arkgate 3.6.0 → 3.6.1

package/CHANGELOG.md

@@ -4,6 +4,29 @@ All notable changes to ArkGate (`arkgate`; formerly `ark-runtime-kernel`) are do
 
 ## Unreleased
 
+## 3.6.1 — 2026-07-17
+
+Codex project-scoped MCP fix. **No breaking** CLI, MCP tool, or `ark.config.json` changes.
+**No gate weaken.**
+
+### Fixed
+
+- **Codex MCP follows the active repository:** `--install-agent-gates --tools codex` now writes
+  `.codex/config.toml` with relative project paths. Each repository owns its primary `ark`
+  binding, so `ark upgrade` no longer leaves Codex resolving `ark://manifest` through another
+  permanent project registered in the global home config.
+- **Doctor effective-config honesty:** Codex advisory-MCP capability and adoption checks prefer
+  a valid project `.codex/config.toml`; an unrelated `$CODEX_HOME` primary no longer produces a
+  false `write-path-none` or `codex-home-multi-project` warning.
+- **Ephemeral worktree cleanup:** roots under `.claude/worktrees`, `.codex/worktrees`, or
+  `.grok/worktrees` are treated as temporary instead of permanent global MCP owners.
+
+### Changed
+
+- `$CODEX_HOME/config.toml` remains an explicit compatibility fallback via `--codex-home`.
+  Normal `--tools codex` installs no longer mutate the global MCP registry, and skills-only
+  home refreshes cannot accidentally rebind its primary server.
+
 ## 3.6.0 — 2026-07-17
 
 Phase X closes: the doctor learns to see **physical shape** and agents get a governed way to

package/README.md

@@ -16,10 +16,9 @@ and makes sure a “green” check means something real.
 
 </div>
 
-> **ArkGate 3.4.0** is current stable: opt-in capability walls (`pure: true` or
-> `capabilities.deny` per layer, enforced on every adapter), the advisory ambient-state sensor,
-> and the measured pre-tool path — completing 3.3's evidence slice.
-> [Release notes](docs/releases/3.4.0.md).
+> **ArkGate 3.6.1** is current stable: Codex MCP configuration is project-scoped, doctor
+> recognizes the effective project binding, and stale agent worktrees no longer become
+> permanent global MCP owners. [Release notes](docs/releases/3.6.1.md).
 
 ---
 
@@ -383,7 +382,7 @@ for real systems. Details: [production-hardening.md](https://github.com/pedrokni
 | Security reporting | [SECURITY.md](SECURITY.md) |
 | Demos | [docs/demos/](docs/demos/) |
 | Examples | [examples/](examples/README.md) |
-| Latest release (3.1.0) | [release notes](docs/releases/3.1.0.md) · [3.0.0 baseline](docs/releases/3.0.0.md) |
+| Latest release (3.6.1) | [release notes](docs/releases/3.6.1.md) · [3.0.0 baseline](docs/releases/3.0.0.md) |
 | Roadmap and decisions | [ROADMAP.md](ROADMAP.md) · [ADRs](docs/adr/) · [Changelog](CHANGELOG.md) |
 
 ---

package/bin/ark.mjs

@@ -227,8 +227,8 @@ async function upgrade(args) {
   if (status !== 0) return status;
 
   // Codex home skill catalog is $CODEX_HOME/skills/<name>/SKILL.md (repo uses .agents/skills/).
-  // Refresh home when a Codex home exists. --force rewrites temp/upgrade MCP roots to this
-  // project + arkgate-mcp. Non-fatal: a permission error (e.g. sandbox) shouldn't fail upgrade.
+  // Refresh home skills when a Codex home exists. Project MCP is installed above in
+  // .codex/config.toml. Non-fatal: a permission error (e.g. sandbox) shouldn't fail upgrade.
   const codexHomeBase = process.env.CODEX_HOME || path.join(os.homedir(), '.codex');
   if (fs.existsSync(codexHomeBase)) {
     console.log(`\n     Refreshing Codex home (${codexHomeBase})…`);

package/bin/lib/agent-gates.mjs

@@ -8,6 +8,7 @@ export {
   codexArkBlockNeedsRewrite,
   codexConfigPath,
   codexPrimaryTable,
+  codexProjectMcpIsValid,
   codexProjectSlug,
   codexPromptsDir,
   codexSkillsDir,
@@ -23,6 +24,7 @@ export {
 export {
   PREFERRED_MCP_BIN,
   claudeSettings,
+  codexProjectConfig,
   grokHooks,
   grokProjectConfig,
 } from './hook-templates.mjs';

