@longtable/cli 0.1.31 → 0.1.33

package/README.md

@@ -8,9 +8,9 @@ Claude skills, and future MCP surfaces remain generated adapter artifacts.
 
 The basic contract is:
 
-1. seed the researcher profile once
-2. create a workspace for each project
-3. continue the research conversation inside that workspace
+1. approve provider/runtime support once
+2. start each project inside the provider with `$longtable-interview`
+3. create or resume a workspace from that interview
 4. preserve decisions, tensions, and evidence as durable project state
 
 ## Install
@@ -26,15 +26,17 @@ config, hooks, or provider runtime files without explicit setup approval.
 
 ```bash
 longtable setup --provider codex
-longtable start
-cd "<project-path>"
+cd "<research-folder>"
 codex
 ```
 
+Then invoke `$longtable-interview` inside Codex.
+
 `longtable setup --provider codex` is the permission-first setup route. It asks
 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.
+strongly it may interrupt research decisions, and whether to show the
+provider-native interview launch steps. `longtable init` remains only as a
+deprecated compatibility alias.
 
 Return later:
 
@@ -44,7 +46,7 @@ longtable resume
 codex
 ```
 
-## What `longtable start` Creates
+## What `$longtable-interview` Creates
 
 ```text
 <project>/
@@ -84,7 +86,6 @@ This is how LongTable avoids turning tacit knowledge into fake certainty.
 
 ```bash
 longtable setup
-longtable start
 longtable resume --cwd "<project-path>"
 longtable roles
 longtable ask --cwd "<project-path>" --prompt "..."
@@ -136,12 +137,14 @@ longtable claude install-skills
 
 Codex skills include `longtable`, `longtable-panel`, and generated role-specific
 skills such as `longtable-methods-critic`. If your Codex build exposes explicit
-skill shortcuts, `$longtable` is the manual entry. Do not depend on `/prompts`;
-current Codex builds may reject it.
+skill shortcuts, `$longtable-interview` is the research-start entry and
+`$longtable` is the general router. Do not depend on `/prompts`; current Codex
+builds may reject it.
 
 Claude Code skills include `longtable`, `longtable-panel`, and generated
-role-specific skills such as `longtable-methods-critic`. They are adapter files
-generated from the LongTable role registry.
+role-specific skills such as `longtable-methods-critic`. They also include
+`longtable-interview` for the First Research Shape workflow. They are adapter
+files generated from the LongTable role registry.
 
 ## Panel Orchestration
 

package/dist/cli.js

@@ -6,6 +6,7 @@ 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 { fileURLToPath } from "node:url";
 import { classifyCheckpointTrigger } from "@longtable/checkpoints";
 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";
@@ -15,7 +16,8 @@ import { installCodexPromptAliases, listInstalledCodexPromptAliases, removeCodex
 import { buildPersonaGuidance, parseInvocationDirective } from "./persona-router.js";
 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 { LONGTABLE_MANAGED_HOOK_EVENTS, codexHooksEnabled, enableCodexHooksFeature, getMissingManagedCodexHookEvents, mergeManagedCodexHooksConfig, removeManagedCodexHooks } from "./codex-hooks.js";
+import { appendInvocationRecordToWorkspace, assertWorkspaceNotBlocked, answerWorkspaceQuestion, clearWorkspaceQuestion, createWorkspaceFollowUpQuestions, createWorkspaceQuestion, createOrUpdateProjectWorkspace, inspectProjectWorkspace, loadWorkspaceState, loadProjectContextFromDirectory, repairWorkspaceStateConsistency, renderProjectWorkspaceSummary, syncCurrentWorkspaceView } from "./project-session.js";
 import { buildTeamDebate, buildTeamReview, renderTeamDebateSummary } from "./debate.js";
 import { createPromptRenderer } from "./prompt-renderer.js";
 const VALID_MODES = new Set([
@@ -43,7 +45,7 @@ const ANSI = {
     green: "\u001B[32m"
 };
 const LONGTABLE_MCP_SERVER_NAME = "longtable-state";
-const LONGTABLE_MCP_PACKAGE_VERSION = "0.1.31";
+const LONGTABLE_MCP_PACKAGE_VERSION = "0.1.33";
 const LONGTABLE_MCP_MARKER_START = "# LongTable state MCP START";
 const LONGTABLE_MCP_MARKER_END = "# LongTable state MCP END";
 function style(text, prefix) {
@@ -68,6 +70,20 @@ function renderBrandBanner(title, subtitle) {
     }
     return lines.join("\n");
 }
+function renderInterviewLaunchSteps(provider) {
+    const command = provider === "codex" ? "codex" : "claude";
+    return renderSectionCard("LongTable Interview", [
+        "Setup is permission and runtime calibration, not the research interview.",
+        "The first research conversation now happens inside the provider so the model can listen, reflect, and ask one natural-language follow-up at a time.",
+        "",
+        "Next:",
+        "1. cd \"<research-folder>\"",
+        `2. run \`${command}\``,
+        "3. invoke `$longtable-interview`",
+        "",
+        "The interview will create or resume `.longtable/`, build a First Research Shape, and use option UI only for the final confirmation."
