfigured(codexMcpConfig),
+                ...(codexMcpPackageSpec ? { mcpPackageSpec: codexMcpPackageSpec } : {}),
+                expectedMcpPackageSpec: LONGTABLE_MCP_PACKAGE_SPEC,
+                missingMcpTools,
+                missingResearchSpecificationMcpTools: missingMcpTools.filter((tool) => LONGTABLE_MCP_RESEARCH_SPECIFICATION_TOOLS.includes(tool)),
                 mcpElicitationsAllowed: codexMcpElicitationsAllowed(codexMcpConfig),
                 hooksPath: codexHooksPath,
                 hooksExists: existsSync(codexHooksPath),
@@ -1546,6 +1631,11 @@ function renderDoctorStatus(status) {
             : []),
         `- MCP config: ${status.providers.codex.mcpConfigExists ? "present" : "missing"} (${status.providers.codex.mcpConfigPath})`,
         `- LongTable MCP: ${status.providers.codex.longtableMcpConfigured ? "configured" : "missing"}`,
+        `- MCP package: ${status.providers.codex.mcpPackageSpec ?? "unknown"}${status.providers.codex.mcpPackageSpec === status.providers.codex.expectedMcpPackageSpec ? "" : ` (expected ${status.providers.codex.expectedMcpPackageSpec})`}`,
+        `- MCP managed tools: ${LONGTABLE_MCP_MANAGED_TOOLS.length - status.providers.codex.missingMcpTools.length}/${LONGTABLE_MCP_MANAGED_TOOLS.length} configured`,
+        ...(status.providers.codex.missingResearchSpecificationMcpTools.length > 0
+            ? [`- Research Specification MCP tools: missing ${status.providers.codex.missingResearchSpecificationMcpTools.join(", ")}`]
+            : ["- Research Specification MCP tools: complete"]),
         `- MCP elicitation approval: ${status.providers.codex.mcpElicitationsAllowed ? "allowed" : "not allowed"}`,
         `- Codex hooks file: ${status.providers.codex.hooksExists ? "present" : "missing"} (${status.providers.codex.hooksPath})`,
         `- codex_hooks feature: ${status.providers.codex.codexHooksEnabled ? "enabled" : "missing"}`,
@@ -1594,6 +1684,9 @@ function renderDoctorStatus(status) {
     const canFix = status.providers.codex.missingSkills.length > 0 ||
         status.providers.claude.missingSkills.length > 0 ||
         status.providers.codex.legacyPromptFilesInstalled.length > 0 ||
+        !status.providers.codex.longtableMcpConfigured ||
+        status.providers.codex.mcpPackageSpec !== status.providers.codex.expectedMcpPackageSpec ||
+        status.providers.codex.missingMcpTools.length > 0 ||
         !status.providers.codex.codexHooksEnabled ||
         status.providers.codex.missingManagedHookEvents.length > 0 ||
         (status.setupExists &&
@@ -1604,6 +1697,11 @@ function renderDoctorStatus(status) {
     if (!status.providers.codex.codexHooksEnabled || status.providers.codex.missingManagedHookEvents.length > 0) {
         nextActions.push("longtable codex install-hooks");
     }
+    if (!status.providers.codex.longtableMcpConfigured ||
+        status.providers.codex.mcpPackageSpec !== status.providers.codex.expectedMcpPackageSpec ||
+        status.providers.codex.missingMcpTools.length > 0) {
+        nextActions.push("longtable mcp install --provider codex --write");
+    }
     if (!status.setupExists) {
         nextActions.push("longtable setup --provider codex");
     }
@@ -1643,7 +1741,7 @@ function renderRepairSummary(repair) {
         }
     }
     if (repair.writtenRuntimeConfigs.length > 0) {
-        lines.push("- wrote runtime configs:");
+        lines.push("- wrote configs:");
         for (const target of repair.writtenRuntimeConfigs) {
             lines.push(`  - ${target.provider}: ${target.path}`);
         }
@@ -1699,6 +1797,21 @@ async function repairDoctorStatus(args, status) {
         writtenRuntimeConfigs: [],
         skipped: []
     };
+    const mcpRepairNeeded = !status.providers.codex.longtableMcpConfigured ||
+        status.providers.codex.mcpPackageSpec !== status.providers.codex.expectedMcpPackageSpec ||
+        status.providers.codex.missingMcpTools.length > 0;
+    if (mcpRepairNeeded) {
+        const mcpConfigPath = resolveDoctorCodexMcpConfigPath(args);
+        const block = renderCodexMcpBlock(LONGTABLE_MCP_SERVER_NAME, "npx", ["-y", LONGTABLE_MCP_PACKAGE_SPEC]);
+        await writeCodexMcpConfig(mcpConfigPath, block, LONGTABLE_MCP_SERVER_NAME, {
+            enableElicitations: status.providers.codex.mcpElicitationsAllowed
+        });
+        repair.writtenRuntimeConfigs.push({
+            provider: "codex",
+            path: mcpConfigPath,
+            format: "toml"
+        });
+    }
     if (status.providers.codex.missingSkills.length > 0) {
         repair.installedCodexSkills = (await installCodexSkills(roles, codexDir, skillSurface)).map((skill) => skill.name);
     }
@@ -1789,6 +1902,11 @@ const QUESTION_AUDIT_FIXTURES = [
         prompt: "Protected decision closure pressure: measurement. User prompt: Implement the plan.",
         expectedKinds: ["research_commitment"]
     },
+    {
+        id: "scholarly_access_policy",
+        prompt: "메타분석 논문들의 PDF와 full text를 수집해서 원문 기반으로 코딩해줘.",
+        expectedKinds: ["evidence_risk"]
+    },
     {
         id: "low_stakes_copyedit",
         prompt: "문장 끝 공백만 정리해줘.",
@@ -2347,6 +2465,86 @@ async function recordEvidenceRun(run, workingDirectory) {
     await syncCurrentWorkspaceView(context);
     return evidencePath;
 }
+function nowIso() {
+    return new Date().toISOString();
+}
+function uniqueAccessRoutes(routes) {
+    return [...new Set(routes)];
+}
+function accessReadinessPath(home = homedir()) {
+    return join(home, ".longtable", "access-readiness.json");
+}
+function readAccessReadinessProfile() {
+    const path = accessReadinessPath();
+    if (!existsSync(path)) {
+        return undefined;
+    }
+    try {
+        return JSON.parse(readFileSync(path, "utf8"));
+    }
+    catch {
+        return undefined;
+    }
+}
+function hasPublisherCredentialSignal(records) {
+    return records.some((record) => record.presentEnv.length > 0 || record.credentialStatus !== "missing");
+}
+function readinessPublisherRecord(record) {
+    const safeRecord = { ...record };
+    delete safeRecord.evidenceSnippet;
+    return safeRecord;
+}
+function inferAccessRoutes(records) {
+    const routes = ["metadata"];
+    if (hasPublisherCredentialSignal(records)) {
+        routes.push("publisher_tdm");
+    }
+    return routes;
+}
+function buildAccessReadinessProfile(options) {
+    const publisherRecords = options.publisherRecords ?? summarizeConfiguredPublisherAccess(env);
+    const routes = uniqueAccessRoutes(options.routes?.length ? options.routes : inferAccessRoutes(publisherRecords));
+    const disabled = options.readiness === "disabled";
+    const institutionalMode = options.institutionalAccessMode;
+    const institutionalAccess = routes.includes("institutional")
+        ? {
+            available: true,
+            mode: institutionalMode ?? "unknown",
+            verified: false,
+            note: "LongTable records institutional access readiness only. The researcher must complete VPN/proxy/library login directly."
