@longtable/cli 0.1.19 → 0.1.20

package/README.md

@@ -27,16 +27,15 @@ approval.
 
 ```bash
 longtable setup --provider codex
-longtable init --flow interview
 longtable start
 cd "<project-path>"
 codex
 ```
 
 `longtable setup --provider codex` is the permission-first setup route. It asks
-which runtime surfaces LongTable may enable and explains why each choice matters:
-CLI only, skills, skills + MCP, skills + MCP + sentinel, intervention posture,
-tmux HUD/console, and team discussion mode.
+where LongTable may install support, which runtime surfaces it may enable, how
+strongly it may interrupt research decisions, and whether to create a project
+workspace now. `longtable init` remains only as a deprecated compatibility alias.
 
 Return later:
 
@@ -85,7 +84,7 @@ This is how LongTable avoids turning tacit knowledge into fake certainty.
 ## Commands
 
 ```bash
-longtable init
+longtable setup
 longtable start
 longtable resume --cwd "<project-path>"
 longtable roles

package/dist/cli.js

@@ -8,7 +8,7 @@ import { stdin as input, stdout as output, cwd, exit } from "node:process";
 import { dirname, join, resolve } from "node:path";
 import { homedir } from "node:os";
 import { classifyCheckpointTrigger } from "@longtable/checkpoints";
-import { buildProviderChoices, buildQuickSetupFlow, createPersistedSetupOutput, installRuntimeConfigFromStoredSetup, loadSetupOutput, renderInstallSummary, renderSetupSummary, resolveDefaultRuntimeConfigPath, resolveDefaultSetupPath, saveSetupAndRuntimeConfig, serializeSetupOutput, writeRuntimeConfig } from "@longtable/setup";
+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";
 import { installCodexPromptAliases, listInstalledCodexPromptAliases, removeCodexPromptAliases, resolveCodexPromptsDir } from "./prompt-aliases.js";
@@ -42,7 +42,7 @@ const ANSI = {
     green: "\u001B[32m"
 };
 const LONGTABLE_MCP_SERVER_NAME = "longtable-state";
-const LONGTABLE_MCP_PACKAGE_VERSION = "0.1.19";
+const LONGTABLE_MCP_PACKAGE_VERSION = "0.1.20";
 const LONGTABLE_MCP_MARKER_START = "# LongTable state MCP START";
 const LONGTABLE_MCP_MARKER_END = "# LongTable state MCP END";
 function style(text, prefix) {
@@ -78,9 +78,9 @@ function usage() {
         "  Run `longtable ...` in your terminal, not inside the Codex chat box.",
         "  After `longtable start`, move into the created project directory and open `codex` there.",
         "",
-        "  longtable init [--flow quickstart|interview] [--provider codex|claude] [--career-stage <stage>] [--experience novice|intermediate|advanced] [--checkpoint low|balanced|high] [--field <field>] [--authorship-signal <text>] [--entry-mode explore|review|critique|draft|commit] [--weakest-domain theory|methodology|measurement|analysis|writing] [--panel-preference synthesis_only|show_on_conflict|always_visible] [--json] [--no-install] [--install-skills] [--install-prompts]",
-        "  longtable setup [--provider codex|claude] [--json] [--dir <path>] [--skills-dir <path>] [--runtime-path <file>] [--setup-path <file>]",
-        "  longtable start [--path <dir>] [--name <project>] [--goal <text>] [--blocker <text>] [--perspectives <role[,role]>] [--disagreement synthesis_only|show_on_conflict|always_visible] [--setup <path>] [--json]",
+        "  longtable setup [--provider codex|claude] [--install-scope user|project|none] [--surfaces cli_only|skills|skills_mcp|skills_mcp_sentinel] [--intervention advisory|balanced|strong] [--workspace create|later] [--project-dir <path>] [--json] [--dir <path>] [--skills-dir <path>] [--runtime-path <file>] [--setup-path <file>]",
+        "  longtable init [deprecated alias for setup; full legacy flags still supported for automation]",
+        "  longtable start [--path <dir>] [--name <project>] [--goal <text>] [--blocker <text>] [--research-object research_question|theory_framework|measurement_instrument|study_design|analysis_plan|manuscript] [--gap-risk known_gap|suspected_tacit_assumptions|diagnose] [--protected-decision theory|measurement|method|evidence_citation|authorship_voice|submission_public_sharing] [--perspectives <role[,role]>] [--disagreement synthesis_only|show_on_conflict|always_visible] [--setup <path>] [--json]",
         "  longtable resume [--cwd <path>] [--json]",
         "  longtable doctor [--cwd <path>] [--fix] [--json] [--codex-dir <path>] [--claude-dir <path>] [--codex-prompts-dir <path>] [--codex-runtime-path <file>] [--claude-runtime-path <file>]",
         "  longtable status [--cwd <path>] [--fix] [--json] [--codex-dir <path>] [--claude-dir <path>] [--codex-prompts-dir <path>] [--codex-runtime-path <file>] [--claude-runtime-path <file>]",