+    ]);
+}
 function renderProgressBar(current, total) {
     const width = 10;
     const filled = Math.max(1, Math.round((current / total) * width));
@@ -77,14 +93,14 @@ function usage() {
     return [
         "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 research starts inside Codex or Claude with `$longtable-interview` after setup.",
         "",
         "  longtable setup [--provider codex|claude] [--install-scope user|project|none] [--surfaces cli_only|skills|skills_mcp|skills_mcp_sentinel] [--intervention advisory|balanced|strong] [--checkpoint-ui off|interactive|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 start [deprecated fallback] [--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] [--no-interview]",
         "  longtable resume [--cwd <path>] [--json]",
-        "  longtable doctor [--cwd <path>] [--fix] [--json] [--codex-dir <path>] [--codex-config <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>] [--codex-config <path>] [--claude-dir <path>] [--codex-prompts-dir <path>] [--codex-runtime-path <file>] [--claude-runtime-path <file>]",
+        "  longtable doctor [--cwd <path>] [--fix] [--json] [--codex-dir <path>] [--codex-config <path>] [--hooks-path <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>] [--codex-config <path>] [--hooks-path <path>] [--claude-dir <path>] [--codex-prompts-dir <path>] [--codex-runtime-path <file>] [--claude-runtime-path <file>]",
         "  longtable roles [--json]",
         "  longtable show [--json] [--path <file>]",
         "  longtable install [--json] [--path <file>] [--runtime-path <file>]",
@@ -98,6 +114,7 @@ function usage() {
         "  longtable ask [--prompt <text>] [--print] [--json] [--setup <path>] [--cwd <path>]",
         "  longtable clarify --prompt <task-context> [--provider codex|claude] [--required|--advisory] [--print] [--cwd <path>] [--json] [--force]",
         "  longtable question --prompt <decision-context> [--title <text>] [--text <question>] [--provider codex|claude] [--required|--advisory] [--print] [--cwd <path>] [--json]",
+        "  longtable clear-question --question <id> --reason <text> [--cwd <path>] [--json]",
         "  longtable panel [--prompt <text>] [--role <role[,role]>] [--mode review|critique|draft|commit] [--visibility synthesis_only|show_on_conflict|always_visible] [--print] [--json] [--setup <path>] [--cwd <path>]",
         "  longtable decide [--question <id>] --answer <value-or-text> [--rationale <text>] [--provider codex|claude] [--cwd <path>] [--json]",
         "  longtable explore|review|critique|draft|commit|submit [--prompt <text>] [--role <role[,role]>] [--panel] [--show-conflicts] [--show-deliberation] [--print] [--json] [--stage <stage>] [--setup <path>] [--cwd <path>]",
@@ -106,7 +123,9 @@ function usage() {
         "  longtable codex remove-skills [--dir <path>]",
         "  longtable codex install-prompts [--dir <path>]",
         "  longtable codex remove-prompts [--dir <path>]",
-        "  longtable codex status [--dir <path>] [--json]",
+        "  longtable codex install-hooks [--codex-config <path>] [--hooks-path <path>] [--json]",
+        "  longtable codex remove-hooks [--codex-config <path>] [--hooks-path <path>] [--json]",
+        "  longtable codex status [--dir <path>] [--codex-config <path>] [--hooks-path <path>] [--json]",
         "  longtable claude install-skills [--dir <path>]",
         "  longtable claude remove-skills [--dir <path>]",
         "  longtable claude status [--dir <path>] [--json]",
@@ -114,9 +133,9 @@ function usage() {
         "",
         "Examples:",
         "  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",
+        "  cd \"<research-folder>\" && codex",
+        "  $longtable-interview",
+        "  longtable start --no-interview --path ~/Research/My-Project --name \"AI Adoption Meta-Analysis\" --goal \"Narrow the review question\"",
         "  longtable doctor",