package/bin/lib/ci-and-commands.mjs

@@ -238,10 +238,8 @@ export function mcpJson(root) {
   }, null, 2)}\n`;
 }
 
-// Sample for docs/ — `ark-check --install-agent-gates --tools codex` auto-merges the real
-// block (with absolute paths) into ~/.codex/config.toml. This copy is a reference only, so
-// it flags the two gotchas of hand-editing the global config: absolute paths (config.toml is
-// loaded without the project as cwd) and the required restart.
+// Optional home fallback reference. Normal Codex installs write the project-scoped
+// `.codex/config.toml`; `--codex-home` is for older clients or an explicit global binding.
 export function codexTomlSnippet(root) {
   const { command, args } = execCommandParts(root, PREFERRED_MCP_BIN, [
     '--root',
@@ -250,10 +248,9 @@ export function codexTomlSnippet(root) {
     '/absolute/path/to/project/ark.config.json',
   ]);
   const argsToml = args.map((value) => `"${value}"`).join(', ');
-  return `# Add to ~/.codex/config.toml (or $CODEX_HOME/config.toml), then RESTART Codex —
-# it does not hot-load MCP servers. Use ABSOLUTE paths: config.toml is global, so
-# "." would resolve against Codex's launch dir, not this project. Prefer:
-#   ark-check --install-agent-gates --tools codex   (auto-merges the absolute paths)
+  return `# Optional global fallback for older Codex clients. Modern Codex uses the generated
+# project-scoped .codex/config.toml instead. If you install this fallback manually, restart
+# Codex and keep ABSOLUTE paths because $CODEX_HOME/config.toml is global.
 [mcp_servers.ark]
 command = "${command}"
 args = [${argsToml}]

package/bin/lib/codex-home.mjs

@@ -47,6 +47,7 @@ export function isTempOrUpgradeRoot(p) {
     /\/tmp\//i.test(n) ||
     /\/Temp\//i.test(n) ||
     /ark-upgrade/i.test(n) ||
+    /\/(?:\.claude|\.codex|\.grok)\/worktrees\//i.test(n) ||
     /\/T\/(?:ark-|grok-)/i.test(n) ||
     /[\\/]AppData[\\/]Local[\\/]Temp[\\/]/i.test(n)
   );
@@ -144,6 +145,23 @@ export function codexScopedTableForRoot(tomlText, absRoot) {
   return null;
 }
 
+/** True when project TOML owns the primary Ark MCP binding for that project. */
+export function codexProjectMcpIsValid(tomlText, projectRoot) {
+  const resolvedRoot = path.resolve(projectRoot);
+  const primary = codexPrimaryTable(tomlText);
+  if (!primary?.root || !/\b(ark|arkgate)-mcp\b/.test(primary.block)) return false;
+  const config = primary.block.match(/"--config"\s*,\s*"([^"]+)"/)?.[1];
+  if (!config) return false;
+  try {
+    return (
+      path.resolve(resolvedRoot, primary.root) === resolvedRoot &&
+      path.resolve(resolvedRoot, config) === path.join(resolvedRoot, 'ark.config.json')
+    );
+  } catch {
+    return false;
+  }
+}
+
 /** Extract --root from primary [mcp_servers.ark]. */
 export function extractCodexArkRootFromToml(tomlText) {
   return codexPrimaryTable(tomlText)?.root ?? null;
@@ -236,14 +254,11 @@ export function assessCodexHomeMcp(tomlText, absRoot) {
       message: scopedTable
         ? `Codex primary [mcp_servers.ark] is bound to another project (${rootArg}); ` +
           `this project is registered as [mcp_servers.${scopedTable}]. ` +
-          `Codex may still prefer the primary binding for ark://manifest — rebind if this repo should own it.`
+          `Install the project-scoped binding so this repo owns ark://manifest when active.`
         : `Codex home primary MCP --root is another permanent project ` +
           `(${rootArg || 'missing'} ≠ ${resolvedRoot}). ` +
-          `Install without --force adds a scoped [mcp_servers.ark_<slug>] table and leaves primary unchanged; ` +
-          `--force rebinds primary to this project.`,
-      fixArgs: scopedTable
-        ? '--install-agent-gates --tools codex --force'
-        : '--install-agent-gates --tools codex',
+          `Install the project-scoped binding for this repo; the global primary can remain unchanged.`,
+      fixArgs: '--install-agent-gates --tools codex',
     };
   }
 

package/bin/lib/gate-files.mjs

@@ -125,7 +125,7 @@ const COMPACT_HOST_FILES = {
   claude: ['.claude/settings.json'],
   grok: ['.grok/config.toml', '.grok/hooks/ark-write-gate.json'],
   cursor: ['.cursor/mcp.json'],
-  codex: ['.codex/hooks.json'],
+  codex: ['.codex/hooks.json', '.codex/config.toml'],
   windsurf: ['.windsurf/rules/ark.md'],
   cline: ['.clinerules/ark.md'],
   copilot: ['.github/copilot-instructions.md'],

package/bin/lib/hook-templates.mjs

@@ -73,8 +73,28 @@ export function codexHooks(root) {
   }, null, 2)}\n`;
 }
 
+// Codex project config: modern Codex resolves .codex/config.toml from the active
+// project, so the primary `ark` binding can stay local instead of competing in
+// the user's global $CODEX_HOME across every adopted repository.
+export function codexProjectConfig(root) {
+  const { command, args } = execCommandParts(root, PREFERRED_MCP_BIN, [
+    '--root',
+    '.',
+    '--config',
+    'ark.config.json',
+  ]);
+  const esc = (value) => value.replace(/\\/g, '\\\\').replace(/"/g, '\\"');
+  const argsToml = args.map((value) => `"${esc(value)}"`).join(', ');
+  return `# Generated by ark-check --install-agent-gates (Codex project scope).
+# Restart Codex after changes; MCP servers are loaded when the project session starts.
+[mcp_servers.ark]
+command = "${esc(command)}"
+args = [${argsToml}]
+`;
+}
+
 // Grok Build project config: MCP registration (commit-friendly relative paths — unlike
-// Codex's global config.toml, Grok loads .grok/config.toml from the project).
+// the optional Codex home fallback, Grok loads .grok/config.toml from the project).
 export function grokProjectConfig(root) {
   const { command, args } = execCommandParts(root, PREFERRED_MCP_BIN, [
     '--root',