@@ -109,7 +109,7 @@ function usage() {
         "  longtable mcp install --provider all",
         "",
         "Examples:",
-        "  longtable init --flow interview --provider codex --install-skills",
+        "  longtable setup --provider codex",
         "  longtable start",
         "  longtable start --path ~/Research/My-Project --name \"AI Adoption Meta-Analysis\" --goal \"Narrow the review question\"",
         "  cd \"<project-path>\" && codex",
@@ -563,77 +563,72 @@ async function collectInteractiveAnswers(initialFlow) {
 }
 function buildPermissionSetupChoices() {
     return {
+        installScope: [
+            {
+                id: "user",
+                label: "User-level provider config",
+                description: "Why: available across projects. What you get: writes to ~/.codex or ~/.claude. Tradeoff: broader machine-level change."
+            },
+            {
+                id: "project",
+                label: "Current project only",
+                description: "Why: keeps LongTable local to this repository. What you get: project-scoped runtime files when supported. Tradeoff: not available elsewhere."
+            },
+            {
+                id: "none",
+                label: "Do not install provider files",
+                description: "Why: safest permission boundary. What you get: CLI setup record only. Tradeoff: no provider-native skills or MCP config."
+            }
+        ],
         surfaces: [
             {
                 id: "cli_only",
                 label: "CLI only",
-                description: "Why: least invasive. Tradeoff: no natural in-provider LongTable entrypoints."
+                description: "Why: least invasive. What you get: setup record and CLI commands. Tradeoff: no natural in-provider LongTable entrypoints."
             },
             {
                 id: "skills",
                 label: "Skills",
-                description: "Why: enables natural LongTable skill routing. Tradeoff: writes provider skill files."
+                description: "Why: enables natural LongTable skill routing. What you get: provider skills. Tradeoff: writes provider skill files."
             },
             {
                 id: "skills_mcp",
                 label: "Skills + MCP",
-                description: "Why: adds structured state access. Tradeoff: writes provider config for MCP transport."
+                description: "Why: adds structured state access. What you get: skills and MCP config. Tradeoff: writes provider config for MCP transport."
             },
             {
                 id: "skills_mcp_sentinel",
                 label: "Skills + MCP + Sentinel",
-                description: "Why: prepares advisory gap/tacit monitoring. Tradeoff: LongTable may nudge research turns."
+                description: "Why: prepares advisory gap/tacit monitoring. What you get: skills, MCP, and sentinel approval. Tradeoff: LongTable may nudge research turns."
             }
         ],
         intervention: [
             {
                 id: "advisory",
                 label: "Advisory",
-                description: "Why: notices gaps without blocking. Tradeoff: you may still miss hard commitments."
+                description: "Why: notices gaps without blocking. What you get: light nudges. Tradeoff: you may still miss hard commitments."
             },
             {
                 id: "balanced",
                 label: "Balanced",
-                description: "Why: blocks clear theory, measurement, method, or evidence commitments. Tradeoff: occasional stops."
+                description: "Why: blocks clear theory, measurement, method, or evidence commitments. What you get: recommended checkpoints. Tradeoff: occasional stops."
             },
             {
                 id: "strong",
                 label: "Strong",
-                description: "Why: maximizes judgment protection. Tradeoff: more interruption before closure."
+                description: "Why: maximizes judgment protection. What you get: stricter checkpoints. Tradeoff: more interruption before closure."
             }
         ],
-        tmux: [
-            {
-                id: "standard",
-                label: "Standard chat",
-                description: "Why: portable default. Tradeoff: checkpoints and gaps are less persistently visible."
-            },
+        workspace: [
             {
-                id: "hud",
-                label: "Research HUD",
-                description: "Why: keeps goals, blockers, and pending checkpoints visible. Requires tmux."
