@longtable/cli 0.1.29 → 0.1.31

package/dist/cli.js

@@ -2,13 +2,12 @@
 import { existsSync, readFileSync, statSync } from "node:fs";
 import { mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
 import { execSync } from "node:child_process";
-import { emitKeypressEvents } from "node:readline";
 import { createInterface } from "node:readline/promises";
 import { stdin as input, stdout as output, cwd, env, exit } from "node:process";
 import { dirname, join, resolve } from "node:path";
 import { homedir } from "node:os";
 import { classifyCheckpointTrigger } from "@longtable/checkpoints";
-import { assessSearchSourceCapabilities, buildResearchSearchIntent, runResearchSearch } from "./search/index.js";
+import { assessSearchSourceCapabilities, buildResearchSearchIntent, buildSearchCapabilitySnapshot, parsePublisherTarget, probePublisherAccess, publisherConfigs, runResearchSearch, searchCapabilitySnapshotPath, 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";
@@ -18,6 +17,7 @@ import { PERSONA_DEFINITIONS, listRoleDefinitions } from "./personas.js";
 import { buildPanelFallback, renderPanelSummary } from "./panel.js";
 import { appendInvocationRecordToWorkspace, assertWorkspaceNotBlocked, answerWorkspaceQuestion, createWorkspaceFollowUpQuestions, createWorkspaceQuestion, createOrUpdateProjectWorkspace, inspectProjectWorkspace, loadWorkspaceState, loadProjectContextFromDirectory, renderProjectWorkspaceSummary, syncCurrentWorkspaceView } from "./project-session.js";
 import { buildTeamDebate, buildTeamReview, renderTeamDebateSummary } from "./debate.js";
+import { createPromptRenderer } from "./prompt-renderer.js";
 const VALID_MODES = new Set([
     "explore",
     "review",
@@ -43,7 +43,7 @@ const ANSI = {
     green: "\u001B[32m"
 };
 const LONGTABLE_MCP_SERVER_NAME = "longtable-state";
-const LONGTABLE_MCP_PACKAGE_VERSION = "0.1.29";
+const LONGTABLE_MCP_PACKAGE_VERSION = "0.1.31";
 const LONGTABLE_MCP_MARKER_START = "# LongTable state MCP START";
 const LONGTABLE_MCP_MARKER_END = "# LongTable state MCP END";
 function style(text, prefix) {
@@ -89,7 +89,10 @@ 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 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] [--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,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>]",
@@ -136,6 +139,10 @@ function parseArgs(argv) {
     else if (command === "codex" || command === "claude" || command === "mcp") {
         startIndex = 2;
     }
+    else if (command === "search" && maybeSubcommand && !maybeSubcommand.startsWith("--")) {
+        subcommand = maybeSubcommand;
+        startIndex = 2;
+    }
     else if (directCommand) {
         subcommand = undefined;
         startIndex = 1;
@@ -164,11 +171,6 @@ function parseArgs(argv) {
     }
     return { command, subcommand, values };
 }
-function renderChoices(choices) {
-    return choices
-        .map((choice, index) => `${index + 1}. ${choice.label} — ${choice.description}`)
-        .join("\n");
-}
 function buildSetupFlowChoices() {
     return [
         {
@@ -212,23 +214,6 @@ function questionSection(questionId) {
 function formatModeLabel(mode) {
     return `${mode[0].toUpperCase()}${mode.slice(1)}`;
 }
-function moveCursorUp(lines) {
-    return lines > 0 ? `\u001B[${lines}A` : "";
-}
-function clearLine() {
-    return "\u001B[2K\r";
-}
-function renderArrowMenu(prompt, choices, selectedIndex) {
-    const lines = [style(prompt, ANSI.bold), style("Use ↑/↓ and Enter.", ANSI.dim)];
-    for (let index = 0; index < choices.length; index += 1) {
-        const prefix = index === selectedIndex ? style(">", `${ANSI.bold}${ANSI.green}`) : " ";
-        lines.push(`${prefix} ${choices[index].label} - ${choices[index].description}`);
-    }
-    return lines.join("\n");
-}
-function countRenderedLines(text) {
-    return text.split("\n").length;
-}
 function stripWrappingQuotes(value) {
     const trimmed = value.trim();
     if ((trimmed.startsWith("\"") && trimmed.endsWith("\"")) ||
@@ -295,186 +280,14 @@ async function verifyWritableWorkspaceParent(projectPath) {
         ].join("\n"));
     }
 }
-async function promptChoiceByNumber(rl, prompt, choices) {
-    while (true) {
-        const answer = await rl.question(`${prompt}\n${renderChoices(choices)}\nSelect one number: `);
-        const numeric = Number(answer.trim());
-        if (!Number.isInteger(numeric) || numeric < 1 || numeric > choices.length) {
-            console.log("Invalid selection. Enter one of the listed numbers.");
-            continue;
-        }
-        const choice = choices[numeric - 1];
-        if (choice.fallbackToText) {
-            const freeText = await rl.question("Type your custom value: ");
-            if (!freeText.trim()) {
-                console.log("Custom value cannot be empty.");
-                continue;
-            }
-            return freeText.trim();
-        }
-        return choice.id;
-    }
+async function promptText(prompt, required) {
+    return createPromptRenderer().text(prompt, { required });
 }
-async function promptText(rl, prompt, required) {
-    while (true) {
-        const answer = (await rl.question(`${prompt}\n> `)).trim();
-        if (!required) {
-            return answer || undefined;
-        }
-        if (answer) {
-            return answer;
-        }
-        console.log("This answer cannot be empty.");
-    }
+async function promptChoice(prompt, choices) {
+    return createPromptRenderer().select(prompt, choices);
 }
-async function promptChoiceWithArrows(rl, prompt, choices) {
-    const stream = input;
-    if (!stream.isTTY || !output.isTTY) {
-        return promptChoiceByNumber(rl, prompt, choices);
-    }
-    const previousRawMode = stream.isRaw;
-    let selectedIndex = 0;
-    let lastRenderLineCount = 0;
-    return await new Promise((resolve, reject) => {
-        function draw(first = false) {
-            const renderedText = renderArrowMenu(prompt, choices, selectedIndex);
-            const rendered = renderedText.split("\n");
-            if (!first && lastRenderLineCount > 0) {
-                output.write(moveCursorUp(lastRenderLineCount));
-            }
-            for (const line of rendered) {
-                output.write(clearLine());
-                output.write(`${line}\n`);
-            }
-            lastRenderLineCount = countRenderedLines(renderedText);
-        }
-        function cleanup() {
-            stream.off("keypress", onKeypress);
-            if (stream.isTTY) {
-                stream.setRawMode(previousRawMode ?? false);
-            }
-            output.write("\u001B[?25h");
-        }
-        async function handleChoice(choice) {
-            cleanup();
-            if (choice.fallbackToText) {