+        }
+        : undefined;
+    return {
+        version: 1,
+        updatedAt: nowIso(),
+        readiness: options.readiness,
+        metadataSources: [...SEARCH_SOURCES],
+        routes: disabled ? [] : routes,
+        ...(institutionalAccess ? { institutionalAccess } : {}),
+        publisherTdm: disabled
+            ? "deferred"
+            : routes.includes("publisher_tdm")
+                ? hasPublisherCredentialSignal(publisherRecords) ? "configured" : "unknown"
+                : "not_configured",
+        oaOnly: !disabled && routes.includes("oa_full_text") && !routes.includes("institutional") && !routes.includes("publisher_tdm"),
+        manualPdfAllowed: !disabled && routes.includes("manual_pdf"),
+        storesSecrets: false,
+        requiresCheckpointBeforeSearch: options.readiness === "deferred",
+        requiresCheckpointBeforeFullText: options.readiness !== "disabled",
+        ...(disabled ? {} : {
+            publisherAccess: {
+                contactEmailPresent: Boolean(env.LONGTABLE_CONTACT_EMAIL?.trim()),
+                records: publisherRecords.map(readinessPublisherRecord)
+            }
+        })
+    };
+}
+async function saveAccessReadinessProfile(profile) {
+    const profilePath = accessReadinessPath();
+    await mkdir(dirname(profilePath), { recursive: true });
+    await writeJsonFile(profilePath, profile);
+    return profilePath;
+}
 function renderPublisherAccessRecord(record) {
     const envSummary = record.missingEnv.length > 0
         ? `missing ${record.missingEnv.join(", ")}`
@@ -2381,12 +2579,6 @@ function renderPublisherAccessRecords(title, records, capabilityPath) {
     }
     return lines.join("\n");
 }
-async function saveSearchCapabilityRecords(records) {
-    const snapshotPath = searchCapabilitySnapshotPath();
-    await mkdir(dirname(snapshotPath), { recursive: true });
-    await writeJsonFile(snapshotPath, buildSearchCapabilitySnapshot(records, env));
-    return snapshotPath;
-}
 async function probeAllPublishers(doi) {
     const records = [];
     for (const publisher of publisherConfigs()) {
@@ -2398,9 +2590,48 @@ async function probeAllPublishers(doi) {
     }
     return records;
 }
-async function runSearchProbe(args) {
+function renderAccessReadinessProfile(profile, profilePath = accessReadinessPath()) {
+    const lines = [
+        "LongTable Scholarly Access Readiness",
+        `- profile: ${profilePath}`,
+        `- readiness: ${profile.readiness}`,
+        `- routes: ${profile.routes.length > 0 ? profile.routes.join(", ") : "none"}`,
+        `- metadata sources: ${profile.metadataSources.join(", ")}`,
+        `- OA-only: ${profile.oaOnly ? "yes" : "no"}`,
+        `- manual PDF allowed: ${profile.manualPdfAllowed ? "yes" : "no"}`,
+        `- publisher/TDM: ${profile.publisherTdm}`,
+        `- stores secrets: ${profile.storesSecrets ? "yes" : "no"}`,
+        `- checkpoint before search: ${profile.requiresCheckpointBeforeSearch ? "yes" : "no"}`,
+        `- checkpoint before full text: ${profile.requiresCheckpointBeforeFullText ? "yes" : "no"}`
+    ];
+    if (profile.institutionalAccess) {
+        lines.push(`- institutional access: ${profile.institutionalAccess.mode}; verified: no`);
+        lines.push(`  note: ${profile.institutionalAccess.note}`);
+    }
+    if (profile.publisherAccess) {
+        lines.push(`- contact email: ${profile.publisherAccess.contactEmailPresent ? "present" : "missing"}`);
+        lines.push(`- publisher adapters: ${profile.publisherAccess.records.length}`);
+    }
+    return lines.join("\n");
+}
+function renderAccessDoctor(profile, records, profilePath) {
+    const metadataCapabilities = assessSearchSourceCapabilities([...SEARCH_SOURCES], env);
+    const lines = [
+        "LongTable Scholarly Access Doctor",
+        `- readiness profile: ${profile ? "present" : "missing"} (${profilePath})`,
+        `- metadata sources: ${metadataCapabilities.map((capability) => `${capability.source}:${capability.enabled ? "available" : "needs_config"}`).join(", ")}`,
+        "- institutional access: LongTable cannot verify VPN/proxy/SSO until the researcher logs in.",
+        "- secrets: LongTable stores env var names and capability status only, never credential values.",
+        renderPublisherAccessRecords("Publisher API/TDM adapters", records)
+    ];
+    if (!profile) {
+        lines.push("- next: run `longtable access setup` before PDF collection or full-text extraction.");
+    }
+    return lines.join("\n");
+}
+async function runAccessProbe(args) {
     if (typeof args.doi !== "string" || !args.doi.trim()) {
-        throw new Error("`longtable search probe` requires --doi <doi>.");
+        throw new Error("`longtable access probe` requires --doi <doi>.");
     }
     const publisher = parsePublisherTarget(args.publisher);
     const record = await probePublisherAccess({
@@ -2416,7 +2647,7 @@ async function runSearchProbe(args) {
     }
     return [record];
 }
-async function runSearchDoctor(args) {
+async function collectAccessDoctorRecords(args) {
     let records;
     if (typeof args.doi === "string" && args.doi.trim()) {
         if (args.publisher === "all") {
@@ -2434,104 +2665,148 @@ async function runSearchDoctor(args) {
     else {
         records = summarizeConfiguredPublisherAccess(env);
     }
-    const snapshotPath = searchCapabilitySnapshotPath();
-    const snapshotExists = existsSync(snapshotPath);
+    return records;
+}
+async function runAccessDoctor(args) {
+    const records = await collectAccessDoctorRecords(args);
+    const profilePath = accessReadinessPath();
+    const profile = readAccessReadinessProfile();
     if (args.json === true) {
         console.log(JSON.stringify({
-            capabilityFile: snapshotPath,
-            capabilityFileExists: snapshotExists,
+            readinessFile: profilePath,
+            readinessFileExists: Boolean(profile),
+            readiness: profile,
+            metadataSources: assessSearchSourceCapabilities([...SEARCH_SOURCES], env),
             records
         }, null, 2));
     }
     else {
-        console.log(renderPublisherAccessRecords("LongTable Search Publisher Access Doctor", records, snapshotPath));
-        if (!snapshotExists) {
-            console.log("- saved capabilities: none yet; run `longtable search setup` to record non-secret capability status.");
-        }
+        console.log(renderAccessDoctor(profile, records, profilePath));
     }
     return records;
 }
-async function promptPublisherDoi(rl, label, defaultDoi) {
-    const prompt = defaultDoi
-        ? `${label} test DOI [${defaultDoi}, Enter to reuse, skip to skip]: `
-        : `${label} test DOI (Enter to skip): `;
-    const answer = (await rl.question(prompt)).trim();
-    if (!answer && defaultDoi) {