+                id: "create",
+                label: "Yes, create one now",
+                description: "Why: durable state needs .longtable/. What you get: decision log and CURRENT.md. Tradeoff: asks project-specific questions now."
             },
             {
-                id: "console",
-                label: "Research console",
-                description: "Why: enables a richer tmux layout for HUD and team discussion. Requires tmux."
-            }
-        ],
-        team: [
-            {
-                id: "off",
-                label: "Off",
-                description: "Why: simplest. Tradeoff: panel disagreement stays inside one LongTable response."
-            },
-            {
-                id: "panel",
-                label: "Structured panel",
-                description: "Why: role disagreement is visible without tmux. Tradeoff: not parallel."
-            },
-            {
-                id: "tmux_team",
-                label: "Tmux team discussion",
-                description: "Why: opens role panes for parallel debate. Tradeoff: terminal complexity and cleanup."
+                id: "later",
+                label: "No, prepare runtime only",
+                description: "Why: keeps setup short. What you get: runtime support without project state. Tradeoff: no durable research memory until `longtable start`."
             }
         ]
     };
@@ -645,6 +640,65 @@ function checkpointIntensityFromIntervention(choice) {
         return "low";
     return "balanced";
 }
+function shouldInstallSkills(scope, surfaces) {
+    return scope !== "none" && surfaces !== "cli_only";
+}
+function shouldInstallMcp(scope, surfaces) {
+    return scope !== "none" && (surfaces === "skills_mcp" || surfaces === "skills_mcp_sentinel");
+}
+function setupProjectRoot(args) {
+    return resolve(normalizeUserPath(typeof args["project-dir"] === "string" && args["project-dir"].trim()
+        ? args["project-dir"].trim()
+        : cwd()));
+}
+function setupInstallDir(provider, scope, customDir, projectRoot) {
+    if (customDir)
+        return customDir;
+    if (scope === "project")
+        return join(projectRoot, provider === "codex" ? ".codex" : ".claude", "skills");
+    return undefined;
+}
+function setupPathForScope(scope, args, projectRoot) {
+    if (typeof args["setup-path"] === "string")
+        return args["setup-path"];
+    if (scope === "project")
+        return join(projectRoot, ".longtable", "setup.json");
+    return undefined;
+}
+function runtimePathForScope(provider, scope, args, projectRoot) {
+    if (typeof args["runtime-path"] === "string")
+        return args["runtime-path"];
+    if (scope !== "project")
+        return undefined;
+    return join(projectRoot, ".longtable", provider === "codex" ? "codex-runtime.toml" : "claude-runtime.json");
+}
+function mcpArgsForScope(provider, scope, args, projectRoot) {
+    if (scope !== "project")
+        return args;
+    return {
+        ...args,
+        ...(provider === "codex" && typeof args["codex-config"] !== "string"
+            ? { "codex-config": join(projectRoot, ".codex", "config.toml") }
+            : {}),
+        ...(provider === "claude" && typeof args["claude-settings"] !== "string"
+            ? { "claude-settings": join(projectRoot, ".claude", "settings.json") }
+            : {})
+    };
+}
+function parseSetupInstallScope(value) {
+    return value === "user" || value === "project" || value === "none" ? value : undefined;
+}
+function parseSetupSurface(value) {
+    return value === "cli_only" || value === "skills" || value === "skills_mcp" || value === "skills_mcp_sentinel"
+        ? value
+        : undefined;
+}
+function parseSetupIntervention(value) {
+    return value === "advisory" || value === "balanced" || value === "strong" ? value : undefined;
+}
+function parseSetupWorkspace(value) {
+    return value === "create" || value === "later" ? value : undefined;
+}
 async function runSetup(args) {
     const json = args.json === true;
     const rl = createInterface({ input, output });
@@ -653,27 +707,30 @@ async function runSetup(args) {
             ? (args.provider === "claude" ? "claude" : "codex")
             : await promptChoice(rl, "Which provider should LongTable configure?", buildProviderChoices()));
         const choices = buildPermissionSetupChoices();
-        const surfaces = await promptChoice(rl, [
+        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 = await promptChoice(rl, "How strongly may LongTable interrupt research decisions?", choices.intervention);