-                const freeText = await rl.question("Type your custom value: ");
-                if (!freeText.trim()) {
-                    resolve(await promptChoiceWithArrows(rl, prompt, choices));
-                    return;
-                }
-                resolve(freeText.trim());
-                return;
-            }
-            resolve(choice.id);
-        }
-        function onKeypress(_, key) {
-            if (key.ctrl && key.name === "c") {
-                cleanup();
-                reject(new Error("Setup cancelled."));
-                return;
-            }
-            if (key.name === "up") {
-                selectedIndex = selectedIndex === 0 ? choices.length - 1 : selectedIndex - 1;
-                draw();
-                return;
-            }
-            if (key.name === "down") {
-                selectedIndex = selectedIndex === choices.length - 1 ? 0 : selectedIndex + 1;
-                draw();
-                return;
-            }
-            if (key.name === "return") {
-                void handleChoice(choices[selectedIndex]);
-            }
-        }
-        emitKeypressEvents(stream);
-        stream.setRawMode(true);
-        output.write("\u001B[?25l");
-        draw(true);
-        stream.on("keypress", onKeypress);
-    });
-}
-async function promptChoice(rl, prompt, choices) {
-    return promptChoiceWithArrows(rl, prompt, choices);
-}
-async function promptMultiChoice(rl, prompt, choices) {
-    const stream = input;
-    if (!stream.isTTY || !output.isTTY) {
-        const answer = await rl.question(`${prompt}\nType comma-separated ids or leave blank for auto.\n> `);
-        return answer
-            .split(",")
-            .map((part) => part.trim())
-            .filter(Boolean);
-    }
-    const previousRawMode = stream.isRaw;
-    let selectedIndex = 0;
-    const selected = new Set();
-    let lastRenderLineCount = 0;
-    return await new Promise((resolvePromise, reject) => {
-        function draw(first = false) {
-            const lines = [prompt, "Use ↑/↓, Space to toggle, and Enter to confirm."];
-            for (let index = 0; index < choices.length; index += 1) {
-                const choice = choices[index];
-                const pointer = index === selectedIndex ? ">" : " ";
-                const marker = selected.has(choice.id) ? "[x]" : "[ ]";
-                lines.push(`${pointer} ${marker} ${choice.label} - ${choice.description}`);
-            }
-            const renderedText = lines.join("\n");
-            if (!first && lastRenderLineCount > 0) {
-                output.write(moveCursorUp(lastRenderLineCount));
-            }
-            for (const line of lines) {
-                output.write(clearLine());
-                output.write(`${line}\n`);
-            }
-            lastRenderLineCount = countRenderedLines(renderedText);
-        }
-        function cleanup() {
-            stream.off("keypress", onKeypress);
-            if (stream.isTTY) {
-                stream.setRawMode(previousRawMode ?? false);
-            }
-            output.write("\u001B[?25h");
-        }
-        function onKeypress(_, key) {
-            if (key.ctrl && key.name === "c") {
-                cleanup();
-                reject(new Error("Setup cancelled."));
-                return;
-            }
-            if (key.name === "up") {
-                selectedIndex = selectedIndex === 0 ? choices.length - 1 : selectedIndex - 1;
-                draw();
-                return;
-            }
-            if (key.name === "down") {
-                selectedIndex = selectedIndex === choices.length - 1 ? 0 : selectedIndex + 1;
-                draw();
-                return;
-            }
-            if (key.name === "space") {
-                const id = choices[selectedIndex].id;
-                if (selected.has(id)) {
-                    selected.delete(id);
-                }
-                else {
-                    selected.add(id);
-                }
-                draw();
-                return;
-            }
-            if (key.name === "return") {
-                cleanup();
-                resolvePromise([...selected]);
-            }
-        }
-        emitKeypressEvents(stream);
-        stream.setRawMode(true);
-        output.write("\u001B[?25l");
-        draw(true);
-        stream.on("keypress", onKeypress);
-    });
+async function promptMultiChoice(prompt, choices) {
+    return createPromptRenderer().multiselect(prompt, choices);
 }
 function hasCompleteFlagInput(args) {
     const required = ["provider", "career-stage", "experience", "checkpoint"];
@@ -509,58 +322,52 @@ function toSetupAnswers(args) {
     };
 }
 async function collectInteractiveAnswers(initialFlow) {
-    const rl = createInterface({ input, output });
-    try {
-        const flow = initialFlow ??
-            (await promptChoice(rl, "How would you like to set up LongTable?", buildSetupFlowChoices()));
-        console.log("");
-        console.log(renderSetupHeader(flow));
-        console.log("");
-        const provider = await promptChoice(rl, "Which provider do you want to configure?", buildProviderChoices());
-        const answers = {
-            field: "unspecified",
-            currentProjectType: "unspecified research task"
-        };
-        const questions = buildQuickSetupFlow(flow);
-        for (let index = 0; index < questions.length; index += 1) {
-            const question = questions[index];
-            const prompt = renderQuestionHeader(index + 1, questions.length, questionSection(question.id), question.prompt);
-            let value;
-            if (question.kind === "text") {
-                value = await promptText(rl, prompt, question.required);
-            }
-            else if (question.choices) {
-                value = await promptChoice(rl, prompt, question.choices);
-            }
-            if (!value) {
-                continue;
-            }
-            if (question.id === "careerStage")
-                answers.careerStage = value;
-            if (question.id === "experienceLevel")
-                answers.experienceLevel = value;
-            if (question.id === "preferredCheckpointIntensity") {
-                answers.preferredCheckpointIntensity = value;
-            }
-            if (question.id === "humanAuthorshipSignal" && value !== "other") {
-                answers.humanAuthorshipSignal = value;
-            }
-            if (question.id === "preferredEntryMode")
-                answers.preferredEntryMode = value;
-            if (question.id === "weakestDomain")
-                answers.weakestDomain = value;
-            if (question.id === "panelPreference")
-                answers.panelPreference = value;
+    const flow = initialFlow ??