-        return defaultDoi;
-    }
-    if (!answer || /^skip$/i.test(answer)) {
-        return undefined;
+async function publisherRecordsForAccessSetup(args, routes) {
+    const defaultDoi = typeof args.doi === "string" ? args.doi : undefined;
+    if (!routes.includes("publisher_tdm")) {
+        return summarizeConfiguredPublisherAccess(env);
     }
-    return answer;
-}
-async function runInteractiveSearchSetup(defaultDoi) {
-    const rl = createInterface({ input, output });
-    const records = [];
-    try {
-        console.log("LongTable publisher access setup");
-        console.log("LongTable does not store API keys or TDM tokens. It reads environment variables and records only non-secret capability results.");
-        console.log("");
-        for (const publisher of publisherConfigs()) {
-            console.log(`${publisher.label}`);
-            console.log(`  required env: ${publisher.requiredEnv.join(", ")}`);
-            if (publisher.optionalEnv.length > 0) {
-                console.log(`  optional env: ${publisher.optionalEnv.join(", ")}`);
-            }
-            console.log(`  ${publisher.setupHint}`);
-            const doi = await promptPublisherDoi(rl, publisher.label, defaultDoi);
-            if (doi) {
-                records.push(await probePublisherAccess({
-                    doi,
-                    publisher: publisher.publisher,
-                    env
-                }));
-            }
-            else {
-                const summary = summarizeConfiguredPublisherAccess(env)
-                    .find((record) => record.publisher === publisher.publisher);
-                if (summary) {
-                    records.push(summary);
-                }
-            }
-            console.log(renderPublisherAccessRecord(records[records.length - 1]));
-            console.log("");
-        }
+    if (defaultDoi) {
+        return probeAllPublishers(defaultDoi);
     }
-    finally {
-        rl.close();
+    if (input.isTTY && output.isTTY && args.json !== true) {
+        const doi = await promptText("Optional DOI for publisher/TDM probing. Leave blank to record env-var readiness only.", false);
+        return doi
+            ? await probeAllPublishers(doi)
+            : summarizeConfiguredPublisherAccess(env);
     }
-    return records;
+    return summarizeConfiguredPublisherAccess(env);
 }
-async function runSearchSetup(args) {
-    const defaultDoi = typeof args.doi === "string" ? args.doi : undefined;
-    const records = input.isTTY && output.isTTY && args.json !== true
-        ? await runInteractiveSearchSetup(defaultDoi)
-        : defaultDoi
-            ? await probeAllPublishers(defaultDoi)
-            : summarizeConfiguredPublisherAccess(env);
-    const snapshotPath = await saveSearchCapabilityRecords(records);
+async function runInteractiveAccessSetup(args) {
+    const readiness = await promptChoice("Scholarly Access Readiness\n\nWill this machine/account use scholarly search or full-text access?", [
+        { id: "configured", label: "Configure now", description: "Record access capability without storing secrets." },
+        { id: "deferred", label: "Ask later", description: "Defer setup and require an access checkpoint before search or extraction." },
+        { id: "disabled", label: "Do not use", description: "This project will use metadata/manual notes without scholarly full-text access." }
+    ]);
+    if (readiness !== "configured") {
+        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: "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." },
+        { id: "manual_pdf", label: "Manual PDFs", description: "Researcher supplies PDFs; LongTable organizes/probes allowed extraction." },
+        { id: "unknown", label: "Unknown", description: "Keep access uncertain and require a checkpoint before full-text work." }
+    ]);
+    const routes = uniqueAccessRoutes(routeSelections.length > 0 ? routeSelections : ["metadata"]);
+    const institutionalAccessMode = routes.includes("institutional")
+        ? await promptChoice("How will institutional access be completed? The researcher handles login/MFA directly.", [
+            { id: "vpn", label: "VPN", description: "Researcher connects through school or institutional VPN." },
+            { id: "library_proxy", label: "Library proxy", description: "Researcher uses proxy links or library resolver." },
+            { id: "browser_sso", label: "Browser SSO", description: "Researcher logs into library/publisher SSO in the browser." },
+            { id: "unknown", label: "Unknown", description: "The route exists but is not yet specified." }
+        ])
+        : undefined;
+    const publisherRecords = await publisherRecordsForAccessSetup(args, routes);
+    return buildAccessReadinessProfile({
+        readiness,
+        routes,
+        institutionalAccessMode,
+        publisherRecords
+    });
+}
+async function runAccessSetup(args) {
+    const records = typeof args.doi === "string" && args.doi.trim()
+        ? await probeAllPublishers(args.doi)
+        : summarizeConfiguredPublisherAccess(env);
+    const profile = input.isTTY && output.isTTY && args.json !== true
+        ? await runInteractiveAccessSetup(args)
+        : buildAccessReadinessProfile({
+            readiness: "configured",
+            routes: inferAccessRoutes(records),
+            publisherRecords: records
+        });
+    const profilePath = await saveAccessReadinessProfile(profile);
     if (args.json === true) {
         console.log(JSON.stringify({
-            capabilityFile: snapshotPath,
-            snapshot: buildSearchCapabilitySnapshot(records, env)
+            readinessFile: profilePath,
+            profile
         }, null, 2));
         return;
     }
-    console.log(renderPublisherAccessRecords("LongTable Search Publisher Access Setup", records, snapshotPath));
+    console.log(renderAccessReadinessProfile(profile, profilePath));
 }
-async function runSearch(subcommand, args) {
-    if (subcommand === "probe") {
-        await runSearchProbe(args);
+async function runAccessStatus(args) {
+    const profilePath = accessReadinessPath();
+    const profile = readAccessReadinessProfile();
+    if (args.json === true) {
+        console.log(JSON.stringify({
+            readinessFile: profilePath,
+            readinessFileExists: Boolean(profile),
+            readiness: profile
+        }, null, 2));
         return;
     }
-    if (subcommand === "doctor" || subcommand === "status") {
-        await runSearchDoctor(args);
+    if (!profile) {
+        console.log([
+            "LongTable Scholarly Access Readiness",
+            `- profile: missing (${profilePath})`,
+            "- next: run `longtable access setup` before PDF collection or full-text extraction."