package/bin/lib/install-migrate.mjs

@@ -15,6 +15,7 @@ import {
   codexSkillsDir,
   codexConfigPath,
   isTempOrUpgradeRoot,
+  upsertCodexMcpTable,
   usesDefaultCodexHome,
   wireCodexMcp,
 } from './codex-home.mjs';
@@ -22,6 +23,7 @@ import {
   PREFERRED_MCP_BIN,
   claudeSettings,
   codexHooks,
+  codexProjectConfig,
   grokHooks,
   grokProjectConfig,
 } from './hook-templates.mjs';
@@ -279,6 +281,7 @@ export function runInstallAgentGates(args) {
     }
     if (tools.has('codex')) {
       templates.push(['.codex/hooks.json', codexHooks(root)]);
+      templates.push(['.codex/config.toml', codexProjectConfig(root)]);
       if (!args.compact) templates.push(['docs/ark-codex-config.toml', codexTomlSnippet(root)]);
     }
     if (tools.has('grok')) {
@@ -341,14 +344,29 @@ export function runInstallAgentGates(args) {
     }
   }
 
-  const results = templates.map(([relativePath, content]) =>
-    writeTemplate(
+  const results = templates.map(([relativePath, content]) => {
+    if (relativePath === '.codex/config.toml') {
+      const fullPath = path.join(root, relativePath);
+      let existing = '';
+      try {
+        existing = fs.readFileSync(fullPath, 'utf8');
+      } catch {
+        // A missing project config starts from the generated Ark table.
+      }
+      const tableStart = content.indexOf('[mcp_servers.ark]');
+      const generatedPrelude = tableStart > 0 ? content.slice(0, tableStart) : '';
+      const mergeBase = generatedPrelude ? existing.replace(generatedPrelude, '') : existing;
+      const merged = upsertCodexMcpTable(mergeBase, 'ark', content);
+      if (merged === existing) return { relativePath, status: 'skipped' };
+      return writeTemplate(root, relativePath, merged, true);
+    }
+    return writeTemplate(
       root,
       relativePath,
       content,
       args.force || (args.compact && relativePath === 'AGENTS.md' && priorCompactHost !== null)
-    )
-  );
+    );
+  });
 
   console.log('Ark agent gate templates:');
   let staleSkipped = 0;
@@ -427,11 +445,8 @@ export function runInstallAgentGates(args) {
     }
   }
 
-  // Auto-wire the ark MCP server into Codex's home config.toml. Claude and Cursor get
-  // machine-readable registrations (.claude/settings.json, .cursor/mcp.json) written as repo
-  // templates above; Codex reads MCP servers only from ~/.codex/config.toml, so it needs a
-  // home-dir merge instead. Fires whenever Codex is in play so `ark://manifest` is live
-  // without a manual copy step.
+  // Optional legacy/home fallback. Normal Codex installs use the project-scoped
+  // .codex/config.toml above, avoiding cross-project primary binding conflicts.
   //
   // Skip home MCP mutation when the project root is a temp/upgrade scratch *and*
   // CODEX_HOME is the default (~/.codex). Fixtures and agent smokes must not rewrite
@@ -439,7 +454,7 @@ export function runInstallAgentGates(args) {
   // home *skills* below; MCP binding of a temp root into default home is never safe.
   // A redirected CODEX_HOME (tests/isolation) may still wire as requested.
   let codexMcp = null;
-  const wantCodexWire = !args.compact && (tools.has('codex') || args.codexHome);
+  const wantCodexWire = !args.compact && !args.skillsOnly && args.codexHome;
   const skipHomeWire =
     wantCodexWire && isTempOrUpgradeRoot(root) && usesDefaultCodexHome();
   if (wantCodexWire && !skipHomeWire) {
@@ -475,7 +490,7 @@ export function runInstallAgentGates(args) {
   }
   if (codexMcp?.status === 'failed') {
     console.error(
-      `\nWarning: Codex home MCP registration failed (${codexMcp.message}). Repo gates were written; fix ~/.codex access or re-run with --tools codex --force.`
+      `\nWarning: Codex home MCP registration failed (${codexMcp.message}). Repo gates were written; fix ~/.codex access or re-run with --codex-home --force.`
     );
   }
   if (writeRequest.host) {