         "  longtable roles",
         "  longtable ask --prompt \"연구를 시작하고 싶어. 지금 어디서부터 좁혀야 할지 모르겠어.\"",
@@ -130,7 +149,7 @@ function parseArgs(argv) {
     const values = {};
     let subcommand = maybeSubcommand;
     const modeCommand = command && VALID_MODES.has(command);
-    const directCommand = command && ["init", "setup", "start", "resume", "doctor", "status", "roles", "show", "install", "mcp", "codex", "claude", "ask", "clarify", "question", "panel", "decide", "sentinel", "team", "search"].includes(command);
+    const directCommand = command && ["init", "setup", "start", "resume", "doctor", "status", "roles", "show", "install", "mcp", "codex", "claude", "ask", "clarify", "question", "clear-question", "panel", "decide", "sentinel", "team", "search"].includes(command);
     let startIndex = 1;
     if (modeCommand) {
         subcommand = undefined;
@@ -447,13 +466,13 @@ function buildPermissionSetupChoices() {
         workspace: [
             {
                 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."
+                label: "Show interview launch steps",
+                description: "Why: research should start inside the provider. What you get: setup finishes with Codex/Claude + $longtable-interview steps. Tradeoff: workspace creation waits for the in-provider interview."
             },
             {
                 id: "later",
                 label: "No, prepare runtime only",
-                description: "Why: keeps setup short. What you get: runtime support without project state. Tradeoff: no durable research memory until `longtable start`."
+                description: "Why: keeps setup short. What you get: runtime support without project state. Tradeoff: no durable research memory until `$longtable-interview` creates or resumes a workspace."
             }
         ]
     };
@@ -575,6 +594,8 @@ async function runSetup(args) {
         interventionPosture: effectiveIntervention,
         checkpointUiMode: checkpointUi,
         workspaceCreationPreference: workspacePreference,
+        officialStartSurface: "$longtable-interview",
+        setupPosture: "permission_first",
         teamMode: "panel"
     };
     if (surfaces === "skills_mcp_sentinel") {
@@ -617,7 +638,12 @@ async function runSetup(args) {
             runtime: result,
             installedSkills: installedSkills.map((skill) => skill.name),
             mcpInstall,
-            workspacePreference
+            workspacePreference,
+            nextStep: {
+                surface: "$longtable-interview",
+                command: provider === "codex" ? "codex" : "claude",
+                description: "Open the provider in the research folder and invoke `$longtable-interview`."
+            }
         }, null, 2));
         return;
     }
@@ -646,12 +672,11 @@ async function runSetup(args) {
         console.log("Background sentinel approval recorded.");
         console.log("Hook installation remains opt-in; LongTable will not install hooks without an explicit hook command.");
     }
+    console.log("");
+    console.log(renderInterviewLaunchSteps(provider));
     if (workspacePreference === "create") {
         console.log("");
-        console.log("Project workspace requested. LongTable will now run `longtable start` with an adaptive start interview.");
-        await runStart({
-            setup: result.setupTarget.path
-        });
+        console.log("Workspace launch requested. Open the provider in your research folder and run `$longtable-interview`; the interview will create `.longtable/` there.");
     }
 }
 function perspectiveChoices() {
@@ -849,6 +874,7 @@ function normalizePerspectiveList(value) {
         .filter(Boolean);
 }
 async function collectProjectInterview(setup, args) {
+    const skipResearchInterview = args["no-interview"] === true;
     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;
@@ -863,11 +889,11 @@ async function collectProjectInterview(setup, args) {