-        const tmuxMode = await promptChoice(rl, "Should LongTable recommend a tmux-based research interface?", choices.tmux);
-        const teamMode = await promptChoice(rl, "Should LongTable enable agent/team discussion mode?", choices.team);
+        const intervention = parseSetupIntervention(args.intervention) ?? await promptChoice(rl, "How strongly may LongTable interrupt research decisions?", choices.intervention);
+        const workspacePreference = parseSetupWorkspace(args.workspace) ?? await promptChoice(rl, "Should LongTable create a project workspace now?", choices.workspace);
+        const projectRoot = setupProjectRoot(args);
         const outputValue = createPersistedSetupOutput({
             field: "unspecified",
             careerStage: "unspecified",
             experienceLevel: "advanced",
             preferredCheckpointIntensity: checkpointIntensityFromIntervention(intervention),
             preferredEntryMode: "explore",
-            panelPreference: teamMode === "off" ? "show_on_conflict" : "always_visible"
+            panelPreference: "show_on_conflict"
         }, provider, "quickstart");
         outputValue.initialState.explicitState = {
             ...outputValue.initialState.explicitState,
+            installScope,
             runtimeSurfaces: surfaces,
             interventionPosture: intervention,
-            tmuxMode,
-            teamMode
+            workspaceCreationPreference: workspacePreference,
+            tmuxMode: "standard",
+            teamMode: "panel"
         };
         if (surfaces === "skills_mcp_sentinel") {
             outputValue.initialState.inferredHypotheses.push({
@@ -683,44 +740,64 @@ async function runSetup(args) {
                 status: "confirmed"
             });
         }
-        const result = await saveSetupAndRuntimeConfig(outputValue, {
-            setupPath: typeof args["setup-path"] === "string" ? args["setup-path"] : undefined,
-            runtimePath: typeof args["runtime-path"] === "string" ? args["runtime-path"] : undefined
-        });
-        const installedSkills = surfaces === "cli_only"
+        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(), typeof args["skills-dir"] === "string" ? args["skills-dir"] : typeof args.dir === "string" ? args.dir : undefined)
-                : await installClaudeSkills(listRoleDefinitions(), typeof args["skills-dir"] === "string" ? args["skills-dir"] : typeof args.dir === "string" ? args.dir : undefined);
-        const mcpRequested = surfaces === "skills_mcp" || surfaces === "skills_mcp_sentinel";
-        if (mcpRequested && !json) {
-            console.log("");
-            console.log("MCP setup is approved. To write provider config now, run:");
-            console.log(`- longtable mcp install --provider ${provider} --write`);
+                ? await installCodexSkills(listRoleDefinitions(), scopedInstallDir)
+                : await installClaudeSkills(listRoleDefinitions(), scopedInstallDir);
+        let mcpInstall;
+        if (shouldInstallMcp(installScope, surfaces)) {
+            mcpInstall = await installMcpForSetup(provider, mcpArgsForScope(provider, installScope, args, projectRoot));
         }
         if (json) {
             console.log(JSON.stringify({
                 setup: outputValue,
                 runtime: result,
                 installedSkills: installedSkills.map((skill) => skill.name),
-                mcpRequested,
-                tmuxMode,
-                teamMode
+                mcpInstall,
+                workspacePreference
             }, null, 2));
             return;
         }
         console.log("");
         console.log(renderSetupSummary(outputValue));
         console.log("");
-        console.log(renderInstallSummary(result));
+        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 (tmuxMode !== "standard") {
+        if (mcpInstall) {
             console.log("");
-            console.log("Tmux recommendation:");
-            console.log("- macOS: brew install tmux");
-            console.log("- Ubuntu/Debian: sudo apt install tmux");
-            console.log("- Start HUD in an existing tmux session: longtable hud --tmux");
-            console.log("- Start a discussion team: longtable team --tmux --prompt \"...\"");
+            console.log(renderMcpInstallSummary(mcpInstall));
+        }
+        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 research-object and gap-risk prompts.");
+            await runStart({
+                setup: result.setupTarget.path
+            });
         }
     }
     finally {
@@ -734,6 +811,33 @@ function perspectiveChoices() {
         description: persona.shortDescription