+        ].join("\n"));
         return;
     }
+    console.log(renderAccessReadinessProfile(profile, profilePath));
+}
+async function runAccess(subcommand, args) {
     if (subcommand === "setup") {
-        await runSearchSetup(args);
+        await runAccessSetup(args);
+        return;
+    }
+    if (subcommand === "status") {
+        await runAccessStatus(args);
         return;
     }
+    if (subcommand === "doctor") {
+        await runAccessDoctor(args);
+        return;
+    }
+    if (subcommand === "probe") {
+        await runAccessProbe(args);
+        return;
+    }
+    if (!subcommand) {
+        await runAccessStatus(args);
+        return;
+    }
+    throw new Error(`Unknown access subcommand: ${subcommand}`);
+}
+function movedSearchAccessCommand(subcommand) {
+    return new Error(`\`longtable search ${subcommand}\` has moved. Use \`longtable access ${subcommand}\`.`);
+}
+async function runSearch(subcommand, args) {
+    if (subcommand === "setup" || subcommand === "doctor" || subcommand === "status" || subcommand === "probe") {
+        throw movedSearchAccessCommand(subcommand);
+    }
     if (subcommand) {
         throw new Error(`Unknown search subcommand: ${subcommand}`);
     }
@@ -3524,6 +3799,10 @@ async function main() {
         await runMcpSubcommand(subcommand, values);
         return;
     }
+    if (command === "access") {
+        await runAccess(subcommand, values);
+        return;
+    }
     if (command === "search") {
         await runSearch(subcommand, values);
         return;

package/dist/longtable-codex-native-hook.js

@@ -131,6 +131,11 @@ function looksLikeResearchCommitmentPrompt(prompt) {
         /\b(change|revise|update|replace|reframe|modify|alter)\b/i.test(prompt) ||
         /바꾸|변경|수정|교체|전환|재설정/.test(prompt));
 }
+function looksLikeAccessSensitiveResearchAction(prompt) {
+    const normalized = prompt.trim();
+    return /\b(pdf|full[- ]?text|tdm|publisher api|institutional access|library login|vpn|proxy|subscription|paper collection|source collection|corpus|download)\b/i.test(normalized)
+        || /PDF|원문|전문|기관\s*구독|기관구독|구독|VPN|프록시|도서관|라이브러리|TDM|논문\s*수집|문헌\s*수집|코퍼스|다운로드/.test(normalized);
+}
 function looksLikeQuestionGenerationPrompt(prompt) {
     return /\b(needed questions?|necessary questions?|question generation|clarifying questions?|ask questions?)\b/i.test(prompt)
         || /필요한\s*질문|질문을\s*(모두|많이|생성)|질문\s*생성|물어봐|질문해/.test(prompt);
@@ -184,11 +189,12 @@ function shouldSurfaceInterviewContext(prompt) {
     return looksLikeExplicitInterviewPrompt(prompt) || looksLikeResearchStateConfirmationPrompt(prompt);
 }
 function shouldCreateRequiredQuestionsForPrompt(prompt) {
-    return !looksLikeLongTableProductOrToolingPrompt(prompt) && looksLikeResearchCommitmentPrompt(prompt);
+    return !looksLikeLongTableProductOrToolingPrompt(prompt) &&
+        (looksLikeResearchCommitmentPrompt(prompt) || looksLikeAccessSensitiveResearchAction(prompt));
 }
 function shouldApplyProtectedDecisionClosure(runtime, prompt) {
     return Boolean(runtime.context.session.protectedDecision) &&
-        shouldCreateRequiredQuestionsForPrompt(prompt) &&
+        looksLikeResearchCommitmentPrompt(prompt) &&
         !looksLikeQuestionGenerationPrompt(prompt) &&
         !looksLikeMultiCommitmentChangePrompt(prompt);
 }

package/dist/project-session.d.ts

@@ -1,4 +1,4 @@
-import type { DecisionRecord, InvocationRecord, LongTableQuestionObligation, ProviderKind, QuestionOption, QuestionGenerationResult, QuestionOpportunity, QuestionSurface, QuestionRecord, ResearchState } from "@longtable/core";
+import type { DecisionRecord, InvocationRecord, LongTableQuestionObligation, ProviderKind, QuestionOption, QuestionCommitmentFamily, QuestionEpistemicBasis, QuestionGenerationResult, QuestionOpportunity, QuestionSurface, QuestionRecord, ResearchState } from "@longtable/core";
 import type { SetupPersistedOutput } from "@longtable/setup";
 export type ProjectDisagreementPreference = "synthesis_only" | "show_on_conflict" | "always_visible";
 export type StartInterviewSignal = "phenomenon" | "audience" | "artifact" | "evidence" | "assumption" | "decision_risk" | "voice";
@@ -221,6 +221,8 @@ export interface LongTableWorkspaceInspection {
         id: string;
         title: string;
         question: string;
+        commitmentFamily?: QuestionCommitmentFamily;
+        epistemicBasis?: QuestionEpistemicBasis;
         options: string[];
         required: boolean;
     }>;
@@ -235,6 +237,8 @@ export interface LongTableWorkspaceInspection {
         id: string;
         checkpointKey: string;
         summary: string;
+        commitmentFamily?: QuestionCommitmentFamily;
+        epistemicBasis?: QuestionEpistemicBasis;
         selectedOption?: string;
         timestamp: string;
     }>;
@@ -329,6 +333,8 @@ export declare function createWorkspaceQuestion(options: {
     displayReason?: string;
     provider?: ProviderKind;
     required?: boolean;
+    commitmentFamily?: QuestionCommitmentFamily;
+    epistemicBasis?: QuestionEpistemicBasis;
 }): Promise<{
     question: QuestionRecord;
     state: ResearchState;

package/dist/project-session.js

@@ -140,6 +140,15 @@ function renderResearchSpecificationSummary(specification, locale) {
     if (specification.methodAnalysis.analysisOptions.length > 0) {
         lines.push(`- ${korean ? "분석 옵션" : "Analysis options"}: ${specification.methodAnalysis.analysisOptions.join("; ")}`);
     }
+    if (specification.evidenceAccess.requiredSources?.length) {
+        lines.push(`- ${korean ? "필요 근거원" : "Required sources"}: ${specification.evidenceAccess.requiredSources.join("; ")}`);
+    }
+    if (specification.evidenceAccess.accessRequirements?.length) {
+        lines.push(`- ${korean ? "Corpus and Access Plan" : "Corpus and Access Plan"}: ${specification.evidenceAccess.accessRequirements.join("; ")}`);
+    }
+    if (specification.evidenceAccess.evidenceStandards?.length) {
+        lines.push(`- ${korean ? "근거 기준" : "Evidence standards"}: ${specification.evidenceAccess.evidenceStandards.join("; ")}`);