package/bin/lib/mcp-adoption.mjs

@@ -7,7 +7,11 @@ import path from 'node:path';
 import { arkCommand } from '../ark-shared.mjs';
 import { CORE_LAYER_NAMES } from './core-layers.mjs';
 import { falseGreenAdoptionGap } from './field-install.mjs';
-import { assessCodexHomeMcp, codexConfigPath } from './codex-home.mjs';
+import {
+  assessCodexHomeMcp,
+  codexConfigPath,
+  codexProjectMcpIsValid,
+} from './codex-home.mjs';
 import { detectWritePathCapabilities } from './write-path-detect.mjs';
 import { detectActiveAgentHost, skillTemplateNames } from './skill-install.mjs';
 import { detectDeployPathQuality } from './deploy-path.mjs';
@@ -19,7 +23,7 @@ export const COMMAND_GATE_TEXT_FILES = [
   '.claude/settings.json', 'AGENTS.md', '.cursor/rules/ark.mdc', '.windsurf/rules/ark.md',
   '.clinerules/ark.md', '.github/copilot-instructions.md', '.kiro/steering/ark.md',
   '.roo/rules/ark.md', '.continue/rules/ark.md', 'GEMINI.md', 'package.json',
-  '.grok/hooks/ark-write-gate.json', '.grok/config.toml',
+  '.grok/hooks/ark-write-gate.json', '.grok/config.toml', '.codex/config.toml',
 ];
 export const COMMAND_GATE_JSON_FILES = ['.mcp.json', '.cursor/mcp.json'];
 // Primary CLI names (product) + one-major aliases. migrate-commands must strip ALL of these
@@ -148,7 +152,10 @@ export function collectAdoptionGaps(root, config, coverage) {
         dir: '.codex',
         // Official Codex REPO skill catalog (Agent Skills standard) — not .codex/prompts.
         skill: (n) => path.join(root, '.agents', 'skills', n, 'SKILL.md'),
-        extras: [['.codex/hooks.json', 'hooks']],
+        extras: [
+          ['.codex/hooks.json', 'hooks'],
+          ['.codex/config.toml', 'project MCP config'],
+        ],
         toolsFlag: 'codex',
       },
     ];
@@ -183,7 +190,17 @@ export function collectAdoptionGaps(root, config, coverage) {
 
   // --- Codex home MCP (temp path / wrong root / multi-project) ---
   let codexHome = null;
-  if (adopted && !isProducer) {
+  const codexProjectMcp = (() => {
+    try {
+      return codexProjectMcpIsValid(
+        fs.readFileSync(path.join(root, '.codex', 'config.toml'), 'utf8'),
+        root
+      );
+    } catch {
+      return false;
+    }
+  })();
+  if (adopted && !isProducer && !codexProjectMcp) {
     const codexFile = codexConfigPath();
     let toml = '';
     try {

package/bin/lib/write-path-capabilities.mjs

@@ -8,6 +8,7 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import {
+  codexProjectMcpIsValid,
   codexConfigPath,
   listCodexArkServerTables,
 } from './codex-home.mjs';
@@ -154,6 +155,11 @@ function mcpEvidence(root, relativePath) {
 }
 
 function codexMcpEvidence(root) {
+  const projectFile = path.join(root, '.codex', 'config.toml');
+  const projectText = readText(projectFile);
+  const projectRegistered = codexProjectMcpIsValid(projectText, root);
+  if (projectRegistered) return ['.codex/config.toml'];
+
   const file = codexConfigPath();
   const text = readText(file);
   const resolvedRoot = path.resolve(root);