+        (await promptChoice("How would you like to set up LongTable?", buildSetupFlowChoices()));
+    console.log("");
+    console.log(renderSetupHeader(flow));
+    console.log("");
+    const provider = await promptChoice("Which provider do you want to configure?", buildProviderChoices());
+    const answers = {
+        field: "unspecified",
+        currentProjectType: "unspecified research task"
+    };
+    const questions = buildQuickSetupFlow(flow);
+    for (let index = 0; index < questions.length; index += 1) {
+        const question = questions[index];
+        const prompt = renderQuestionHeader(index + 1, questions.length, questionSection(question.id), question.prompt);
+        let value;
+        if (question.kind === "text") {
+            value = await promptText(prompt, question.required);
+        }
+        else if (question.choices) {
+            value = await promptChoice(prompt, question.choices);
+        }
+        if (!value) {
+            continue;
         }
-        return {
-            flow,
-            provider,
-            answers: answers
-        };
-    }
-    finally {
-        rl.close();
+        if (question.id === "careerStage")
+            answers.careerStage = value;
+        if (question.id === "experienceLevel")
+            answers.experienceLevel = value;
+        if (question.id === "preferredCheckpointIntensity") {
+            answers.preferredCheckpointIntensity = value;
+        }
+        if (question.id === "humanAuthorshipSignal" && value !== "other") {
+            answers.humanAuthorshipSignal = value;
+        }
+        if (question.id === "preferredEntryMode")
+            answers.preferredEntryMode = value;
+        if (question.id === "weakestDomain")
+            answers.weakestDomain = value;
+        if (question.id === "panelPreference")
+            answers.panelPreference = value;
     }
+    return {
+        flow,
+        provider,
+        answers: answers
+    };
 }
 function buildPermissionSetupChoices() {
     return {
@@ -728,129 +535,123 @@ function checkpointUiIntervention(intervention, checkpointUi) {
 }
 async function runSetup(args) {
     const json = args.json === true;
-    const rl = createInterface({ input, output });
-    try {
-        const provider = (typeof args.provider === "string"
-            ? (args.provider === "claude" ? "claude" : "codex")
-            : await promptChoice(rl, "Which provider should LongTable configure?", buildProviderChoices()));
-        const choices = buildPermissionSetupChoices();
-        const installScope = parseSetupInstallScope(args["install-scope"]) ?? await promptChoice(rl, "Where may LongTable install runtime support?", choices.installScope);
-        const surfaces = parseSetupSurface(args.surfaces) ?? await promptChoice(rl, [
-            "Which LongTable runtime surfaces should be enabled?",
-            "This is a permission choice because skills, MCP, and sentinel support write provider-facing runtime files."
-        ].join("\n"), choices.surfaces);
-        const intervention = parseSetupIntervention(args.intervention) ?? await promptChoice(rl, "How strongly may LongTable interrupt research decisions?", choices.intervention);
-        const parsedCheckpointUi = parseSetupCheckpointUi(args["checkpoint-ui"]);
-        const checkpointUiEligible = provider === "codex" && installScope !== "none" && shouldInstallMcp(installScope, surfaces);
-        if (parsedCheckpointUi && checkpointUiRequiresMcp(parsedCheckpointUi) && !checkpointUiEligible) {
-            throw new Error("`--checkpoint-ui interactive|strong` requires Codex with an MCP runtime surface.");
-        }
-        const checkpointUi = parsedCheckpointUi ?? (checkpointUiEligible
-            ? await promptChoice(rl, [
-                "Should Codex use UI Researcher Checkpoints when MCP elicitation is available?",
-                "This writes Codex MCP elicitation approval only when you choose an interactive mode."
-            ].join("\n"), choices.checkpointUi)
-            : "off");
-        const workspacePreference = parseSetupWorkspace(args.workspace) ?? await promptChoice(rl, "Should LongTable create a project workspace now?", choices.workspace);
-        const projectRoot = setupProjectRoot(args);
-        const effectiveIntervention = checkpointUiIntervention(intervention, checkpointUi);
-        const outputValue = createPersistedSetupOutput({
-            field: "unspecified",
-            careerStage: "unspecified",
-            experienceLevel: "advanced",
-            preferredCheckpointIntensity: checkpointIntensityFromIntervention(effectiveIntervention),
-            checkpointUiMode: checkpointUi,
-            preferredEntryMode: "explore",
-            panelPreference: "show_on_conflict"
-        }, provider, "quickstart");
-        outputValue.initialState.explicitState = {
-            ...outputValue.initialState.explicitState,
-            installScope,
-            runtimeSurfaces: surfaces,
-            interventionPosture: effectiveIntervention,
-            checkpointUiMode: checkpointUi,
-            workspaceCreationPreference: workspacePreference,
-            teamMode: "panel"
-        };
-        if (surfaces === "skills_mcp_sentinel") {
-            outputValue.initialState.inferredHypotheses.push({
-                hypothesis: "Researcher approved advisory Gap/Tacit Sentinel setup.",
-                confidence: 0.95,
-                evidence: ["Selected Skills + MCP + Sentinel during permission-first setup."],
-                status: "confirmed"
-            });
-        }
-        const setupPath = setupPathForScope(installScope, args, projectRoot);
-        const runtimePath = runtimePathForScope(provider, installScope, args, projectRoot);
-        const result = installScope === "none"
-            ? {
-                provider,
-                setupTarget: await saveSetupOutput(outputValue, setupPath)
-            }
-            : await saveSetupAndRuntimeConfig(outputValue, {
-                setupPath,
-                runtimePath
-            });
-        const scopedInstallDir = setupInstallDir(provider, installScope, typeof args["skills-dir"] === "string" ? args["skills-dir"] : typeof args.dir === "string" ? args.dir : undefined, projectRoot);
-        const installedSkills = !shouldInstallSkills(installScope, surfaces)
-            ? []
-            : provider === "codex"
-                ? await installCodexSkills(listRoleDefinitions(), scopedInstallDir)
-                : await installClaudeSkills(listRoleDefinitions(), scopedInstallDir);
-        let mcpInstall;
-        if (shouldInstallMcp(installScope, surfaces)) {
-            mcpInstall = await installMcpForSetup(provider, {
-                ...mcpArgsForScope(provider, installScope, args, projectRoot),
-                ...(provider === "codex" && checkpointUiRequiresMcp(checkpointUi)
-                    ? { "checkpoint-ui": checkpointUi }
-                    : {})
-            });
-        }
-        if (json) {
-            console.log(JSON.stringify({
-                setup: outputValue,
-                runtime: result,
-                installedSkills: installedSkills.map((skill) => skill.name),
-                mcpInstall,
-                workspacePreference
-            }, null, 2));
-            return;
+    const provider = (typeof args.provider === "string"
+        ? (args.provider === "claude" ? "claude" : "codex")
+        : await promptChoice("Which provider should LongTable configure?", buildProviderChoices()));
+    const choices = buildPermissionSetupChoices();
+    const installScope = parseSetupInstallScope(args["install-scope"]) ?? await promptChoice("Where may LongTable install runtime support?", choices.installScope);
+    const surfaces = parseSetupSurface(args.surfaces) ?? await promptChoice([
+        "Which LongTable runtime surfaces should be enabled?",
+        "This is a permission choice because skills, MCP, and sentinel support write provider-facing runtime files."