     }));
 }
+function researchObjectChoices() {
+    return [
+        { id: "research_question", label: "Research question", description: "The main question, problem, or contribution boundary." },
+        { id: "theory_framework", label: "Theory framework", description: "Constructs, theory choice, or conceptual model." },
+        { id: "measurement_instrument", label: "Measurement/instrument", description: "Variables, scales, instruments, or operationalization." },
+        { id: "study_design", label: "Study design", description: "Methods, sample, intervention, or data collection design." },
+        { id: "analysis_plan", label: "Analysis plan", description: "Analytic strategy, models, coding, or interpretation plan." },
+        { id: "manuscript", label: "Manuscript", description: "Drafting, revision, voice, evidence, or submission writing." }
+    ];
+}
+function gapRiskChoices() {
+    return [
+        { id: "known_gap", label: "I know the gap", description: "The blocker is explicit and can be tracked directly." },
+        { id: "suspected_tacit_assumptions", label: "I suspect tacit assumptions", description: "There may be hidden commitments or unstated premises." },
+        { id: "diagnose", label: "Ask LongTable to diagnose it", description: "Let LongTable classify likely gaps during the session." }
+    ];
+}
+function protectedDecisionChoices() {
+    return [
+        { id: "theory", label: "Theory", description: "Do not let theory or construct choices settle quietly." },
+        { id: "measurement", label: "Measurement", description: "Do not let variables, scales, or instruments settle quietly." },
+        { id: "method", label: "Method", description: "Do not let design, sampling, or procedure choices settle quietly." },
+        { id: "evidence_citation", label: "Evidence/citation", description: "Do not let unsupported source or citation choices settle quietly." },
+        { id: "authorship_voice", label: "Authorship/voice", description: "Do not let writing voice or authorial judgment disappear quietly." },
+        { id: "submission_public_sharing", label: "Submission/public sharing", description: "Do not let public-facing commitments settle quietly." }
+    ];
+}
 function normalizePerspectiveList(value) {
     if (!value?.trim()) {
         return [];
@@ -748,6 +852,9 @@ async function collectProjectInterview(setup, args) {
         !(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 });
@@ -763,23 +870,29 @@ async function collectProjectInterview(setup, args) {
             console.log("");
         }
         const projectName = (typeof args.name === "string" && args.name.trim()) ||
-            (await promptText(rl, renderQuestionHeader(1, 6, "Project interview", "What should this project be called?"), true));
+            (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, 6, "Project interview", `Which parent directory should contain this project?\nLongTable will create this folder:\n${suggestedPath}`), true)), projectName));
+            : 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, 6, "Current session", "What are you trying to accomplish in this session?"), true));
+            (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, 6, "Current session", "What is the main blocker or uncertainty right now?"), false));
+            (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(5, 6, "Perspectives", "Which perspectives do you already know you want at the table? Leave everything unchecked for auto."), perspectiveChoices());
+            : 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(6, 6, "Disagreement", "How visible should disagreement between perspectives be in this project by default?"), [
+            (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",
@@ -801,6 +914,9 @@ async function collectProjectInterview(setup, args) {
             projectPath: projectPath.trim(),
             currentGoal: currentGoal.trim(),
             ...(currentBlocker?.trim() ? { currentBlocker: currentBlocker.trim() } : {}),
+            researchObject: researchObject.trim(),
+            gapRisk: gapRisk.trim(),
+            protectedDecision: protectedDecision.trim(),
             requestedPerspectives,
             disagreementPreference: disagreementPreference
         };
@@ -859,6 +975,11 @@ async function readPersistAnswers(args) {
     throw new Error("persist-init requires either --answers-json, --stdin, or the full set of setup flags.");
 }
 async function runInit(args) {
+    if (!hasCompleteFlagInput(args)) {
+        console.error("`longtable init` is deprecated. Use `longtable setup` for permission-first runtime setup.");