+    }
     if (specification.epistemicAlignment.conflictResolutionRule) {
         lines.push(`- ${korean ? "충돌 조정 규칙" : "Conflict rule"}: ${specification.epistemicAlignment.conflictResolutionRule}`);
     }
@@ -154,6 +163,43 @@ function renderResearchSpecificationSummary(specification, locale) {
     }
     return lines;
 }
+function renderResearchSpecificationStatus(session, locale) {
+    if (!session.firstResearchShape && !session.researchSpecification) {
+        return [];
+    }
+    const korean = locale === "ko";
+    if (!session.researchSpecification) {
+        return [
+            "",
+            korean ? "## Research Specification 상태" : "## Research Specification Status",
+            korean
+                ? "- 상태: First Research Shape는 있지만 Research Specification은 아직 없습니다."
+                : "- Status: First Research Shape exists, but Research Specification is missing.",
+            korean
+                ? "- 의미: First Research Shape는 짧은 핸들/재개 인덱스이며, 인터뷰 종료나 연구 명세 확정이 아닙니다."
+                : "- Meaning: First Research Shape is a short handle/resume index, not interview closure or a confirmed research specification.",
+            korean
+                ? "- 다음 프로토콜: 충분한 내용이 있으면 `summarize_research_specification`으로 preview를 만들고 `confirm_research_specification`으로 저장/한 질문 더/섹션 수정/열어두기를 확인합니다."
+                : "- Next protocol: when enough detail exists, run `summarize_research_specification` to create the preview, then `confirm_research_specification` to confirm, ask one more question, revise a section, or keep it open."
+        ];
+    }
+    const status = session.researchSpecification.confirmedAt
+        ? "confirmed"
+        : session.researchSpecification.status ?? "draft";
+    if (status === "confirmed") {
+        return [];
+    }
+    return [
+        "",
+        korean ? "## Research Specification 상태" : "## Research Specification Status",
+        korean
+            ? `- 상태: ${status}. Research Specification은 저장되어 있지만 아직 확정된 종료 지점이 아닙니다.`
+            : `- Status: ${status}. Research Specification exists, but it is not a confirmed closure point yet.`,
+        korean
+            ? "- 다음 프로토콜: 명세를 업데이트한 뒤 `confirm_research_specification`으로 다시 preview 확인을 받아야 합니다."
+            : "- Next protocol: update the specification, then return to `confirm_research_specification` for another preview confirmation."
+    ];
+}
 function buildCurrentGuide(project, session, recentInvocations = [], pendingQuestions = [], pendingObligations = []) {
     const locale = normalizeLocale(session.locale ?? project.locale);
     const openQuestions = session.openQuestions && session.openQuestions.length > 0
@@ -182,6 +228,7 @@ function buildCurrentGuide(project, session, recentInvocations = [], pendingQues
             `- 다음 액션: ${nextAction}`,
             `- 관점: ${session.requestedPerspectives.length > 0 ? session.requestedPerspectives.join(", ") : "auto"}`,
             `- disagreement: ${session.disagreementPreference}`,
+            ...renderResearchSpecificationStatus(session, locale),
             "",
             "## 열린 질문",
             ...openQuestions.map((question) => `- ${question}`),
@@ -201,7 +248,7 @@ function buildCurrentGuide(project, session, recentInvocations = [], pendingQues
                     "## 대기 중인 결정 질문",
                     ...pendingQuestions.map((record) => {
                         const options = formatQuestionOptionValues(record).join("/");
-                        return `- ${record.id}: ${record.prompt.question} (${options})`;
+                        return `- ${record.id}: ${record.prompt.question}${formatQuestionMetadata(record)} (${options})`;
                     }),
                     "- 답변 기록: `longtable decide --question <id> --answer <value>`"
                 ]
@@ -257,6 +304,7 @@ function buildCurrentGuide(project, session, recentInvocations = [], pendingQues
         `- Next action: ${nextAction}`,
         `- Perspectives: ${session.requestedPerspectives.length > 0 ? session.requestedPerspectives.join(", ") : "auto"}`,
         `- Disagreement: ${session.disagreementPreference}`,
+        ...renderResearchSpecificationStatus(session, locale),
         "",
         "## Open Questions",
         ...openQuestions.map((question) => `- ${question}`),
@@ -276,7 +324,7 @@ function buildCurrentGuide(project, session, recentInvocations = [], pendingQues
                 "## Pending Decision Questions",
                 ...pendingQuestions.map((record) => {
                     const options = formatQuestionOptionValues(record).join("/");
-                    return `- ${record.id}: ${record.prompt.question} (${options})`;
+                    return `- ${record.id}: ${record.prompt.question}${formatQuestionMetadata(record)} (${options})`;
                 }),
                 "- Record an answer: `longtable decide --question <id> --answer <value>`"
             ]
@@ -366,6 +414,13 @@ function formatQuestionOptionValues(record) {
     }
     return values;
 }
+function formatQuestionMetadata(record) {
+    const parts = [
+        record.commitmentFamily ? `commitment: ${record.commitmentFamily}` : "",
+        record.epistemicBasis ? `basis: ${record.epistemicBasis}` : ""
+    ].filter(Boolean);
+    return parts.length > 0 ? ` [${parts.join("; ")}]` : "";
+}
 function summarizeWorkspaceInspection(context, state) {
     const questions = state.questionLog ?? [];
     const pendingQuestions = questions.filter((record) => record.status === "pending");
@@ -426,6 +481,8 @@ function summarizeWorkspaceInspection(context, state) {
             id: record.id,
             title: record.prompt.title,
             question: record.prompt.question,
+            ...(record.commitmentFamily ? { commitmentFamily: record.commitmentFamily } : {}),
+            ...(record.epistemicBasis ? { epistemicBasis: record.epistemicBasis } : {}),
             options: formatQuestionOptionValues(record),
             required: record.prompt.required
         })),
@@ -440,6 +497,8 @@ function summarizeWorkspaceInspection(context, state) {