+    ].join("\n"), choices.surfaces);
+    const intervention = parseSetupIntervention(args.intervention) ?? await promptChoice("How strongly may LongTable interrupt research decisions?", choices.intervention);
+    const parsedCheckpointUi = parseSetupCheckpointUi(args["checkpoint-ui"]);
+    const checkpointUiEligible = provider === "codex" && installScope !== "none" && shouldInstallMcp(installScope, surfaces);
+    if (parsedCheckpointUi && checkpointUiRequiresMcp(parsedCheckpointUi) && !checkpointUiEligible) {
+        throw new Error("`--checkpoint-ui interactive|strong` requires Codex with an MCP runtime surface.");
+    }
+    const checkpointUi = parsedCheckpointUi ?? (checkpointUiEligible
+        ? await promptChoice([
+            "Should Codex use UI Researcher Checkpoints when MCP elicitation is available?",
+            "This writes Codex MCP elicitation approval only when you choose an interactive mode."
+        ].join("\n"), choices.checkpointUi)
+        : "off");
+    const workspacePreference = parseSetupWorkspace(args.workspace) ?? await promptChoice("Should LongTable create a project workspace now?", choices.workspace);
+    const projectRoot = setupProjectRoot(args);
+    const effectiveIntervention = checkpointUiIntervention(intervention, checkpointUi);
+    const outputValue = createPersistedSetupOutput({
+        field: "unspecified",
+        careerStage: "unspecified",
+        experienceLevel: "advanced",
+        preferredCheckpointIntensity: checkpointIntensityFromIntervention(effectiveIntervention),
+        checkpointUiMode: checkpointUi,
+        preferredEntryMode: "explore",
+        panelPreference: "show_on_conflict"
+    }, provider, "quickstart");
+    outputValue.initialState.explicitState = {
+        ...outputValue.initialState.explicitState,
+        installScope,
+        runtimeSurfaces: surfaces,
+        interventionPosture: effectiveIntervention,
+        checkpointUiMode: checkpointUi,
+        workspaceCreationPreference: workspacePreference,
+        teamMode: "panel"
+    };
+    if (surfaces === "skills_mcp_sentinel") {
+        outputValue.initialState.inferredHypotheses.push({
+            hypothesis: "Researcher approved advisory Gap/Tacit Sentinel setup.",
+            confidence: 0.95,
+            evidence: ["Selected Skills + MCP + Sentinel during permission-first setup."],
+            status: "confirmed"
+        });
+    }
+    const setupPath = setupPathForScope(installScope, args, projectRoot);
+    const runtimePath = runtimePathForScope(provider, installScope, args, projectRoot);
+    const result = installScope === "none"
+        ? {
+            provider,
+            setupTarget: await saveSetupOutput(outputValue, setupPath)
         }
+        : await saveSetupAndRuntimeConfig(outputValue, {
+            setupPath,
+            runtimePath
+        });
+    const scopedInstallDir = setupInstallDir(provider, installScope, typeof args["skills-dir"] === "string" ? args["skills-dir"] : typeof args.dir === "string" ? args.dir : undefined, projectRoot);
+    const installedSkills = !shouldInstallSkills(installScope, surfaces)
+        ? []
+        : provider === "codex"
+            ? await installCodexSkills(listRoleDefinitions(), scopedInstallDir)
+            : await installClaudeSkills(listRoleDefinitions(), scopedInstallDir);
+    let mcpInstall;
+    if (shouldInstallMcp(installScope, surfaces)) {
+        mcpInstall = await installMcpForSetup(provider, {
+            ...mcpArgsForScope(provider, installScope, args, projectRoot),
+            ...(provider === "codex" && checkpointUiRequiresMcp(checkpointUi)
+                ? { "checkpoint-ui": checkpointUi }
+                : {})
+        });
+    }
+    if (json) {
+        console.log(JSON.stringify({
+            setup: outputValue,
+            runtime: result,
+            installedSkills: installedSkills.map((skill) => skill.name),
+            mcpInstall,
+            workspacePreference
+        }, null, 2));
+        return;
+    }
+    console.log("");
+    console.log(renderSetupSummary(outputValue));
+    console.log("");
+    if ("runtimeTarget" in result) {
+        console.log(renderInstallSummary(result));
+    }
+    else {
+        console.log("LongTable setup summary");
+        console.log(`setup path: ${result.setupTarget.path}`);
+        console.log("provider files: not installed by researcher choice");
+    }
+    console.log(`Installed skills: ${installedSkills.length}`);
+    if (mcpInstall) {
         console.log("");
-        console.log(renderSetupSummary(outputValue));
-        console.log("");
-        if ("runtimeTarget" in result) {
-            console.log(renderInstallSummary(result));
-        }
-        else {
-            console.log("LongTable setup summary");
-            console.log(`setup path: ${result.setupTarget.path}`);
-            console.log("provider files: not installed by researcher choice");
-        }
-        console.log(`Installed skills: ${installedSkills.length}`);
-        if (mcpInstall) {
-            console.log("");
-            console.log(renderMcpInstallSummary(mcpInstall));
-            if (provider === "codex" && checkpointUiRequiresMcp(checkpointUi)) {
-                console.log("");
-                console.log("Restart Codex after this config change, then run `longtable doctor` in the project workspace.");
-            }
-        }
-        if (surfaces === "skills_mcp_sentinel") {
+        console.log(renderMcpInstallSummary(mcpInstall));
+        if (provider === "codex" && checkpointUiRequiresMcp(checkpointUi)) {
             console.log("");
-            console.log("Background sentinel approval recorded.");
-            console.log("Hook installation remains opt-in; LongTable will not install hooks without an explicit hook command.");
-        }
-        if (workspacePreference === "create") {
-            console.log("");
-            console.log("Project workspace requested. LongTable will now run `longtable start` with research-object and gap-risk prompts.");
-            await runStart({
-                setup: result.setupTarget.path
-            });
+            console.log("Restart Codex after this config change, then run `longtable doctor` in the project workspace.");
         }
     }
-    finally {
-        rl.close();
+    if (surfaces === "skills_mcp_sentinel") {
+        console.log("");
+        console.log("Background sentinel approval recorded.");
+        console.log("Hook installation remains opt-in; LongTable will not install hooks without an explicit hook command.");
+    }
+    if (workspacePreference === "create") {
+        console.log("");
+        console.log("Project workspace requested. LongTable will now run `longtable start` with an adaptive start interview.");
+        await runStart({
+            setup: result.setupTarget.path
+        });
     }
 }
 function perspectiveChoices() {
@@ -887,6 +688,157 @@ function protectedDecisionChoices() {
         { id: "submission_public_sharing", label: "Submission/public sharing", description: "Do not let public-facing commitments settle quietly." }