+        await runSetup(args);
+        return;
+    }
     const json = args.json === true;
     const installRuntime = args["no-install"] !== true;
     const installPrompts = args["install-prompts"] === true;
@@ -1056,6 +1177,34 @@ function renderMcpInstallSummary(result) {
     }
     return lines.join("\n").trimEnd();
 }
+async function installMcpForSetup(provider, args) {
+    const serverName = typeof args.name === "string" && args.name.trim()
+        ? args.name.trim()
+        : LONGTABLE_MCP_SERVER_NAME;
+    const packageSpec = resolveMcpPackageSpec(args);
+    const command = typeof args.command === "string" && args.command.trim() ? args.command.trim() : "npx";
+    const mcpArgs = command === "npx" ? ["-y", packageSpec] : [packageSpec];
+    const targets = [];
+    if (provider === "codex") {
+        const path = resolveCodexMcpConfigPath(args);
+        const block = renderCodexMcpBlock(serverName, command, mcpArgs);
+        const content = await writeCodexMcpConfig(path, block, serverName);
+        targets.push({ provider, path, format: "toml", content });
+    }
+    if (provider === "claude") {
+        const path = resolveClaudeMcpSettingsPath(args);
+        const content = await writeClaudeMcpSettings(path, serverName, command, mcpArgs);
+        targets.push({ provider, path, format: "json", content });
+    }
+    return {
+        serverName,
+        packageSpec,
+        command,
+        args: mcpArgs,
+        write: true,
+        targets
+    };
+}
 async function runMcpSubcommand(subcommand, args) {
     if (!subcommand || subcommand === "install" || subcommand === "print-config") {
         const serverName = typeof args.name === "string" && args.name.trim()
@@ -1268,7 +1417,7 @@ function renderDoctorStatus(status) {
         nextActions.push("longtable doctor --fix");
     }
     if (!status.setupExists) {
-        nextActions.push("longtable init --flow interview --provider codex --install-skills");
+        nextActions.push("longtable setup --provider codex");
     }
     if (!status.workspace.found) {
         nextActions.push("longtable start");
@@ -1360,7 +1509,7 @@ async function repairDoctorStatus(args, status) {
         repair.removedLegacyPromptFiles = await removeCodexPromptAliases(codexPromptsDir);
     }
     if (!status.setupExists) {
-        repair.skipped.push("runtime configs require a researcher setup; run `longtable init --flow interview --provider codex` first");
+        repair.skipped.push("runtime configs require setup approval; run `longtable setup --provider codex` first");
         return repair;
     }
     const setup = await loadSetupOutput(setupOverride);
@@ -2304,7 +2453,7 @@ async function runStart(args) {
     const setupPath = typeof args.setup === "string" ? args.setup : undefined;
     const existingSetup = await loadOptionalSetup(setupPath);
     if (!existingSetup) {
-        throw new Error("LongTable global setup is missing. Run `longtable init --flow interview` first.");
+        throw new Error("LongTable setup is missing. Run `longtable setup --provider codex` first.");
     }
     const interview = await collectProjectInterview(existingSetup, args);
     await verifyWritableWorkspaceParent(interview.projectPath);
@@ -2313,6 +2462,9 @@ async function runStart(args) {
         projectPath: interview.projectPath,
         currentGoal: interview.currentGoal,
         currentBlocker: interview.currentBlocker,
+        researchObject: interview.researchObject,
+        gapRisk: interview.gapRisk,
+        protectedDecision: interview.protectedDecision,
         requestedPerspectives: interview.requestedPerspectives,
         disagreementPreference: interview.disagreementPreference,
         setup: existingSetup

package/dist/project-session.d.ts

@@ -28,6 +28,9 @@ export interface LongTableSessionRecord {
     projectPath: string;
     currentGoal: string;
     currentBlocker?: string;
+    researchObject?: string;
+    gapRisk?: string;
+    protectedDecision?: string;
     nextAction?: string;
     openQuestions?: string[];
     requestedPerspectives: string[];
@@ -150,6 +153,9 @@ export declare function createOrUpdateProjectWorkspace(options: {
     projectPath: string;
     currentGoal: string;
     currentBlocker?: string;
+    researchObject?: string;
+    gapRisk?: string;
+    protectedDecision?: string;
     requestedPerspectives: string[];
     disagreementPreference: ProjectDisagreementPreference;
     setup: SetupPersistedOutput;

package/dist/project-session.js

@@ -99,6 +99,9 @@ function buildCurrentGuide(project, session, recentInvocations = [], pendingQues