package/dist/index.cjs

@@ -1,4 +1,4 @@
-"use strict";var Se=Object.defineProperty;var yt=Object.getOwnPropertyDescriptor;var gt=Object.getOwnPropertyNames;var mt=Object.prototype.hasOwnProperty;var ht=(e,t)=>{for(var n in t)Se(e,n,{get:t[n],enumerable:!0})},At=(e,t,n,r)=>{if(t&&typeof t=="object"||typeof t=="function")for(let i of gt(t))!mt.call(e,i)&&i!==n&&Se(e,i,{get:()=>t[i],enumerable:!(r=yt(t,i))||r.enumerable});return e};var bt=e=>At(Se({},"__esModule",{value:!0}),e);var an={};ht(an,{ANALYSIS_IR_SCHEMA_VERSION:()=>ge,ARK_ANALYSIS_RESULT_SCHEMA:()=>Ke,ARK_ANALYSIS_RESULT_SCHEMA_VERSION:()=>Ye,ARK_CONFIG_SCHEMA:()=>fe,ARK_CONFIG_SCHEMA_VERSION:()=>at,POLICY_DELTA_SCHEMA_VERSION:()=>Ae,analyzeArchitectureConvergence:()=>ee,analyzeChange:()=>re,analyzePolicyDelta:()=>Ve,analyzeProject:()=>U,classifyArkPolicyDelta:()=>be,collectAnalysisConfigWarnings:()=>Ue,collectForbiddenCapabilityUses:()=>N,createAICodeGate:()=>Te,createAdapterResult:()=>qe,createArchitectureProfile:()=>Q,createArchitectureProfileFromArkConfig:()=>Fe,createElevenLayerArkConfig:()=>je,detectArchitectureCycles:()=>Ie,deterministicHash:()=>P,elevenLayerProfile:()=>Z,evaluateArchitectureGraph:()=>ie,explainViolation:()=>Ge,extractSemanticDependencies:()=>_,loadArkConfigContract:()=>J,loadContract:()=>ne,parseArkConfigJson:()=>ye,policyDeltaAcknowledgementMatches:()=>Ce,preflightChange:()=>He,stableSerialize:()=>L,toAdapterDiagnostic:()=>oe,version:()=>Be});module.exports=bt(an);var Be="3.6.0";var Ye="1.1";function k(e){return typeof e=="string"&&e.length>0?e:void 0}function ze(e,t){return Number.isInteger(e)&&Number(e)>0?Number(e):t}function Ct(e,t,n){return e==="LAYER_IMPORT_VIOLATION"?t.typeOnly||n.targetTypeOnlyExports===!0||n.namedBindingsTypeOnly===!0?"Move the referenced type to a mutually allowed layer, use `import type`, then preflight again.":n.peerIsolation===!0?"Extract the shared dependency to a shared layer, then preflight again.":`Define a port in ${t.fromLayer??"the source layer"}, inject the ${t.toLayer??"outer-layer"} implementation, then preflight again.`:e==="FORBIDDEN_GLOBAL"?`Inject ${t.target??"the capability"} through a port, then preflight again.`:e==="CAPABILITY_VIOLATION"?`Define a ${k(n.capability)??"capability"} port in ${t.fromLayer??"the walled layer"}, bind the implementation outside it, then preflight again.`:e==="CIRCULAR_DEPENDENCY"?"Extract the shared dependency into a third module, then preflight again.":e==="RAW_EVENT_PUBLISH"?"Publish through a registered intent creator, then run Ark again.":e==="PUBLISH_MISSING_SOURCE"?"Add metadata.source to the publish call, then run Ark again.":`Resolve ${e} without weakening ark.config.json, then run Ark again.`}function oe(e,t="error"){let n=k(e.ruleId)??k(e.code)??"ARK_UNKNOWN",r=e.severity==="warning"?"warning":t,i={...k(e.target)?{target:k(e.target)}:{},...k(e.fromLayer)?{fromLayer:k(e.fromLayer)}:{},...k(e.toLayer)?{toLayer:k(e.toLayer)}:{},...typeof e.typeOnly=="boolean"?{typeOnly:e.typeOnly}:{}};return{ruleId:n,severity:r,message:k(e.message)??n,location:{file:k(e.file)??"<unknown>",line:ze(e.line,1),column:ze(e.column,1)},evidence:i,nextAction:k(e.nextAction)??Ct(n,i,e)}}function qe(e){return{schemaVersion:"1.1",valid:e.valid,diagnostics:[...(e.violations??[]).map(t=>oe(t,"error")),...(e.warnings??[]).map(t=>oe(t,"warning"))]}}var 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Set([...n.keys(),...r.keys()]);for(let[l,o]of[...s].sort(([g],[f])=>g.localeCompare(f)))a.has(l)||i.has(l)||c.has(l)||!p.has(o.from)&&!p.has(o.to)||t.push({...X("unplanned",o,`${o.from} -> ${o.to} was added without a matching planned dependency.`,"dependency-added"),actualOperation:"added"});let y=new Set(e.changeMap.map.files.filter(l=>l.operation==="delete").map(l=>l.path));for(let[l,o]of[...a].sort(([g],[f])=>g.localeCompare(f)))s.has(l)||y.has(o.from)||y.has(o.to)||!p.has(o.from)&&!p.has(o.to)||t.push({...X("unplanned",o,`${o.from} -> ${o.to} was removed without a planned file deletion.`,"dependency-removed"),actualOperation:"removed"});let u={satisfied:0,missing:1,contradictory:2,unplanned:3};t.sort((l,o)=>u[l.classification]-u[o.classification]||(l.subject===o.subject?0:l.subject==="file"?-1:1)||l.id.localeCompare(o.id));let m={satisfied:t.filter(l=>l.classification==="satisfied").length,missing:t.filter(l=>l.classification==="missing").length,contradictory:t.filter(l=>l.classification==="contradictory").length,unplanned:t.filter(l=>l.classification==="unplanned").length};return{schemaVersion:"1.0",readOnly:!0,changeMapHash:e.changeMap.hash,structurallyConverged:m.missing===0&&m.contradictory===0&&m.unplanned===0,behavioralCompletion:"not-evaluated",summary:m,findings:t}}var Ae="1.0";function C(e,t){e.push({id:`${t.classification}:${t.path}:${t.kind}`,path:t.path,classification:t.classification,message:t.message,...t.classification==="weakening"||t.classification==="judgment-required"?{nextAction:`Restore the previous protection at ${t.path}, then run ArkGate again.`}:{},...t.before===void 0?{}:{before:t.before},...t.after===void 0?{}:{after:t.after}})}function w(e){return[...new Set(e??