             id: record.id,
             checkpointKey: record.checkpointKey,
             summary: record.summary,
+            ...(record.commitmentFamily ? { commitmentFamily: record.commitmentFamily } : {}),
+            ...(record.epistemicBasis ? { epistemicBasis: record.epistemicBasis } : {}),
             ...(record.selectedOption ? { selectedOption: record.selectedOption } : {}),
             timestamp: record.timestamp
         })),
@@ -486,9 +545,12 @@ function buildProjectAgentsMd(project, session) {
         "- Begin exploratory work with clarifying or tension questions before recommending a direction.",
         "- For `$longtable-interview`, ask one natural-language question at a time, reflect with `LongTable hears: ...`, record turns when MCP is available, and avoid early reader/reviewer or theory/method/measurement classification.",
         "- Do not summarize `$longtable-interview` because a fixed number of turns has passed; wait for content-based readiness around research object, focal uncertainty, boundary, evidence/material, protected decision, and next action.",
+        "- First Research Shape is a short handle/resume index, not the default closure point.",
         "- After the First Research Shape, create a Research Specification when the interview has enough detail to preserve scope, construct ontology, theory framing, coding rules, method options, evidence/access requirements, epistemic alignment, protected decisions, open questions, and next actions.",
+        "- If a confirmed First Research Shape exists without a Research Specification, continue directly into the next Research Specification question instead of asking shape-level continue/revise/restart questions.",
+        "- If the researcher chooses `ask_one_more` or `revise_section` at Research Specification confirmation, answer that gap and return to the Research Specification Preview before ending the interview.",
         "- Do not let unrelated pending Researcher Checkpoints interrupt `$longtable-interview`; mention them only as separate unresolved checkpoints unless the researcher is confirming, saving, or recording a research decision.",
-        "- Use structured options only at the final First Research Shape confirmation or at true checkpoint boundaries.",
+        "- Use structured options at the final Research Specification confirmation, at explicit short-handle stop points, or at true checkpoint boundaries.",
         "- If you foreground role perspectives, disclose them with `LongTable consulted: ...`.",
         "- Keep one accountable synthesis, but do not hide meaningful disagreement.",
         ...(session.disagreementPreference === "always_visible"
@@ -1219,8 +1281,8 @@ function questionPriority(spec) {
     const requiredWeight = spec.kind === "research_commitment" || spec.required ? 20 : 0;
     return (byKey[spec.key] ?? 0) + confidenceWeight + requiredWeight;
 }
-function followUpQuestionOptions(first, second, third, fourth) {
-    return [first, second, third, ...(fourth ? [fourth] : [])];
+function followUpQuestionOptions(first, second, third, ...rest) {
+    return [first, second, third, ...rest];
 }
 export function buildQuestionOpportunitySpecs(prompt, options = {}) {
     const normalized = prompt.toLowerCase();
@@ -1285,8 +1347,26 @@ export function buildQuestionOpportunitySpecs(prompt, options = {}) {
         /\brandom[- ]?effects\b/i,
         /분석\s*계획|분석\s*방법|메타\s*분석|분석\s*(?:모형|모델)|통계\s*(?:모형|모델)|구조\s*방정식|경로\s*모형|조절효과|랜덤\s*효과/
     ]);
+    const accessCue = includesAny(normalized, [
+        /\b(pdf|full[- ]?text|tdm|publisher api|institutional access|library login|vpn|proxy|subscription|paper collection|source collection|corpus|download)\b/i,
+        /PDF|원문|전문|기관\s*구독|기관구독|구독|VPN|프록시|도서관|라이브러리|TDM|논문\s*수집|문헌\s*수집|코퍼스|다운로드/
+    ]);
     const decisionFamilyCount = [scopeCue, theoryCue, measurementCodingCue, methodCue, analysisCue]
         .filter(Boolean).length;
+    if (accessCue) {
+        push({
+            key: "scholarly_access_policy",
+            kind: "evidence_risk",
+            title: "Scholarly access policy",
+            question: "What scholarly access route should LongTable use before collecting PDFs, full text, or subscription-only evidence?",
+            whyNow: "Full-text access decisions can change the corpus, inclusion bias, reproducibility, and TDM permission boundary.",
+            options: followUpQuestionOptions({ value: "oa_only", label: "OA-only", description: "Use only open-access PDF or full text.", recommended: true }, { value: "institutional_access", label: "Institutional access", description: "Include VPN/proxy/library-login access after the researcher completes login." }, { value: "publisher_tdm", label: "Publisher API/TDM", description: "Use configured publisher API/TDM credentials and record entitlement checks." }, { value: "manual_pdf", label: "Manual PDFs", description: "Use PDFs supplied by the researcher and record provenance." }, { value: "metadata_only", label: "Metadata only", description: "Do not collect full text yet." }),
+            confidence: "high",
+            autoEligible: true,
+            required: true,
+            cues: ["scholarly_access", "full_text", "corpus"]
+        });
+    }
     if (decisionActionCue && decisionFamilyCount >= 2) {
         push({
             key: "research_direction_change_commitment",
@@ -1619,7 +1699,7 @@ export function buildQuestionOpportunitySpecs(prompt, options = {}) {
     }
     let selected = options.autoOnly === true ? specs.filter((spec) => spec.autoEligible) : specs;
     if (options.requiredOnly === true) {
-        selected = selected.filter((spec) => spec.kind === "research_commitment");
+        selected = selected.filter((spec) => spec.kind === "research_commitment" || spec.required);
     }
     if (normalized.includes("protected decision closure pressure")) {
         selected = selected.filter((spec) => spec.key === "protected_decision_closure");
@@ -1641,6 +1721,70 @@ export function generateQuestionOpportunities(prompt, options = {}) {