     ];
 }
+function compactAnswer(value, maxLength = 180) {
+    const firstLine = value
+        .split(/\r?\n/)
+        .map((line) => line.trim())
+        .find(Boolean) ?? "";
+    return firstLine.length > maxLength ? `${firstLine.slice(0, maxLength - 1)}…` : firstLine;
+}
+function answerIncludes(answer, patterns) {
+    return patterns.some((pattern) => pattern.test(answer));
+}
+function classifyStartInterviewSignal(answer) {
+    const normalized = answer.toLowerCase();
+    if (answerIncludes(normalized, [/\bvoice\b/, /\bauthor(ship)?\b/, /\bwriting\b/, /저자|목소리|문체|글쓰기/])) {
+        return "voice";
+    }
+    if (answerIncludes(normalized, [/\breader\b/, /\breviewer\b/, /\bvenue\b/, /\bjournal\b/, /\baudience\b/, /독자|심사자|저널|학회|대상/])) {
+        return "audience";
+    }
+    if (answerIncludes(normalized, [/\bpaper\b/, /\bproposal\b/, /\bmanuscript\b/, /\bdraft\b/, /\bdeliverable\b/, /논문|제안서|원고|초안|산출물/])) {
+        return "artifact";
+    }
+    if (answerIncludes(normalized, [/\bevidence\b/, /\bdata\b/, /\bsource\b/, /\bcitation\b/, /\bliterature\b/, /\bmeasure\b/, /\bscale\b/, /\binstrument\b/, /근거|자료|데이터|문헌|인용|측정|척도|도구/])) {
+        return "evidence";
+    }
+    if (answerIncludes(normalized, [/\bassum/, /\btacit\b/, /\bimplicit\b/, /\bpremise\b/, /전제|암묵|가정|숨겨진/])) {
+        return "assumption";
+    }
+    if (answerIncludes(normalized, [/\bdecid/, /\bchoose\b/, /\bcommit\b/, /\bsettle\b/, /\block\b/, /결정|선택|확정|고정/])) {
+        return "decision_risk";
+    }
+    return "phenomenon";
+}
+function inferResearchObjectFromAnswers(answers) {
+    const joined = answers.join("\n").toLowerCase();
+    if (answerIncludes(joined, [/\bmeasure\b/, /\bscale\b/, /\binstrument\b/, /\bvariable\b/, /\bconstruct\b/, /측정|척도|변수|구성개념|도구/])) {
+        return "measurement_instrument";
+    }
+    if (answerIncludes(joined, [/\bmethod\b/, /\bdesign\b/, /\bsample\b/, /\binterview\b/, /\bexperiment\b/, /\bparticipant\b/, /방법|설계|표본|인터뷰|실험|참여자/])) {
+        return "study_design";
+    }
+    if (answerIncludes(joined, [/\btheory\b/, /\bframework\b/, /\bmodel\b/, /\bconcept\b/, /이론|프레임워크|모형|개념/])) {
+        return "theory_framework";
+    }
+    if (answerIncludes(joined, [/\banalysis\b/, /\bmodel\b/, /\bcoding\b/, /\bstatistic\b/, /분석|모델|코딩|통계/])) {
+        return "analysis_plan";
+    }
+    if (answerIncludes(joined, [/\bpaper\b/, /\bmanuscript\b/, /\bdraft\b/, /\bwriting\b/, /논문|원고|초안|글쓰기/])) {
+        return "manuscript";
+    }
+    return "research_question";
+}
+function inferGapRiskFromSignals(signals) {
+    if (signals.includes("assumption") || signals.includes("decision_risk")) {
+        return "suspected_tacit_assumptions";
+    }
+    if (signals.includes("evidence")) {
+        return "known_gap";
+    }
+    return "diagnose";
+}
+function inferProtectedDecisionFromAnswers(answers) {
+    const joined = answers.join("\n").toLowerCase();
+    if (answerIncludes(joined, [/\bmeasure\b/, /\bscale\b/, /\binstrument\b/, /\bvariable\b/, /측정|척도|변수|도구/])) {
+        return "measurement";
+    }
+    if (answerIncludes(joined, [/\bmethod\b/, /\bdesign\b/, /\bsample\b/, /\binterview\b/, /\bexperiment\b/, /방법|설계|표본|인터뷰|실험/])) {
+        return "method";
+    }
+    if (answerIncludes(joined, [/\bevidence\b/, /\bsource\b/, /\bcitation\b/, /\bliterature\b/, /근거|출처|인용|문헌/])) {
+        return "evidence_citation";
+    }
+    if (answerIncludes(joined, [/\bvoice\b/, /\bauthor(ship)?\b/, /\bwriting\b/, /저자|목소리|문체|글쓰기/])) {
+        return "authorship_voice";
+    }
+    if (answerIncludes(joined, [/\bsubmit\b/, /\bpublication\b/, /\bjournal\b/, /\bvenue\b/, /투고|출판|저널|학회|공개/])) {
+        return "submission_public_sharing";
+    }
+    if (answerIncludes(joined, [/\btheory\b/, /\bframework\b/, /\bconstruct\b/, /이론|프레임워크|구성개념/])) {
+        return "theory";
+    }
+    return undefined;
+}
+function uniqueSignals(turns) {
+    return [...new Set(turns.map((turn) => turn.signal))];
+}
+function renderStartInterviewPrompt(turn, total, question, context) {
+    return [
+        `LongTable Start Interview  Turn ${turn}/${total}`,
+        context ? `Context: ${context}` : undefined,
+        question
+    ].filter(Boolean).join("\n");
+}
+async function collectAdaptiveStartInterview(args) {
+    if (!args.needsResearchSeed) {
+        return {};
+    }
+    const createdAt = new Date().toISOString();
+    const turns = [];
+    async function ask(question, purpose, context) {
+        const answer = await promptText(renderStartInterviewPrompt(turns.length + 1, 5, question, context), true);
+        if (!answer?.trim()) {
+            return undefined;
+        }
+        turns.push({
+            index: turns.length + 1,
+            question,
+            answer: answer.trim(),
+            signal: classifyStartInterviewSignal(answer),
+            purpose
+        });
+        return answer.trim();
+    }
+    let currentGoal = args.currentGoal;
+    let currentBlocker = args.currentBlocker;
+    if (!currentGoal) {
+        const opening = await ask("What scene, problem, or moment made you want to start this research?", "Open from the researcher's lived entry point instead of a taxonomy.");
+        currentGoal = opening ? compactAnswer(opening) : undefined;
+    }
+    const openingContext = currentGoal ? compactAnswer(currentGoal, 120) : undefined;
+    if (!currentBlocker) {
+        const blocker = await ask("In that scene, what still feels least explained or hardest to justify?", "Name the first uncertainty without asking the researcher to classify it as theory, method, or measurement.", openingContext);
+        currentBlocker = blocker ? compactAnswer(blocker) : undefined;
+    }
+    const readerContext = currentBlocker ? compactAnswer(currentBlocker, 120) : openingContext;
+    await ask("If this research succeeds, what should a reader or reviewer understand differently?", "Locate the audience-facing contribution before proposing a direction.", readerContext);
+    await ask("What material would you inspect first to make this research concrete: a case, dataset, text, instrument, draft, or literature trail?", "Convert the opening story into a first inspectable research move.", readerContext);
+    const answers = turns.map((turn) => turn.answer);
+    const inferredSignals = uniqueSignals(turns);
+    const summary = [
+        currentGoal ? `Opening: ${compactAnswer(currentGoal, 120)}.` : "",
+        currentBlocker ? `First uncertainty: ${compactAnswer(currentBlocker, 120)}.` : "",
+        inferredSignals.length > 0 ? `Early lenses: ${inferredSignals.join(", ")}.` : ""
+    ].filter(Boolean).join(" ");
+    return {
+        currentGoal,
+        currentBlocker,
+        startInterview: {
+            mode: "adaptive",
+            openingStyle: "scene_problem",
+            createdAt,
+            completedAt: new Date().toISOString(),
+            turnCount: turns.length,
+            turns,
+            inferredSignals,
+            summary: summary || "Adaptive start interview completed."
