arkgate 3.6.0 → 3.7.0

package/CHANGELOG.md

@@ -4,6 +4,75 @@ All notable changes to ArkGate (`arkgate`; formerly `ark-runtime-kernel`) are do
 
 ## Unreleased
 
+## 3.7.0 — 2026-07-17
+
+Phase Y turns field feedback into explicit decision memory, more honest design/parse advisories,
+safer skill-driven edits, and one confirmed purity-bypass closure. **No breaking** CLI, MCP tool,
+analysis IR, or `ark.config.json` changes. **No product-policy gate weakening. No automatic
+reshape or codemod.**
+
+### Added
+
+- **Recorded reshape decisions (Y01):** `.ark/reshape-decisions.json` can explicitly accept,
+  defer, or reject a physical-cohesion pilot with a required reason and optional `reviewBy`.
+  Current deferred/rejected decisions suppress only repeated pilot pressure; the underlying
+  facts remain visible. Stale, expired, malformed, duplicate, or oversized records suppress
+  nothing, and doctor/HTML surfaces render the lifecycle.
+- **Hollow-persistence advisory (Y02):** the existing `handler-in-persistence` smell now sees
+  static framework HTTP imports/re-exports, route definitions, and handler shapes inside
+  Persistence-role modules. It stays advisory and judgment-only, with a bounded and explicit
+  inspection envelope.
+- **Parse-health honesty (Y03):** doctor JSON/human output and the HTML report expose governed
+  files with parser diagnostics through additive `parseHealth` totals and a deterministic,
+  overflow-aware file list. The existing AST is reused; the verdict and exit code are unchanged.
+- **Exact `process` module dual (Y08):** `forbiddenGlobals: ["process"]` now owns exact value
+  imports of `process` and `node:process` across CLI cold/warm cache, pure IR, atomic preflight,
+  AICodeGate/MCP, and ESLint. It emits one `FORBIDDEN_GLOBAL` voice; type-only forms within the
+  documented TypeScript envelope, subpaths, and `child_process` remain excluded.
+
+### Changed
+
+- **Mechanical-edit hygiene (Y04):** `ark-fix`, `ark-autopilot`, and `ark-loop` now require
+  injected headers to merge into an existing doc block, typed `defineRoute<…>` calls to retain
+  their generics/shape, and convention-only placeholder modules to remain uncreated. A
+  deterministic eval guards all three outcomes.
+- **Cycle budgets (Y05):** package and Linux hook/doctor p95 ceilings were re-measured once from
+  clean 3.6.1 candidates with evidence-backed headroom, preserving fixed release guardrails.
+- **Confidence budget:** Y08 adds multi-form ESLint regressions while the full-suite branch floor
+  is recalibrated from 85% to 84.5%; statement/function/line floors and mutation gates are
+  unchanged.
+
+### Fixed
+
+- **Portable peer isolation:** slice identities are case-normalized, so mixed-case paths do not
+  produce a false cross-slice violation on case-insensitive filesystems. Repositories that differ
+  only by path case intentionally share the portable identity.
+- **Convergence remediation direction:** an unplanned removed dependency now tells the user to
+  restore it; an unplanned added dependency still tells the user to remove it.
+
+## 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 3.7.0** is current stable: Phase Y adds explicit reshape decisions, hollow-
+> persistence and parse-health advisories, safer mechanical edits, and exact `process` module-
+> dual enforcement. [Release notes](docs/releases/3.7.0.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 (3.7.0) | [release notes](docs/releases/3.7.0.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-check.mjs