     };
 }
 const FOLLOW_UP_PROMPT_PREFIX = "Follow-up prompt:";
+function compactMetadataText(parts) {
+    return parts
+        .flatMap((part) => Array.isArray(part) ? part : [part])
+        .filter((part) => Boolean(part && part.trim()))
+        .join(" ")
+        .replace(/\s+/g, " ")
+        .trim()
+        .toLowerCase();
+}
+function textMatchesAny(text, patterns) {
+    return patterns.some((pattern) => pattern.test(text));
+}
+const COMMITMENT_FAMILY_BY_CHECKPOINT = [
+    [/product|meta_decision/, "product_policy"],
+    [/research_question|research_direction|scope|boundary|inclusion|exclusion/, "scope"],
+    [/theory|construct|conceptual/, "construct"],
+    [/measurement|coding|codebook|extraction/, "coding"],
+    [/method|analysis|panel_disagreement|team_debate|review/, "method"],
+    [/evidence|scholarly_access|source_authority/, "evidence"],
+    [/knowledge_gap|tacit_assumption|epistemic/, "epistemic_authority"]
+];
+function inferCommitmentFamily(input) {
+    const checkpointKey = (input.checkpointKey ?? "").toLowerCase();
+    const matched = COMMITMENT_FAMILY_BY_CHECKPOINT.find(([pattern]) => pattern.test(checkpointKey));
+    if (matched)
+        return matched[1];
+    if (input.triggerFamily === "meta_decision")
+        return "product_policy";
+    if (input.triggerFamily === "evidence")
+        return "evidence";
+    const text = compactMetadataText([input.title, input.question, input.prompt, input.rationale]);
+    if (textMatchesAny(text, [/checkpoint policy/, /hook ux/, /product language/, /\breadme\b/, /제품 언어|체크포인트 정책|훅|리드미/])) {
+        return "product_policy";
+    }
+    return undefined;
+}
+function inferEpistemicBasis(input) {
+    const text = compactMetadataText([input.title, input.question, input.prompt, input.rationale]);
+    const bases = [];
+    if (textMatchesAny(text, [/\bresearcher\b/, /\bhuman\b/, /\byour judgment\b/, /\byour knowledge\b/, /연구자|인간|사람|너의\s*판단|당신의\s*판단|내\s*지식|사용자/])) {
+        bases.push("researcher_knowledge");
+    }
+    if (textMatchesAny(text, [/\bproject state\b/, /\bworkspace\b/, /\bcurrent\.md\b/, /\.longtable\b/, /\bstate\.json\b/, /\bdataset\b/, /\bcodebook\b/, /\bcoding sheet\b/, /프로젝트\s*상태|워크스페이스|데이터셋|코드북|코딩\s*시트/])) {
+        bases.push("project_state");
+    }
+    if (textMatchesAny(text, [/\bexternal evidence\b/, /\bliterature\b/, /\bpaper\b/, /\bpdf\b/, /\bsource\b/, /\bcitation\b/, /\breference\b/, /\bfull[- ]?text\b/, /외부\s*근거|문헌|논문|원문|전문|출처|인용|레퍼런스/])) {
+        bases.push("external_evidence");
+    }
+    if (textMatchesAny(text, [/\bcodex\b/, /\bllm\b/, /\blanguage model\b/, /\bmodel judgment\b/, /\bai inference\b/, /\bassistant judgment\b/, /코덱스|언어\s*모델|모델\s*판단|AI\s*추론|LLM/])) {
+        bases.push("ai_inference");
+    }
+    const unique = [...new Set(bases)];
+    if (unique.length > 1)
+        return "mixed";
+    return unique[0];
+}
+function resolveQuestionRecordMetadata(input) {
+    const commitmentFamily = input.commitmentFamily ?? inferCommitmentFamily(input);
+    const epistemicBasis = input.epistemicBasis ?? inferEpistemicBasis(input);
+    return {
+        ...(commitmentFamily ? { commitmentFamily } : {}),
+        ...(epistemicBasis ? { epistemicBasis } : {})
+    };
+}
 function hasFollowUpPrompt(record, prompt) {
     return record.prompt.rationale.includes(`${FOLLOW_UP_PROMPT_PREFIX} ${prompt}`);
 }
@@ -1678,31 +1822,43 @@ export async function createWorkspaceFollowUpQuestions(options) {
     if (specsToCreate.length === 0) {
         return { questions: pendingMatches, state, created: false, alreadyAnswered: false };
     }
-    const questions = specsToCreate.map((spec) => ({
-        id: createId("question_record"),
-        createdAt,
-        updatedAt: createdAt,
-        status: "pending",
-        prompt: {
-            id: createId("question_prompt"),
-            checkpointKey: `follow_up_${spec.key}`,
+    const questions = specsToCreate.map((spec) => {
+        const checkpointKey = `follow_up_${spec.key}`;
+        const rationale = [
+            spec.whyNow,
+            `Question kind: ${spec.kind}`,
+            `Question confidence: ${spec.confidence}`,
+            `${FOLLOW_UP_PROMPT_PREFIX} ${options.prompt}`
+        ];
+        const metadata = resolveQuestionRecordMetadata({
+            checkpointKey,
             title: spec.title,
             question: spec.question,
-            type: "single_choice",
-            options: spec.options,
-            allowOther: true,
-            otherLabel: "Other",
-            required: options.required ?? spec.required,
-            source: "runtime_guidance",
-            rationale: [
-                spec.whyNow,
-                `Question kind: ${spec.kind}`,
-                `Question confidence: ${spec.confidence}`,
-                `${FOLLOW_UP_PROMPT_PREFIX} ${options.prompt}`
-            ],
-            preferredSurfaces: preferredSurfaces
-        }
-    }));
+            prompt: options.prompt,
+            rationale
+        });
+        return {
+            id: createId("question_record"),
+            createdAt,
+            updatedAt: createdAt,
+            status: "pending",
+            ...metadata,
+            prompt: {
+                id: createId("question_prompt"),
+                checkpointKey,
+                title: spec.title,
+                question: spec.question,
+                type: "single_choice",
+                options: spec.options,
+                allowOther: true,
+                otherLabel: "Other",
+                required: options.required ?? spec.required,
+                source: "runtime_guidance",
+                rationale,
+                preferredSurfaces: preferredSurfaces
+            }
+        };
+    });
     const updated = appendQuestionRecords(state, questions);
     await writeFile(options.context.stateFilePath, JSON.stringify(updated, null, 2), "utf8");
     await syncCurrentWorkspaceView(options.context);
@@ -1716,16 +1872,35 @@ export async function createWorkspaceQuestion(options) {
     });