+        },
+        inferredResearchObject: inferResearchObjectFromAnswers(answers),
+        inferredGapRisk: inferGapRiskFromSignals(inferredSignals),
+        inferredProtectedDecision: inferProtectedDecisionFromAnswers(answers)
+    };
+}
 function normalizePerspectiveList(value) {
     if (!value?.trim()) {
         return [];
@@ -897,82 +849,76 @@ function normalizePerspectiveList(value) {
         .filter(Boolean);
 }
 async function collectProjectInterview(setup, args) {
+    const providedPerspectives = normalizePerspectiveList(typeof args.perspectives === "string" ? args.perspectives : undefined);
+    const providedGoal = typeof args.goal === "string" && args.goal.trim() ? args.goal.trim() : undefined;
+    const providedBlocker = typeof args.blocker === "string" && args.blocker.trim() ? args.blocker.trim() : undefined;
+    const providedResearchObject = typeof args["research-object"] === "string" && args["research-object"].trim()
+        ? args["research-object"].trim()
+        : undefined;
+    const providedGapRisk = typeof args["gap-risk"] === "string" && args["gap-risk"].trim()
+        ? args["gap-risk"].trim()
+        : undefined;
+    const providedProtectedDecision = typeof args["protected-decision"] === "string" && args["protected-decision"].trim()
+        ? args["protected-decision"].trim()
+        : undefined;
     const needsInteractivePrompts = !(typeof args.name === "string" && args.name.trim()) ||
         !(typeof args.path === "string" && args.path.trim()) ||
-        !(typeof args.goal === "string" && args.goal.trim()) ||
-        typeof args.blocker !== "string" ||
-        !(typeof args["research-object"] === "string" && args["research-object"].trim()) ||
-        !(typeof args["gap-risk"] === "string" && args["gap-risk"].trim()) ||
-        !(typeof args["protected-decision"] === "string" && args["protected-decision"].trim()) ||
-        normalizePerspectiveList(typeof args.perspectives === "string" ? args.perspectives : undefined).length === 0 ||
-        !(typeof args.disagreement === "string" && args.disagreement.trim());
-    const rl = createInterface({ input, output });
-    try {
-        if (needsInteractivePrompts) {
-            console.log("");
-            console.log(renderBrandBanner("LongTable", "Project workspace interview"));
-            console.log("");
-            console.log(renderSectionCard("LongTable Project Start", [
-                "We will create a project workspace and a session memory seed for today's work.",
-                "At the end, LongTable will tell you exactly which directory to open in Codex."
-            ]));
-            console.log("");
-        }
-        const projectName = (typeof args.name === "string" && args.name.trim()) ||
-            (await promptText(rl, renderQuestionHeader(1, 9, "Project interview", "What should this project be called?"), true));
-        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()
-            ? normalizeUserPath(args.path.trim())
-            : resolveInteractiveProjectPath((await promptText(rl, renderQuestionHeader(2, 9, "Project interview", `Which parent directory should contain this project?\nLongTable will create this folder:\n${suggestedPath}`), true)), projectName));
-        const currentGoal = (typeof args.goal === "string" && args.goal.trim()) ||
-            (await promptText(rl, renderQuestionHeader(3, 9, "Current session", "What are you trying to accomplish in this session?"), true));
-        const currentBlocker = (typeof args.blocker === "string" && args.blocker.trim()) ||
-            (await promptText(rl, renderQuestionHeader(4, 9, "Current session", "What is the main blocker or uncertainty right now?"), false));
-        const researchObject = (typeof args["research-object"] === "string" && args["research-object"].trim()) ||
-            await promptChoice(rl, renderQuestionHeader(5, 9, "Research object", "What kind of research object are we protecting right now?"), researchObjectChoices());
-        const gapRisk = (typeof args["gap-risk"] === "string" && args["gap-risk"].trim()) ||
-            await promptChoice(rl, renderQuestionHeader(6, 9, "Gap/tacit risk", "What is the most likely gap risk at the start of this workspace?"), gapRiskChoices());
-        const protectedDecision = (typeof args["protected-decision"] === "string" && args["protected-decision"].trim()) ||
-            await promptChoice(rl, renderQuestionHeader(7, 9, "Protected decision", "Which decision should LongTable not let you settle quietly?"), protectedDecisionChoices());
-        const requestedPerspectives = normalizePerspectiveList(typeof args.perspectives === "string" ? args.perspectives : undefined).length > 0
-            ? normalizePerspectiveList(typeof args.perspectives === "string" ? args.perspectives : undefined)
-            : await promptMultiChoice(rl, renderQuestionHeader(8, 9, "Perspectives", "Which perspectives do you already know you want at the table? Leave everything unchecked for auto."), perspectiveChoices());
-        const disagreementPreference = (typeof args.disagreement === "string" && args.disagreement.trim()) ||
-            (await promptChoice(rl, renderQuestionHeader(9, 9, "Disagreement", "How visible should disagreement between perspectives be in this project by default?"), [
-                {
-                    id: "synthesis_only",
-                    label: "Synthesis only",
-                    description: "Show one LongTable answer unless I ask for more."