[])].sort()}function T(e,t,n,r,i){let a=w(n),s=w(r),c=new Set(a),p=new Set(s),y=s.filter(m=>!c.has(m)),u=a.filter(m=>!p.has(m));y.length===0&&u.length===0||(y.length>0&&C(e,{kind:"added",path:t,classification:i.added,message:i.addedMessage,before:a,after:s}),u.length>0&&C(e,{kind:"removed",path:t,classification:i.removed,message:i.removedMessage,before:a,after:s}))}function me(e,t,n,r,i,a,s){if(n===r)return;C(e,{kind:r?"enabled":"disabled",path:t,classification:r?i:i==="strengthening"?"weakening":"strengthening",message:r?a:s,before:n,after:r})}function he(e,t){let n=new Map,r=new Set;for(let i of e){let a=t(i);n.has(a)?r.add(a):n.set(a,i)}return{values:n,duplicates:[...r].sort()}}function Kt(e,t,n){let r=he(t,a=>a.name),i=he(n,a=>a.name);(r.duplicates.length>0||i.duplicates.length>0)&&C(e,{kind:"duplicate-layer",path:"$.layers",classification:"judgment-required",message:"Duplicate layer names make policy ownership ambiguous.",before:r.duplicates,after:i.duplicates});for(let a of[...new Set([...r.values.keys(),...i.values.keys()])].sort()){let s=r.values.get(a),c=i.values.get(a),p=`$.layers[${a}]`;if(!s&&c){C(e,{kind:"layer-added",path:p,classification:"judgment-required",message:"A layer was added; verify overlap, ownership, and rule coverage.",after:c});continue}if(s&&!c){C(e,{kind:"layer-removed",path:p,classification:"weakening",message:"Removing a layer can leave its source paths ungoverned.",before:s});continue}if(!s||!c)continue;T(e,`${p}.patterns`,s.patterns,c.patterns,{added:"strengthening",removed:"weakening",addedMessage:"Additional paths are governed by this layer.",removedMessage:"Paths were removed from this layer and may become ungoverned."}),T(e,`${p}.exclude`,s.exclude,c.exclude,{added:"weakening",removed:"strengthening",addedMessage:"Additional paths are excluded from this layer.",removedMessage:"Fewer paths are excluded from this layer."});let y=le(s),u=le(c);T(e,`${p}.forbiddenGlobals`,y.rawGlobals,u.rawGlobals,{added:"strengthening",removed:"weakening",addedMessage:"Additional forbidden globals are enforced in this layer.",removedMessage:"A forbidden-global protection was removed from this layer."}),T(e,`${p}.capabilities`,y.atoms,u.atoms,{added:"strengthening",removed:"weakening",addedMessage:"Additional ambient/import protection is enforced in this layer (coverage atoms).",removedMessage:"An ambient/import protection was lost from this layer (coverage atoms)."}),w(s.intentPrefixes).join("\0")!==w(c.intentPrefixes).join("\0")&&C(e,{kind:"intent-prefixes-changed",path:`${p}.intentPrefixes`,classification:"judgment-required",message:"Intent ownership changed and must be reviewed against publishers and consumers.",before:w(s.intentPrefixes),after:w(c.intentPrefixes)}),me(e,`${p}.mayImportInfrastructure`,s.mayImportInfrastructure===!0,c.mayImportInfrastructure===!0,"weakening","The layer may now import infrastructure directly.","Direct infrastructure imports are no longer allowed for this layer."),me(e,`${p}.optional`,s.optional===!0,c.optional===!0,"weakening","The layer is now optional and can be absent without a strict warning.","The layer is now required when its contract is active.")}}function Wt(e,t,n){let r=s=>`${s.from}->${s.to}`,i=he(t,r),a=he(n,r);(i.duplicates.length>0||a.duplicates.length>0)&&C(e,{kind:"duplicate-rule",path:"$.rules",classification:"judgment-required",message:"Duplicate rule edges make the effective verdict order-dependent.",before:i.duplicates,after:a.duplicates});for(let s of[...new Set([...i.values.keys(),...a.values.keys()])].sort()){let c=i.values.get(s),p=a.values.get(s),y=`$.rules[${s}]`;if(!c&&p){p.allowed===!1&&C(e,{kind:"deny-added",path:y,classification:"strengthening",message:"A denied dependency edge was added.",after:p});continue}if(c&&!p){c.allowed===!1&&C(e,{kind:"deny-removed",path:y,classification:"weakening",message:"A denied dependency edge was removed.",before:c});continue}if(!c||!p)continue;c.allowed!==p.allowed&&C(e,{kind:p.allowed?"deny-disabled":"deny-enabled",path:`${y}.allowed`,classification:p.allowed?"weakening":"strengthening",message:p.allowed?"A previously denied dependency edge is now allowed.":"A dependency edge is now denied.",before:c.allowed,after:p.allowed});let u=c.peerIsolation===!0,m=p.peerIsolation===!0;if(u!==m){let l=c.from===c.to&&p.from===p.to;C(e,{kind:m?"peer-isolation-enabled":"peer-isolation-disabled",path:`${y}.peerIsolation`,classification:l?m?"strengthening":"weakening":"judgment-required",message:l?m?"Cross-slice dependencies inside this layer are now denied.":"Cross-slice dependencies inside this layer are no longer denied.":"Changing peer isolation on a cross-layer edge changes the denial scope.",before:u,after:m})}w(c.sliceFolders).join("\0")!==w(p.sliceFolders).join("\0")&&C(e,{kind:"slice-folders-changed",path:`${y}.sliceFolders`,classification:"judgment-required",message:"Slice 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i!="string")||e.reason.trim().length===0||e.basePolicyHash!==t.basePolicyHash||e.candidatePolicyHash!==t.candidatePolicyHash)return!1;let n=w(e.findingIds),r=w(t.findingIds);return n.length===r.length&&n.every((i,a)=>i===r[a])}function D(e){let t=[];for(let n of e.replace(/\\/g,"/").split("/"))!n||n==="."||(n===".."&&t.length>0&&t.at(-1)!==".."?t.pop():t.push(n));return t.join("/")}function ct(e){return e!==void 0&&/[A-Za-z0-9_$]/.test(e)}function $(e,t){for(;t<e.length&&/\s/.test(e[t]);)t+=1;return t}function te(e,t){let n=e[t];if(n!=="'"&&n!=='"')return;let r=t,i="";for(t+=1;t<e.length;t+=1){let a=e[t];if(a===n)return{value:i,offset:r,excerpt:e.slice(r,t+1)};a==="\\"&&t+1<e.length?(i+=e[t+1],t+=1):i+=a}}function O(e,t,n){return e.startsWith(t,n)&&!ct(e[n-1])&&!ct(e[n+t.length])}function Qt(e,t){if(t=$(e,t+6),e[t]==="(")return te(e,$(e,t+1));let n=!1;if(O(e,"type",t)){let i=$(e,t+4);e[i]!==","&&!O(e,"from",i)&&(n=!0)}let r=lt(e,t,!0);return r&&n?{...r,typeOnly:!0}:r}function 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package/dist/index.d.cts