         : undefined;
     const needsInteractivePrompts = !(typeof args.name === "string" && args.name.trim()) ||
         !(typeof args.path === "string" && args.path.trim()) ||
-        !providedGoal ||
-        !providedBlocker ||
-        !providedResearchObject ||
-        !providedGapRisk ||
-        !providedProtectedDecision;
+        (!skipResearchInterview && (!providedGoal ||
+            !providedBlocker ||
+            !providedResearchObject ||
+            !providedGapRisk ||
+            !providedProtectedDecision));
     if (needsInteractivePrompts) {
         console.log("");
         console.log(renderBrandBanner("LongTable", "Project workspace interview"));
@@ -887,15 +913,17 @@ async function collectProjectInterview(setup, args) {
     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${suggestedPath}`), true)), projectName));
-    const adaptive = await collectAdaptiveStartInterview({
-        currentGoal: providedGoal,
-        currentBlocker: providedBlocker,
-        needsResearchSeed: !providedGoal ||
-            !providedBlocker ||
-            !providedResearchObject ||
-            !providedGapRisk ||
-            !providedProtectedDecision
-    });
+    const adaptive = skipResearchInterview
+        ? {}
+        : await collectAdaptiveStartInterview({
+            currentGoal: providedGoal,
+            currentBlocker: providedBlocker,
+            needsResearchSeed: !providedGoal ||
+                !providedBlocker ||
+                !providedResearchObject ||
+                !providedGapRisk ||
+                !providedProtectedDecision
+        });
     const currentGoal = providedGoal ?? adaptive.currentGoal;
     if (!currentGoal?.trim()) {
         throw new Error("LongTable start needs a current research goal or an opening interview answer.");
@@ -1090,6 +1118,16 @@ function resolveCodexMcpConfigPath(args) {
         ? args["codex-config"].trim()
         : "~/.codex/config.toml"));
 }
+function resolveCodexHooksPath(args) {
+    if (typeof args["hooks-path"] === "string" && args["hooks-path"].trim()) {
+        return resolve(normalizeUserPath(args["hooks-path"]));
+    }
+    const configPath = resolveCodexMcpConfigPath(args);
+    return resolve(dirname(configPath), "hooks.json");
+}
+function resolveCliPackageRoot() {
+    return resolve(fileURLToPath(new URL("..", import.meta.url)));
+}
 function resolveClaudeMcpSettingsPath(args) {
     return resolve(normalizeUserPath(typeof args["claude-settings"] === "string" && args["claude-settings"].trim()
         ? args["claude-settings"].trim()
@@ -1172,6 +1210,56 @@ async function writeClaudeMcpSettings(path, serverName, command, mcpArgs) {
     await writeFile(path, `${updated}\n`, "utf8");
     return `${updated}\n`;
 }
+async function installCodexNativeHooks(args) {
+    const configPath = resolveCodexMcpConfigPath(args);
+    const hooksPath = resolveCodexHooksPath(args);
+    const packageRoot = resolveCliPackageRoot();
+    const existingConfig = existsSync(configPath) ? await readFile(configPath, "utf8") : "";
+    const existingHooks = existsSync(hooksPath) ? await readFile(hooksPath, "utf8") : "";
+    const nextConfig = enableCodexHooksFeature(existingConfig);
+    const nextHooks = mergeManagedCodexHooksConfig(existingHooks, packageRoot);
+    await mkdir(dirname(configPath), { recursive: true });
+    await mkdir(dirname(hooksPath), { recursive: true });
+    await writeFile(configPath, nextConfig, "utf8");
+    await writeFile(hooksPath, nextHooks, "utf8");
+    return {
+        configPath,
+        hooksPath,
+        codexHooksEnabled: codexHooksEnabled(nextConfig),
+        managedEvents: [...LONGTABLE_MANAGED_HOOK_EVENTS],
+        write: true
+    };
+}
+async function removeCodexNativeHooks(args) {
+    const configPath = resolveCodexMcpConfigPath(args);
+    const hooksPath = resolveCodexHooksPath(args);