-                },
-                {
-                    id: "show_on_conflict",
-                    label: "Show on conflict",
-                    description: "Surface disagreement when the perspectives materially diverge."
-                },
-                {
-                    id: "always_visible",
-                    label: "Always visible",
-                    description: "Keep panel opinions visible by default."
-                }
-            ]));
-        return {
-            projectName: projectName.trim(),
-            projectPath: projectPath.trim(),
-            currentGoal: currentGoal.trim(),
-            ...(currentBlocker?.trim() ? { currentBlocker: currentBlocker.trim() } : {}),
-            researchObject: researchObject.trim(),
-            gapRisk: gapRisk.trim(),
-            protectedDecision: protectedDecision.trim(),
-            requestedPerspectives,
-            disagreementPreference: disagreementPreference
-        };
-    }
-    finally {
-        rl.close();
+        !providedGoal ||
+        !providedBlocker ||
+        !providedResearchObject ||
+        !providedGapRisk ||
+        !providedProtectedDecision;
+    if (needsInteractivePrompts) {
+        console.log("");
+        console.log(renderBrandBanner("LongTable", "Project workspace interview"));
+        console.log("");
+        console.log(renderSectionCard("LongTable Project Start", [
+            "LongTable will create a workspace and seed today's research memory.",
+            "The start interview begins from the scene or problem, then LongTable quietly infers the research shape."
+        ]));
+        console.log("");
     }
+    const projectName = (typeof args.name === "string" && args.name.trim()) ||
+        (await promptText(renderQuestionHeader(1, 2, "Workspace", "What should this project be called?"), true));
+    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()
+        ? 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));
+    const adaptive = await collectAdaptiveStartInterview({
+        currentGoal: providedGoal,
+        currentBlocker: providedBlocker,
+        needsResearchSeed: !providedGoal ||
+            !providedBlocker ||
+            !providedResearchObject ||
+            !providedGapRisk ||
+            !providedProtectedDecision
+    });
+    const currentGoal = providedGoal ?? adaptive.currentGoal;
+    if (!currentGoal?.trim()) {
+        throw new Error("LongTable start needs a current research goal or an opening interview answer.");
+    }
+    const currentBlocker = providedBlocker ?? adaptive.currentBlocker;
+    const researchObject = providedResearchObject ?? adaptive.inferredResearchObject;
+    const gapRisk = providedGapRisk ?? adaptive.inferredGapRisk;
+    const protectedDecision = providedProtectedDecision ?? adaptive.inferredProtectedDecision;
+    const disagreementPreference = (typeof args.disagreement === "string" && args.disagreement.trim()
+        ? args.disagreement.trim()
+        : setup.profileSeed.panelPreference ?? "show_on_conflict");
+    return {
+        projectName: projectName.trim(),
+        projectPath: projectPath.trim(),
+        currentGoal: currentGoal.trim(),
+        ...(currentBlocker?.trim() ? { currentBlocker: currentBlocker.trim() } : {}),
+        ...(researchObject?.trim() ? { researchObject: researchObject.trim() } : {}),
+        ...(gapRisk?.trim() ? { gapRisk: gapRisk.trim() } : {}),
+        ...(protectedDecision?.trim() ? { protectedDecision: protectedDecision.trim() } : {}),
+        ...(adaptive.startInterview ? { startInterview: adaptive.startInterview } : {}),
+        requestedPerspectives: providedPerspectives,
+        disagreementPreference
+    };
 }
 function normalizePersistAnswers(raw) {
     return {
@@ -2013,6 +1959,7 @@ function renderEvidenceRunSummary(run, recordedPath) {
         ].filter(Boolean).join(", ");
         lines.push(`  - ${card.title}`);
         lines.push(`    score: ${card.relevanceScore}; support: ${card.citationSupportStatus}; depth: ${card.evidenceDepth}; sources: ${card.sourceRoutes.join(", ")}`);
+        lines.push(`    access: ${card.accessStatus}; verification: ${card.verificationNote}`);
         if (identifiers) {
             lines.push(`    ids: ${identifiers}`);
         }
@@ -2056,7 +2003,194 @@ async function recordEvidenceRun(run, workingDirectory) {
     await syncCurrentWorkspaceView(context);
     return evidencePath;
 }
-async function runSearch(args) {
+function renderPublisherAccessRecord(record) {
+    const envSummary = record.missingEnv.length > 0
+        ? `missing ${record.missingEnv.join(", ")}`
+        : `configured ${record.presentEnv.join(", ") || "none"}`;
+    const lines = [
+        `${record.publisher}:`,
+        `  credential: ${record.credentialStatus} (${envSummary})`,
+        `  entitlement: ${record.entitlementStatus}; tdm: ${record.tdmStatus}; depth: ${record.collectionDepth}`,
+        `  verification: ${record.verificationNote}`
+    ];
+    if (record.testedDoi) {
+        lines.push(`  tested doi: ${record.testedDoi}`);
+    }
+    if (record.endpoint) {
+        lines.push(`  endpoint: ${record.endpoint}`);
+    }
+    if (record.licenseNote) {
+        lines.push(`  license: ${record.licenseNote}`);
+    }
+    if (record.setupHint) {
+        lines.push(`  setup: ${record.setupHint}`);
+    }
+    return lines.join("\n");
+}
+function renderPublisherAccessRecords(title, records, capabilityPath) {
+    const lines = [title];
+    if (capabilityPath) {
+        lines.push(`- capability file: ${capabilityPath}`);
+    }
+    for (const record of records) {
+        lines.push(renderPublisherAccessRecord(record));
+    }
+    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()) {
+        records.push(await probePublisherAccess({
+            doi,
+            publisher: publisher.publisher,
+            env
+        }));
+    }
+    return records;
+}
+async function runSearchProbe(args) {
+    if (typeof args.doi !== "string" || !args.doi.trim()) {
+        throw new Error("`longtable search probe` requires --doi <doi>.");
+    }
+    const publisher = parsePublisherTarget(args.publisher);
+    const record = await probePublisherAccess({
+        doi: args.doi,
+        publisher,
+        env
+    });
+    if (args.json === true) {
+        console.log(JSON.stringify({ record }, null, 2));
+    }
+    else {
+        console.log(renderPublisherAccessRecord(record));
+    }
+    return [record];
+}
+async function runSearchDoctor(args) {
+    let records;
+    if (typeof args.doi === "string" && args.doi.trim()) {
+        if (args.publisher === "all") {
+            records = await probeAllPublishers(args.doi);
+        }
+        else {
+            const publisher = parsePublisherTarget(args.publisher);
+            records = [await probePublisherAccess({
+                    doi: args.doi,
+                    publisher,
+                    env
+                })];
+        }
+    }
+    else {
+        records = summarizeConfiguredPublisherAccess(env);