             "## 지금 초점",
             `- 현재 목표: ${session.currentGoal}`,
             ...(session.currentBlocker ? [`- 현재 blocker: ${session.currentBlocker}`] : []),
+            ...(session.researchObject ? [`- 연구 객체: ${session.researchObject}`] : []),
+            ...(session.gapRisk ? [`- 공백/암묵지 위험: ${session.gapRisk}`] : []),
+            ...(session.protectedDecision ? [`- 보호할 결정: ${session.protectedDecision}`] : []),
             `- 다음 액션: ${nextAction}`,
             `- 관점: ${session.requestedPerspectives.length > 0 ? session.requestedPerspectives.join(", ") : "auto"}`,
             `- disagreement: ${session.disagreementPreference}`,
@@ -148,6 +151,9 @@ function buildCurrentGuide(project, session, recentInvocations = [], pendingQues
         "## Focus Now",
         `- Current goal: ${session.currentGoal}`,
         ...(session.currentBlocker ? [`- Current blocker: ${session.currentBlocker}`] : []),
+        ...(session.researchObject ? [`- Research object: ${session.researchObject}`] : []),
+        ...(session.gapRisk ? [`- Gap/tacit risk: ${session.gapRisk}`] : []),
+        ...(session.protectedDecision ? [`- Protected decision: ${session.protectedDecision}`] : []),
         `- Next action: ${nextAction}`,
         `- Perspectives: ${session.requestedPerspectives.length > 0 ? session.requestedPerspectives.join(", ") : "auto"}`,
         `- Disagreement: ${session.disagreementPreference}`,
@@ -335,6 +341,9 @@ function buildProjectAgentsMd(project, session) {
         `- Project: ${project.projectName}`,
         `- Current goal: ${session.currentGoal}`,
         ...(session.currentBlocker ? [`- Current blocker: ${session.currentBlocker}`] : []),
+        ...(session.researchObject ? [`- Research object: ${session.researchObject}`] : []),
+        ...(session.gapRisk ? [`- Gap/tacit risk: ${session.gapRisk}`] : []),
+        ...(session.protectedDecision ? [`- Protected decision: ${session.protectedDecision}`] : []),
         `- Requested perspectives: ${session.requestedPerspectives.length > 0 ? session.requestedPerspectives.join(", ") : "auto"}`,
         `- Disagreement visibility: ${session.disagreementPreference}`,
         "- These instructions apply to this directory and its children."
@@ -344,8 +353,8 @@ function buildStateSeed(project, session, setup) {
     const state = createEmptyResearchState();
     state.explicitState = {
         field: setup.profileSeed.field ?? "unspecified",
-        careerStage: setup.profileSeed.careerStage,
-        experienceLevel: setup.profileSeed.experienceLevel,
+        careerStage: setup.profileSeed.careerStage ?? "unspecified",
+        experienceLevel: setup.profileSeed.experienceLevel ?? "advanced",
         projectName: project.projectName,
         disagreementPreference: session.disagreementPreference,
         requestedPerspectives: session.requestedPerspectives
@@ -353,6 +362,9 @@ function buildStateSeed(project, session, setup) {
     state.workingState = {
         currentGoal: session.currentGoal,
         ...(session.currentBlocker ? { currentBlocker: session.currentBlocker } : {}),
+        ...(session.researchObject ? { researchObject: session.researchObject } : {}),
+        ...(session.gapRisk ? { gapRisk: session.gapRisk } : {}),
+        ...(session.protectedDecision ? { protectedDecision: session.protectedDecision } : {}),
         ...(session.nextAction ? { nextAction: session.nextAction } : {}),
         openQuestions: session.openQuestions ?? [],
         activeModes: session.activeModes ?? [],
@@ -361,6 +373,9 @@ function buildStateSeed(project, session, setup) {
     if (session.currentBlocker) {
         state.openTensions.push(session.currentBlocker);
     }
+    if (session.gapRisk) {
+        state.openTensions.push(`Gap/tacit risk: ${session.gapRisk}`);
+    }
     if (setup.profileSeed.humanAuthorshipSignal) {
         state.explicitState.humanAuthorshipSignal = setup.profileSeed.humanAuthorshipSignal;
     }
@@ -384,6 +399,21 @@ function buildStateSeed(project, session, setup) {
             importance: "high"
         });
     }
+    if (session.researchObject || session.gapRisk || session.protectedDecision) {
+        state.narrativeTraces.push({
+            id: "project-session-risk-profile",
+            timestamp: nowIso(),
+            source: "longtable-start",
+            traceType: "tension",
+            summary: [
+                session.researchObject ? `Research object: ${session.researchObject}.` : "",
+                session.gapRisk ? `Gap/tacit risk: ${session.gapRisk}.` : "",