@@ -234,7 +234,7 @@ declare function loadArkConfigContract(input: unknown, source?: string): ArkConf
 declare function parseArkConfigJson(json: string, source?: string): ArkConfigLoadResult;
 
 /** ArkGate library version — single source of truth. */
-declare const version = "3.6.0";
+declare const version = "3.6.1";
 
 /** Versioned public result contract shared by every ArkGate enforcement adapter. */
 declare const ARK_ANALYSIS_RESULT_SCHEMA_VERSION: "1.1";

package/dist/index.d.ts

@@ -234,7 +234,7 @@ declare function loadArkConfigContract(input: unknown, source?: string): ArkConf
 declare function parseArkConfigJson(json: string, source?: string): ArkConfigLoadResult;
 
 /** ArkGate library version — single source of truth. */
-declare const version = "3.6.0";
+declare const version = "3.6.1";
 
 /** Versioned public result contract shared by every ArkGate enforcement adapter. */
 declare const ARK_ANALYSIS_RESULT_SCHEMA_VERSION: "1.1";

package/dist/index.js

@@ -1,4 +1,4 @@
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package/docs/agent-guide.md

@@ -368,7 +368,7 @@ npx arkgate-check --install-agent-gates --tools claude,cursor,codex,grok
 |------|-----------------|-------------|
 | Claude Code | `.claude/settings.json` hook + `.mcp.json` / `claude mcp add` | `.claude/skills/<name>/SKILL.md` |
 | Cursor | `.cursor/mcp.json` + `.cursor/rules/ark.mdc` | `.cursor/commands/` |
-| OpenAI Codex | `$CODEX_HOME/config.toml` (global; absolute `--root`; multi-project → secondary `ark_<slug>` unless `--force`; doctor defers non-temp home gaps when session host ≠ Codex — see [ai-gates.md](ai-gates.md)) | **Repo:** `.agents/skills/<name>/SKILL.md`; **home:** `$CODEX_HOME/skills/<name>/SKILL.md` (`--codex-home`) |
+| OpenAI Codex | `.codex/config.toml` (project primary, relative `--root .`); optional legacy `$CODEX_HOME/config.toml` fallback uses absolute roots and scoped secondaries — see [ai-gates.md](ai-gates.md) | **Repo:** `.agents/skills/<name>/SKILL.md`; **home:** `$CODEX_HOME/skills/<name>/SKILL.md` (`--codex-home`) |
 | **Grok Build** | `.grok/hooks/ark-write-gate.json` + `.grok/config.toml` / `.mcp.json` | `.grok/skills/<name>/SKILL.md` |
 
 This is a path reference, not a guarantee table. Full copy-paste setups:

package/docs/ai-gates.md

@@ -263,23 +263,22 @@ npx ark-check --install-agent-gates --tools codex
 The generated hook includes `--hook-repair`, so a rejected patch carries the same structured
 repair envelope as Claude and Grok. Codex still needs hook trust enabled for the project.
 
-Unlike Claude/Cursor (project-local MCP files), **Codex loads MCP servers only from
-`$CODEX_HOME/config.toml`** (default `~/.codex/config.toml`) — a **global** home file.
-Hand-editing with relative `--root .` is wrong: Codex does not use the project as cwd, so
-`.` resolves against the launch directory. Prefer absolute paths, or let Ark write them:
+Modern Codex resolves MCP servers from the active project's `.codex/config.toml`. Ark writes
+that file with relative paths, so every repository owns its primary `ark` binding without
+competing for a global slot:
 
 ```bash
 npx ark-check --install-agent-gates --tools codex
-# optional: install /ark-* skills into $CODEX_HOME/skills/<name>/SKILL.md
+# optional: install /ark-* skills and a legacy global MCP fallback under $CODEX_HOME
 npx ark-check --install-agent-gates --codex-home
 ```
 