+    }
+    const snapshotPath = searchCapabilitySnapshotPath();
+    const snapshotExists = existsSync(snapshotPath);
+    if (args.json === true) {
+        console.log(JSON.stringify({
+            capabilityFile: snapshotPath,
+            capabilityFileExists: snapshotExists,
+            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.");
+        }
+    }
+    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$/i.test(answer)) {
+        return undefined;
+    }
+    return answer;
+}
+async function runInteractiveSearchSetup(defaultDoi) {
+    const rl = createInterface({ input, output });
+    const records = [];
+    try {
+        console.log("LongTable publisher access setup");
+        console.log("LongTable does not store API keys or TDM tokens. It reads environment variables and records only non-secret capability results.");
+        console.log("");
+        for (const publisher of publisherConfigs()) {
+            console.log(`${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("");
+        }
+    }
+    finally {
+        rl.close();
+    }
+    return records;
+}
+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);
+    if (args.json === true) {
+        console.log(JSON.stringify({
+            capabilityFile: snapshotPath,
+            snapshot: buildSearchCapabilitySnapshot(records, env)
+        }, null, 2));
+        return;
+    }
+    console.log(renderPublisherAccessRecords("LongTable Search Publisher Access Setup", records, snapshotPath));
+}
+async function runSearch(subcommand, args) {
+    if (subcommand === "probe") {
+        await runSearchProbe(args);
+        return;
+    }
+    if (subcommand === "doctor" || subcommand === "status") {
+        await runSearchDoctor(args);
+        return;
+    }
+    if (subcommand === "setup") {
+        await runSearchSetup(args);
+        return;
+    }
+    if (subcommand) {
+        throw new Error(`Unknown search subcommand: ${subcommand}`);
+    }
     const workingDirectory = typeof args.cwd === "string" ? args.cwd : cwd();
     const projectContext = await loadProjectContextFromDirectory(workingDirectory);
     const searchInput = {
@@ -2082,7 +2216,8 @@ async function runSearch(args) {
     const run = await runResearchSearch({
         ...searchInput,
         env,
-        allowPartial
+        allowPartial,
+        publisherAccess: args["publisher-access"] === true
     });
     let recordedPath;
     if (args.record === true && run.status !== "blocked") {
@@ -2142,30 +2277,24 @@ async function runQuestion(args) {
         return;
     }
     if (isInteractiveTerminal()) {
-        const rl = createInterface({ input, output });
-        try {
-            console.log(renderBrandBanner("LongTable", "Researcher Checkpoint"));
-            console.log("");
-            const answer = await promptChoice(rl, renderQuestionHeader(1, 1, result.question.prompt.title, result.question.prompt.question), questionRecordToChoices(result.question));
-            const decision = await answerWorkspaceQuestion({
-                context,
-                questionId: result.question.id,
-                answer,
-                provider,
-                surface: "terminal_selector"
-            });
-            console.log("");
-            console.log("LongTable checkpoint decision recorded");
-            console.log(`- question: ${decision.question.id}`);
-            console.log(`- decision: ${decision.decision.id}`);
-            console.log(`- answer: ${decision.decision.selectedOption ?? answer}`);
-            console.log(`- state: ${context.stateFilePath}`);
-            console.log(`- current: ${context.currentFilePath}`);
-            return;
-        }
-        finally {
-            rl.close();
-        }
+        console.log(renderBrandBanner("LongTable", "Researcher Checkpoint"));
+        console.log("");
+        const answer = await promptChoice(renderQuestionHeader(1, 1, result.question.prompt.title, result.question.prompt.question), questionRecordToChoices(result.question));
+        const decision = await answerWorkspaceQuestion({
+            context,
+            questionId: result.question.id,
+            answer,
+            provider,
+            surface: "terminal_selector"
+        });
+        console.log("");
+        console.log("LongTable checkpoint decision recorded");
+        console.log(`- question: ${decision.question.id}`);
+        console.log(`- decision: ${decision.decision.id}`);
+        console.log(`- answer: ${decision.decision.selectedOption ?? answer}`);
+        console.log(`- state: ${context.stateFilePath}`);
+        console.log(`- current: ${context.currentFilePath}`);
+        return;
     }
     const optionValues = [
         ...result.question.prompt.options.map((option) => option.value),
@@ -2256,25 +2385,19 @@ async function answerFollowUpQuestionsInTerminal(context, questions, provider) {
     if (questions.length === 0) {
         return;
     }
-    const rl = createInterface({ input, output });
-    try {
-        console.log(renderBrandBanner("LongTable", "Follow-up Questions"));
-        console.log("");
-        for (let index = 0; index < questions.length; index += 1) {
-            const question = questions[index];
-            const prompt = renderQuestionHeader(index + 1, questions.length, question.prompt.title, question.prompt.question);
-            const answer = await promptChoice(rl, prompt, questionRecordToChoices(question));
-            await answerWorkspaceQuestion({
-                context,
-                questionId: question.id,
-                answer,
-                provider,
-                surface: "terminal_selector"
-            });
-        }
-    }
-    finally {
-        rl.close();
+    console.log(renderBrandBanner("LongTable", "Follow-up Questions"));
+    console.log("");
+    for (let index = 0; index < questions.length; index += 1) {
+        const question = questions[index];
+        const prompt = renderQuestionHeader(index + 1, questions.length, question.prompt.title, question.prompt.question);
+        const answer = await promptChoice(prompt, questionRecordToChoices(question));
+        await answerWorkspaceQuestion({
+            context,
+            questionId: question.id,
+            answer,
+            provider,
+            surface: "terminal_selector"
+        });
     }
 }
 async function runClarify(args) {
@@ -2665,6 +2788,7 @@ async function runStart(args) {
         researchObject: interview.researchObject,
         gapRisk: interview.gapRisk,
         protectedDecision: interview.protectedDecision,
+        startInterview: interview.startInterview,
         requestedPerspectives: interview.requestedPerspectives,
         disagreementPreference: interview.disagreementPreference,
         setup: existingSetup
@@ -2907,7 +3031,7 @@ async function main() {
         return;
     }
     if (command === "search") {
-        await runSearch(values);
+        await runSearch(subcommand, values);
         return;
     }
     if (command === "ask") {