+    const existingHooks = existsSync(hooksPath) ? await readFile(hooksPath, "utf8") : "";
+    const removed = existingHooks ? removeManagedCodexHooks(existingHooks) : { nextContent: null, removedCount: 0 };
+    if (removed.nextContent === null) {
+        await rm(hooksPath, { force: true });
+    }
+    else {
+        await mkdir(dirname(hooksPath), { recursive: true });
+        await writeFile(hooksPath, removed.nextContent, "utf8");
+    }
+    const configContent = existsSync(configPath) ? await readFile(configPath, "utf8") : "";
+    return {
+        configPath,
+        hooksPath,
+        codexHooksEnabled: codexHooksEnabled(configContent),
+        managedEvents: removed.removedCount > 0 ? [...LONGTABLE_MANAGED_HOOK_EVENTS] : [],
+        write: true
+    };
+}
+function renderCodexHookInstallSummary(result) {
+    return [
+        "LongTable Codex hooks",
+        `- config: ${result.configPath}`,
+        `- hooks: ${result.hooksPath}`,
+        `- codex_hooks feature: ${result.codexHooksEnabled ? "enabled" : "missing"}`,
+        `- managed events: ${result.managedEvents.length > 0 ? result.managedEvents.join(", ") : "none"}`
+    ].join("\n");
+}
 function renderMcpInstallSummary(result) {
     const lines = [
         "LongTable MCP transport",
@@ -1358,6 +1446,13 @@ async function collectDoctorStatus(args) {
     const codexMcpConfig = existsSync(codexMcpConfigPath)
         ? await readFile(codexMcpConfigPath, "utf8")
         : "";
+    const codexHooksPath = resolveCodexHooksPath(args);
+    const codexHooksContent = existsSync(codexHooksPath)
+        ? await readFile(codexHooksPath, "utf8")
+        : "";
+    const missingManagedHookEvents = codexHooksContent
+        ? (getMissingManagedCodexHookEvents(codexHooksContent) ?? [...LONGTABLE_MANAGED_HOOK_EVENTS])
+        : [...LONGTABLE_MANAGED_HOOK_EVENTS];
     const expectedCodexSkills = buildCodexSkillSpecs(roles).map((skill) => skill.name);
     const expectedClaudeSkills = buildClaudeSkillSpecs(roles).map((skill) => skill.name);
     const [codexSkills, claudeSkills, codexAliases, workspace] = await Promise.all([
@@ -1386,7 +1481,11 @@ async function collectDoctorStatus(args) {
                 mcpConfigPath: codexMcpConfigPath,
                 mcpConfigExists: existsSync(codexMcpConfigPath),
                 longtableMcpConfigured: codexLongTableMcpConfigured(codexMcpConfig),
-                mcpElicitationsAllowed: codexMcpElicitationsAllowed(codexMcpConfig)
+                mcpElicitationsAllowed: codexMcpElicitationsAllowed(codexMcpConfig),
+                hooksPath: codexHooksPath,
+                hooksExists: existsSync(codexHooksPath),
+                codexHooksEnabled: codexHooksEnabled(codexMcpConfig),
+                missingManagedHookEvents
             },
             claude: {
                 command: "claude",
@@ -1428,6 +1527,9 @@ function renderDoctorStatus(status) {
         `- MCP config: ${status.providers.codex.mcpConfigExists ? "present" : "missing"} (${status.providers.codex.mcpConfigPath})`,
         `- LongTable MCP: ${status.providers.codex.longtableMcpConfigured ? "configured" : "missing"}`,
         `- MCP elicitation approval: ${status.providers.codex.mcpElicitationsAllowed ? "allowed" : "not allowed"}`,
+        `- Codex hooks file: ${status.providers.codex.hooksExists ? "present" : "missing"} (${status.providers.codex.hooksPath})`,
+        `- codex_hooks feature: ${status.providers.codex.codexHooksEnabled ? "enabled" : "missing"}`,
+        `- managed hook coverage: ${status.providers.codex.missingManagedHookEvents.length === 0 ? "complete" : `missing ${status.providers.codex.missingManagedHookEvents.join(", ")}`}`,
         "",
         ...renderProviderDoctorBlock("Claude", status.providers.claude),
         "",
@@ -1438,7 +1540,7 @@ function renderDoctorStatus(status) {
     }
     else {
         const workspace = status.workspace;