     const checkpointKey = options.checkpointKey ?? trigger.signal.checkpointKey;
     const createdAt = nowIso();
+    const title = options.title ?? questionTitleForCheckpoint(trigger.family, checkpointKey);
+    const questionText = options.question ?? questionTextForCheckpoint(trigger.family, options.prompt, checkpointKey);
+    const rationale = [
+        ...trigger.rationale,
+        `Trigger family: ${trigger.family}.`,
+        `Trigger confidence: ${trigger.confidence}.`,
+        `Original prompt: ${options.prompt}`
+    ];
+    const metadata = resolveQuestionRecordMetadata({
+        checkpointKey,
+        triggerFamily: trigger.family,
+        title,
+        question: questionText,
+        prompt: options.prompt,
+        rationale,
+        commitmentFamily: options.commitmentFamily,
+        epistemicBasis: options.epistemicBasis
+    });
     const question = {
         id: createId("question_record"),
         createdAt,
         updatedAt: createdAt,
         status: "pending",
+        ...metadata,
         prompt: {
             id: createId("question_prompt"),
             checkpointKey,
-            title: options.title ?? questionTitleForCheckpoint(trigger.family, checkpointKey),
-            question: options.question ?? questionTextForCheckpoint(trigger.family, options.prompt, checkpointKey),
+            title,
+            question: questionText,
             type: "single_choice",
             options: options.questionOptions ?? optionsForCheckpointTrigger(trigger.family, checkpointKey),
             allowOther: true,
@@ -1733,12 +1908,7 @@ export async function createWorkspaceQuestion(options) {
             required: options.required ?? trigger.requiresQuestionBeforeClosure,
             source: "checkpoint",
             displayReason: options.displayReason ?? trigger.rationale[0],
-            rationale: [
-                ...trigger.rationale,
-                `Trigger family: ${trigger.family}.`,
-                `Trigger confidence: ${trigger.confidence}.`,
-                `Original prompt: ${options.prompt}`
-            ],
+            rationale,
             preferredSurfaces: options.provider === "claude"
                 ? ["native_structured", "numbered"]
                 : ["mcp_elicitation", "numbered"]
@@ -1865,6 +2035,8 @@ export async function answerWorkspaceQuestion(options) {
         level: question.prompt.required ? "adaptive_required" : "recommended",
         mode: "commit",
         summary: `Answered ${question.prompt.title}: ${answer.selectedLabels.join(", ")}`,
+        ...(question.commitmentFamily ? { commitmentFamily: question.commitmentFamily } : {}),
+        ...(question.epistemicBasis ? { epistemicBasis: question.epistemicBasis } : {}),
         selectedOption: answer.selectedValues[0],
         ...(rationale ? { rationale } : {})
     };

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

@@ -1,4 +1,4 @@
-import { type CrossrefTdmDiscovery, type EvidenceCard, type Publisher, type PublisherAccessRecord, type PublisherProbeInput, type PublisherProbeTarget, type SearchCapabilitySnapshot, type SearchFetch } from "./types.js";
+import { type CrossrefTdmDiscovery, type EvidenceCard, type Publisher, type PublisherAccessRecord, type PublisherProbeInput, type PublisherProbeTarget, type SearchFetch } from "./types.js";
 interface PublisherConfig {
     publisher: Publisher;
     label: string;
@@ -12,8 +12,6 @@ export declare function discoverCrossrefTdm(doi: string, env?: Record<string, st
 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 buildSearchCapabilitySnapshot(records: PublisherAccessRecord[], env?: Record<string, string | undefined>): SearchCapabilitySnapshot;
-export declare function searchCapabilitySnapshotPath(home?: string): string;
 export declare function enrichCardsWithPublisherAccess(input: {
     cards: EvidenceCard[];
     env?: Record<string, string | undefined>;

package/dist/search/publisher-access.js

@@ -1,5 +1,3 @@
-import { join } from "node:path";
-import { homedir } from "node:os";
 import { PUBLISHERS } from "./types.js";
 const PUBLISHER_CONFIGS = {
     elsevier: {
@@ -505,17 +503,6 @@ export function summarizeConfiguredPublisherAccess(env = process.env) {
         });
     });
 }
-export function buildSearchCapabilitySnapshot(records, env = process.env) {
-    return {
-        version: 1,
-        updatedAt: now(),
-        contactEmailPresent: Boolean(env.LONGTABLE_CONTACT_EMAIL?.trim()),
-        records
-    };
-}
-export function searchCapabilitySnapshotPath(home = homedir()) {
-    return join(home, ".longtable", "search-capabilities.json");
-}
 function bestAccessStatus(record) {
     if (record.entitlementStatus === "licensed_full_text_available" && record.collectionDepth === "licensed_snippet") {
         return "licensed_full_text_checked";

package/dist/search/types.d.ts

@@ -173,12 +173,6 @@ export interface PublisherAccessRecord {
     evidenceSnippet?: string;
     crossref?: CrossrefTdmDiscovery;
 }
-export interface SearchCapabilitySnapshot {
-    version: 1;
-    updatedAt: string;
-    contactEmailPresent: boolean;
-    records: PublisherAccessRecord[];
-}
 export interface PublisherProbeInput {
     doi: string;
     publisher?: PublisherProbeTarget;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@longtable/cli",
-  "version": "0.1.44",
+  "version": "0.1.47",
   "private": false,
   "description": "Researcher-facing LongTable CLI",
   "type": "module",
@@ -29,12 +29,12 @@
   },
   "dependencies": {
     "@clack/prompts": "^1.2.0",
-    "@longtable/checkpoints": "0.1.44",
-    "@longtable/core": "0.1.44",
-    "@longtable/memory": "0.1.44",
-    "@longtable/provider-claude": "0.1.44",
-    "@longtable/provider-codex": "0.1.44",
-    "@longtable/setup": "0.1.44"
+    "@longtable/checkpoints": "0.1.47",
+    "@longtable/core": "0.1.47",
+    "@longtable/memory": "0.1.47",
+    "@longtable/provider-claude": "0.1.47",
+    "@longtable/provider-codex": "0.1.47",
+    "@longtable/setup": "0.1.47"
   },
   "devDependencies": {
     "@types/node": "^22.10.1",