-Example shape (absolute paths — also what install writes):
+Project-scoped shape:
 
 ```toml
 [mcp_servers.ark]
 command = "npx"
-args = ["arkgate-mcp", "--root", "/absolute/path/to/project", "--config", "/absolute/path/to/project/ark.config.json"]
+args = ["arkgate-mcp", "--root", ".", "--config", "ark.config.json"]
 ```
 
 Then **restart Codex** — it does not hot-load MCP servers. Expect resource `ark://manifest`
@@ -288,11 +287,12 @@ and tools `validate_code`, `ark_check`, `ark_coverage`, `ark_place`.
 Codex uses the best-effort local patch hook plus advisory MCP for discovery/validation and
 `ark-check` as the hard merge backstop. Register all three as soon as the repo is adopted.
 
-### Multi-project Codex (home config last-wins)
+### Legacy Codex home fallback
 
-`[mcp_servers.ark]` is a **single primary** binding. If project A is already registered and
-you install gates for project B **without** `--force`, Ark does **not** silently steal
-primary A. It writes a **scoped secondary** table:
+`$CODEX_HOME/config.toml` remains supported for older clients or an explicit global binding.
+Because it is global, its `[mcp_servers.ark]` is a single primary. If project A is already
+registered and you run `--codex-home` for project B without `--force`, Ark preserves A and
+writes a scoped secondary table:
 
 ```toml
 [mcp_servers.ark]            # primary — still project A
@@ -304,13 +304,15 @@ primary A. It writes a **scoped secondary** table:
 
 | Goal | Command |
 |------|---------|
-| Add B without moving primary | `ark-check --install-agent-gates --tools codex` (no `--force`) |
-| Make B the primary binding | `ark-check --install-agent-gates --tools codex --force` |
+| Install the normal project binding | `ark-check --install-agent-gates --tools codex` |
+| Add B to the legacy home fallback | `ark-check --install-agent-gates --codex-home` |
+| Make B the legacy home primary | `ark-check --install-agent-gates --codex-home --force` |
 | Doctor: primary points at another permanent project | gap id `codex-home-multi-project` (warn if no secondary yet and session host is unknown/Codex; **info + `deferred`** when the session host is known and not Codex — e.g. Grok/Claude/Cursor; info if a scoped secondary is already present) |
-| When using Codex: refresh home skills/MCP | `ark-check --install-agent-gates --skills-only --codex-home --force` |
+| When using Codex: refresh home skills | `ark-check --install-agent-gates --skills-only --codex-home --force` |
 
-`ark-check --doctor` surfaces the multi-project state so you are not left thinking B owns
-`ark://manifest` when only a secondary table exists. **Deferred (fix when using Codex):**
+When a valid project `.codex/config.toml` exists, doctor treats it as the effective binding and
+does not report an unrelated home primary. Without a project binding, doctor surfaces the
+legacy multi-project state. **Deferred (fix when using Codex):**
 non-temp Codex-home gaps (`codex-home-multi-project`, stale `$CODEX_HOME/skills`) are
 severity **info**, marked `deferred: true`, and omitted from Top actions when the session
 host is known and not Codex — `/ark-upgrade` on Grok/Claude is not Incomplete because of

package/docs/enthusiast/how-to-agent-gates.md

@@ -21,7 +21,7 @@ Installs:
 |------|-------------|
 | Claude Code | `.claude/settings.json`, `.claude/skills/` |
 | Cursor | `.cursor/mcp.json`, `.cursor/rules/ark.mdc`, `.cursor/commands/` |
-| Codex | `.codex/hooks.json`, `.agents/skills/`; MCP in `$CODEX_HOME/config.toml` |
+| Codex | `.codex/hooks.json`, `.codex/config.toml`, `.agents/skills/` |
 | **Grok Build** | `.grok/config.toml`, `.grok/hooks/`, `.grok/skills/` |
 
 See the [canonical host support matrix](../../README.md#host-enforcement-support) for the exact

package/docs/package-surface.md

@@ -100,5 +100,5 @@ production deployment would need to satisfy; it is not a readiness certification
 ## Release notes (maintainers)
 
 Ship notes for a version live under [releases/](./releases/) (latest:
-[3.4.0.md](./releases/3.4.0.md)).
+[3.6.1.md](./releases/3.6.1.md)).
 Publish path: signed annotated tag → GitHub Release → `publish-npm.yml` (see [CONTRIBUTING.md](../CONTRIBUTING.md)).

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "arkgate",
-  "version": "3.6.0",
+  "version": "3.6.1",
   "description": "ArkGate — architecture co-pilot for AI TypeScript (write gate, CI gate, plan/loop)",
   "type": "module",
   "main": "./dist/index.cjs",

package/server.json

@@ -6,12 +6,12 @@
     "url": "https://github.com/pedroknigge/arkgate",
     "source": "github"
   },
-  "version": "3.6.0",
+  "version": "3.6.1",
   "packages": [
     {
       "registryType": "npm",
       "identifier": "arkgate",
-      "version": "3.6.0",
+      "version": "3.6.1",
       "runtimeHint": "npx",
       "transport": {
         "type": "stdio"