-        lines.push(`- project: ${workspace.project?.name ?? "unknown"}`, `- root: ${workspace.rootPath ?? "unknown"}`, `- goal: ${workspace.session?.currentGoal ?? "unknown"}`, `- invocations: ${workspace.counts?.invocations ?? 0}`, `- questions: ${workspace.counts?.questions ?? 0} (${workspace.counts?.pendingQuestions ?? 0} pending, ${workspace.counts?.answeredQuestions ?? 0} answered)`, `- decisions: ${workspace.counts?.decisions ?? 0}`);
+        lines.push(`- project: ${workspace.project?.name ?? "unknown"}`, `- root: ${workspace.rootPath ?? "unknown"}`, `- goal: ${workspace.session?.currentGoal ?? "unknown"}`, `- invocations: ${workspace.counts?.invocations ?? 0}`, `- questions: ${workspace.counts?.questions ?? 0} (${workspace.counts?.pendingQuestions ?? 0} pending, ${workspace.counts?.answeredQuestions ?? 0} answered)`, `- obligations: ${workspace.counts?.pendingObligations ?? 0} pending`, `- decisions: ${workspace.counts?.decisions ?? 0}`);
         if ((workspace.recentInvocations ?? []).length > 0) {
             lines.push("- recent invocations:");
             for (const invocation of workspace.recentInvocations ?? []) {
@@ -1452,6 +1554,12 @@ function renderDoctorStatus(status) {
                 lines.push(`  - ${question.id}: ${question.question} (${question.options.join("/")})`);
             }
         }
+        if ((workspace.pendingObligations ?? []).length > 0) {
+            lines.push("- pending obligations:");
+            for (const obligation of workspace.pendingObligations ?? []) {
+                lines.push(`  - ${obligation.id}: ${obligation.prompt}`);
+            }
+        }
         if ((workspace.answerWarnings ?? []).length > 0) {
             lines.push("- answer warnings:");
             for (const warning of workspace.answerWarnings ?? []) {
@@ -1466,11 +1574,16 @@ function renderDoctorStatus(status) {
     const canFix = status.providers.codex.missingSkills.length > 0 ||
         status.providers.claude.missingSkills.length > 0 ||
         status.providers.codex.legacyPromptFilesInstalled.length > 0 ||
+        !status.providers.codex.codexHooksEnabled ||
+        status.providers.codex.missingManagedHookEvents.length > 0 ||
         (status.setupExists &&
             (!status.providers.codex.runtimeExists || !status.providers.claude.runtimeExists));
     if (canFix) {
         nextActions.push("longtable doctor --fix");
     }
+    if (!status.providers.codex.codexHooksEnabled || status.providers.codex.missingManagedHookEvents.length > 0) {
+        nextActions.push("longtable codex install-hooks");
+    }
     if (!status.setupExists) {
         nextActions.push("longtable setup --provider codex");
     }
@@ -1500,6 +1613,15 @@ function renderRepairSummary(repair) {
     if (repair.removedLegacyPromptFiles.length > 0) {
         lines.push(`- removed legacy prompt files: ${repair.removedLegacyPromptFiles.length}`);
     }
+    if (repair.installedCodexHooks) {
+        lines.push("- installed Codex native hooks");
+    }
+    if ((repair.repairedWorkspaceState ?? []).length > 0) {
+        lines.push("- repaired workspace state:");
+        for (const item of repair.repairedWorkspaceState ?? []) {
+            lines.push(`  - ${item}`);
+        }
+    }
     if (repair.writtenRuntimeConfigs.length > 0) {
         lines.push("- wrote runtime configs:");
         for (const target of repair.writtenRuntimeConfigs) {
@@ -1551,6 +1673,8 @@ async function repairDoctorStatus(args, status) {
         installedCodexSkills: [],
         installedClaudeSkills: [],
         removedLegacyPromptFiles: [],
+        installedCodexHooks: false,
+        repairedWorkspaceState: [],
         writtenRuntimeConfigs: [],
         skipped: []
     };
@@ -1563,8 +1687,16 @@ async function repairDoctorStatus(args, status) {
     if (status.providers.codex.legacyPromptFilesInstalled.length > 0) {
         repair.removedLegacyPromptFiles = await removeCodexPromptAliases(codexPromptsDir);