+                session.protectedDecision ? `Protected decision: ${session.protectedDecision}.` : ""
+            ].filter(Boolean).join(" "),
+            visibility: "explicit",
+            importance: "high"
+        });
+    }
     return JSON.stringify(state, null, 2);
 }
 async function removeLegacyRootFiles(projectPath) {
@@ -908,9 +938,9 @@ export async function createOrUpdateProjectWorkspace(options) {
             locale,
             globalSetupSummary: {
                 field: options.setup.profileSeed.field ?? "unspecified",
-                careerStage: options.setup.profileSeed.careerStage,
-                experienceLevel: options.setup.profileSeed.experienceLevel,
-                checkpointIntensity: options.setup.profileSeed.preferredCheckpointIntensity,
+                careerStage: options.setup.profileSeed.careerStage ?? "unspecified",
+                experienceLevel: options.setup.profileSeed.experienceLevel ?? "advanced",
+                checkpointIntensity: options.setup.profileSeed.preferredCheckpointIntensity ?? "balanced",
                 ...(options.setup.profileSeed.humanAuthorshipSignal
                     ? { humanAuthorshipSignal: options.setup.profileSeed.humanAuthorshipSignal }
                     : {}),
@@ -931,6 +961,9 @@ export async function createOrUpdateProjectWorkspace(options) {
         projectPath,
         currentGoal: options.currentGoal,
         ...(options.currentBlocker ? { currentBlocker: options.currentBlocker } : {}),
+        ...(options.researchObject ? { researchObject: options.researchObject } : {}),
+        ...(options.gapRisk ? { gapRisk: options.gapRisk } : {}),
+        ...(options.protectedDecision ? { protectedDecision: options.protectedDecision } : {}),
         nextAction: buildNextAction({
             schemaVersion: 1,
             id: sessionId,
@@ -939,6 +972,9 @@ export async function createOrUpdateProjectWorkspace(options) {
             projectPath,
             currentGoal: options.currentGoal,
             ...(options.currentBlocker ? { currentBlocker: options.currentBlocker } : {}),
+            ...(options.researchObject ? { researchObject: options.researchObject } : {}),
+            ...(options.gapRisk ? { gapRisk: options.gapRisk } : {}),
+            ...(options.protectedDecision ? { protectedDecision: options.protectedDecision } : {}),
             requestedPerspectives: options.requestedPerspectives,
             disagreementPreference: options.disagreementPreference
         }),
@@ -950,6 +986,9 @@ export async function createOrUpdateProjectWorkspace(options) {
             projectPath,
             currentGoal: options.currentGoal,
             ...(options.currentBlocker ? { currentBlocker: options.currentBlocker } : {}),
+            ...(options.researchObject ? { researchObject: options.researchObject } : {}),
+            ...(options.gapRisk ? { gapRisk: options.gapRisk } : {}),
+            ...(options.protectedDecision ? { protectedDecision: options.protectedDecision } : {}),
             requestedPerspectives: options.requestedPerspectives,
             disagreementPreference: options.disagreementPreference
         }),
@@ -964,6 +1003,9 @@ export async function createOrUpdateProjectWorkspace(options) {
             projectPath,
             currentGoal: options.currentGoal,
             ...(options.currentBlocker ? { currentBlocker: options.currentBlocker } : {}),
+            ...(options.researchObject ? { researchObject: options.researchObject } : {}),
+            ...(options.gapRisk ? { gapRisk: options.gapRisk } : {}),
+            ...(options.protectedDecision ? { protectedDecision: options.protectedDecision } : {}),
             requestedPerspectives: options.requestedPerspectives,
             disagreementPreference: options.disagreementPreference
         }),

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@longtable/cli",
-  "version": "0.1.19",
+  "version": "0.1.20",
   "private": false,
   "description": "Researcher-facing LongTable CLI",
   "type": "module",
@@ -28,12 +28,12 @@
     "typecheck": "tsc -p tsconfig.json --noEmit"
   },
   "dependencies": {
-    "@longtable/checkpoints": "0.1.19",
-    "@longtable/core": "0.1.19",
-    "@longtable/memory": "0.1.19",
-    "@longtable/provider-claude": "0.1.19",
-    "@longtable/provider-codex": "0.1.19",
-    "@longtable/setup": "0.1.19"
+    "@longtable/checkpoints": "0.1.20",
+    "@longtable/core": "0.1.20",
+    "@longtable/memory": "0.1.20",
+    "@longtable/provider-claude": "0.1.20",
+    "@longtable/provider-codex": "0.1.20",
+    "@longtable/setup": "0.1.20"
   },
   "devDependencies": {
     "@types/node": "^22.10.1",