     }
+    if (!status.providers.codex.codexHooksEnabled || status.providers.codex.missingManagedHookEvents.length > 0) {
+        await installCodexNativeHooks(args);
+        repair.installedCodexHooks = true;
+    }
     if (!status.setupExists) {
         repair.skipped.push("runtime configs require setup approval; run `longtable setup --provider codex` first");
+        const workspaceContext = await loadProjectContextFromDirectory(typeof args.cwd === "string" ? args.cwd : cwd());
+        if (workspaceContext) {
+            repair.repairedWorkspaceState = (await repairWorkspaceStateConsistency({ context: workspaceContext })).repaired;
+        }
         return repair;
     }
     const setup = await loadSetupOutput(setupOverride);
@@ -1584,6 +1716,10 @@ async function repairDoctorStatus(args, status) {
             format: target.format
         });
     }
+    const workspaceContext = await loadProjectContextFromDirectory(typeof args.cwd === "string" ? args.cwd : cwd());
+    if (workspaceContext) {
+        repair.repairedWorkspaceState = (await repairWorkspaceStateConsistency({ context: workspaceContext })).repaired;
+    }
     return repair;
 }
 async function runDoctor(args) {
@@ -2308,6 +2444,41 @@ async function runQuestion(args) {
     console.log(`- answer: longtable decide --question ${result.question.id} --answer <value>`);
     console.log(`- current: ${context.currentFilePath}`);
 }
+async function runClearQuestion(args) {
+    const workingDirectory = typeof args.cwd === "string" ? args.cwd : cwd();
+    const questionId = typeof args.question === "string" ? args.question.trim() : "";
+    const reason = typeof args.reason === "string" ? args.reason.trim() : "";
+    if (!questionId) {
+        throw new Error("`clear-question` requires --question <id>.");
+    }
+    if (!reason) {
+        throw new Error("`clear-question` requires --reason <text>.");
+    }
+    const context = await loadProjectContextFromDirectory(workingDirectory);
+    if (!context) {
+        throw new Error("No LongTable project workspace was found here. Run this inside a project or pass --cwd.");
+    }
+    const result = await clearWorkspaceQuestion({
+        context,
+        questionId,
+        reason
+    });
+    if (args.json === true) {
+        console.log(JSON.stringify({
+            question: result.question,
+            files: {
+                state: context.stateFilePath,
+                current: context.currentFilePath
+            }
+        }, null, 2));
+        return;
+    }
+    console.log("LongTable question cleared");
+    console.log(`- question: ${result.question.id}`);
+    console.log(`- reason: ${result.question.clearedReason ?? reason}`);
+    console.log(`- state: ${context.stateFilePath}`);
+    console.log(`- current: ${context.currentFilePath}`);
+}
 function isInteractiveTerminal() {
     return Boolean(input.isTTY && output.isTTY);
 }
@@ -2773,6 +2944,26 @@ async function runRoles(args) {
     }
 }
 async function runStart(args) {
+    const hasMinimalFallbackArgs = typeof args.name === "string" &&
+        typeof args.path === "string" &&
+        typeof args.goal === "string";
+    const hasFallbackIntent = args["no-interview"] === true ||
+        hasMinimalFallbackArgs;
+    if (!hasFallbackIntent) {
+        console.log(renderSectionCard("LongTable Start Has Moved", [
+            "`longtable start` is now a fallback for automation and scripted workspace creation.",
+            "The primary research-start experience is provider-native so LongTable can run a real interview instead of a terminal questionnaire.",
+            "",
+            "Use:",
+            "1. longtable setup --provider codex",
+            "2. cd \"<research-folder>\"",
+            "3. codex",
+            "4. $longtable-interview",
+            "",
+            "For automation, pass `--no-interview --json` with `--name`, `--path`, and `--goal`."
+        ]));
+        return;
+    }
     const setupPath = typeof args.setup === "string" ? args.setup : undefined;
     const existingSetup = await loadOptionalSetup(setupPath);
     if (!existingSetup) {
@@ -2890,11 +3081,34 @@ async function runCodexSubcommand(subcommand, args) {
         console.log(`Removed ${removed.length} legacy LongTable prompt files from ${resolveCodexPromptsDir(customDir)}`);
         return;
     }
+    if (subcommand === "install-hooks") {
+        const result = await installCodexNativeHooks(args);
+        if (args.json === true) {
+            console.log(JSON.stringify(result, null, 2));
+            return;
+        }
+        console.log(renderCodexHookInstallSummary(result));
+        console.log("Restart Codex so the native hook config is reloaded.");
+        return;
+    }
+    if (subcommand === "remove-hooks") {
+        const result = await removeCodexNativeHooks(args);
+        if (args.json === true) {
+            console.log(JSON.stringify(result, null, 2));
+            return;
+        }
+        console.log(renderCodexHookInstallSummary(result));
+        return;
+    }
     if (subcommand === "status") {
         const aliases = await listInstalledCodexPromptAliases(customDir);
         const skills = await listInstalledCodexSkills(roles, customDir);
         const setupPath = resolveDefaultSetupPath(typeof args.path === "string" ? args.path : undefined).path;
         const runtimePath = resolveDefaultRuntimeConfigPath("codex", typeof args["runtime-path"] === "string" ? args["runtime-path"] : undefined).path;
+        const configPath = resolveCodexMcpConfigPath(args);
+        const configContent = existsSync(configPath) ? await readFile(configPath, "utf8") : "";
+        const hooksPath = resolveCodexHooksPath(args);
+        const hooksContent = existsSync(hooksPath) ? await readFile(hooksPath, "utf8") : "";
         const status = {
             setupPath,
             setupExists: existsSync(setupPath),
@@ -2903,7 +3117,14 @@ async function runCodexSubcommand(subcommand, args) {
             skillsDir: resolveCodexSkillsDir(customDir),
             skillsInstalled: skills.map((skill) => skill.name),
             promptsDir: resolveCodexPromptsDir(customDir),
-            legacyPromptFilesInstalled: aliases.map((alias) => alias.name)
+            legacyPromptFilesInstalled: aliases.map((alias) => alias.name),
+            codexConfigPath: configPath,
+            codexHooksEnabled: codexHooksEnabled(configContent),
+            hooksPath,
+            hooksExists: existsSync(hooksPath),
+            missingManagedHookEvents: hooksContent
+                ? (getMissingManagedCodexHookEvents(hooksContent) ?? [...LONGTABLE_MANAGED_HOOK_EVENTS])
+                : [...LONGTABLE_MANAGED_HOOK_EVENTS]
         };
         if (args.json === true) {
             console.log(JSON.stringify(status, null, 2));
@@ -2933,6 +3154,10 @@ async function runCodexSubcommand(subcommand, args) {
                 console.log(`  - ${alias.name}`);
             }
         }
+        console.log(`- codex config: ${status.codexConfigPath}`);
+        console.log(`- codex_hooks feature: ${status.codexHooksEnabled ? "enabled" : "missing"}`);
+        console.log(`- hooks file: ${status.hooksExists ? "present" : "missing"} (${status.hooksPath})`);
+        console.log(`- managed hook coverage: ${status.missingManagedHookEvents.length === 0 ? "complete" : `missing ${status.missingManagedHookEvents.join(", ")}`}`);
         return;
     }
     throw new Error("Unknown codex subcommand.");
@@ -3046,6 +3271,10 @@ async function main() {
         await runQuestion(values);
         return;
     }
+    if (command === "clear-question") {
+        await runClearQuestion(values);
+        return;
+    }
     if (command === "panel") {
         await runPanelCommand(values);
         return;

package/dist/codex-hooks.d.ts

@@ -0,0 +1,22 @@
+export declare const LONGTABLE_MANAGED_HOOK_EVENTS: readonly ["SessionStart", "PreToolUse", "PostToolUse", "UserPromptSubmit", "Stop"];
+type ManagedHookEventName = (typeof LONGTABLE_MANAGED_HOOK_EVENTS)[number];
+type JsonObject = Record<string, unknown>;
+export interface ManagedCodexHooksConfig {
+    hooks: Record<ManagedHookEventName, Array<Record<string, unknown>>>;
+}
+interface ParsedCodexHooksConfig {
+    root: JsonObject;
+    hooks: JsonObject;
+}
+export interface RemoveManagedCodexHooksResult {
+    nextContent: string | null;
+    removedCount: number;
+}
+export declare function buildManagedCodexHooksConfig(packageRoot: string): ManagedCodexHooksConfig;
+export declare function parseCodexHooksConfig(content: string): ParsedCodexHooksConfig | null;
+export declare function getMissingManagedCodexHookEvents(content: string): ManagedHookEventName[] | null;
+export declare function mergeManagedCodexHooksConfig(existingContent: string | null | undefined, packageRoot: string): string;
+export declare function removeManagedCodexHooks(existingContent: string): RemoveManagedCodexHooksResult;
+export declare function enableCodexHooksFeature(existing: string): string;
+export declare function codexHooksEnabled(config: string): boolean;
+export {};