@@ -1133,7 +1133,7 @@ async function main() {
     );
   }
 
-  const { violations, warnings, safety } = runArchitectureScan({
+  const { violations, warnings, safety, parseHealth } = runArchitectureScan({
     root,
     config,
     manifest,
@@ -1148,7 +1148,7 @@ async function main() {
       configPath: path.isAbsolute(args.config) ? args.config : path.join(root, args.config),
       configMissing: !fs.existsSync(path.isAbsolute(args.config) ? args.config : path.join(root, args.config)),
       safety,
-      ts,
+      ts, parseHealth,
     });
     return;
   }
@@ -1320,7 +1320,7 @@ async function main() {
       originJustCreated: !existingOrigin,
       adoption: adoptionForReport,
       designDepth,
-      advisories: computeDoctorAdvisories(root, config, coverage, rules, files, ts),
+      advisories: computeDoctorAdvisories(root, config, coverage, rules, files, ts, parseHealth),
     };
     const html = args.beginner
       ? renderBeginnerHtmlReport(reportPayload)

package/bin/ark-layer-match.mjs

@@ -138,6 +138,7 @@ export function layerForRelativePath(relPath, layers) {
 /**
  * Extract the slice id under a known folder name.
  * Includes the parent folder so `features/auth` ≠ `modules/auth`.
+ * Identity is case-normalized for portable results across filesystems.
  * `src/features/auth/api.ts` + folders `["features"]` → `"features/auth"`.
  */
 export function sliceIdForPath(relPath, sliceFolders) {
@@ -149,7 +150,7 @@ export function sliceIdForPath(relPath, sliceFolders) {
     const folders = new Set(sliceFolders.map((s) => String(s).toLowerCase()));
     for (let i = 0; i < parts.length - 1; i += 1) {
         if (folders.has(parts[i].toLowerCase())) {
-            return `${parts[i]}/${parts[i + 1]}`;
+            return `${parts[i].toLowerCase()}/${parts[i + 1].toLowerCase()}`;
         }
     }
     return undefined;

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/analysis-engine.mjs

@@ -1,10 +1,10 @@
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d=s.path.replace(/\\/g,"/"),f=v(s.path);if(!f||f===".."||f.startsWith("../")||d.startsWith("/")||/^[A-Za-z]:\//.test(d)||d.includes("\0")){a.push({ruleId:"INVALID_CHANGE_PATH",file:"<change-set>",line:1,message:"Every change requires a safe, non-empty project-relative path."});continue}if(i.has(f)){a.push({ruleId:"DUPLICATE_CHANGE_PATH",file:f,line:1,message:`The atomic change set contains more than one operation for ${f}.`});continue}i.add(f),"delete"in s&&s.delete&&!n.has(f)&&a.push({ruleId:"DELETE_TARGET_MISSING",file:f,line:1,message:`Cannot delete ${f} because it is not present in the supplied base tree.`}),r.push("delete"in s&&s.delete?{path:f,delete:!0}:{path:f,content:"content"in s?s.content:""})}e.changes.length===0&&a.push({ruleId:"CHANGE_SET_EMPTY",file:"<change-set>",line:1,message:"Atomic preflight requires at least one create, update, or delete."});let o=me({...e,changes:r}),l=new Map(o.ir.files.map(s=>[s.path,s])),p=o.ir.violations.filter(s=>s.ruleId==="CAPABILITY_VIOLATION").map(s=>({ruleId:s.ruleId,file:s.evidence.file,line:s.evidence.line,target:s.symbol,capability:s.capability,message:s.message})),u=he({config:e.contract.config,rules:e.contract.config.rules,files:o.ir.files.map(s=>s.path),contentViolations:p,edges:o.ir.edges.filter(s=>!!s.fromLayer).map(s=>({from:s.from,fromLayer:s.fromLayer,...s.to?{to:s.to}:{},...s.toLayer?{toLayer:s.toLayer}:{},line:s.evidence.line,kind:"import"}))}),m=r.map(s=>{let d=v(s.path),f=n.get(d),y=l.get(d);return{path:d,operation:"delete"in 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o){if(!s.name){a.push(I("CONFIG_LAYER_WITHOUT_NAME","A configured layer is missing a name."));continue}u.has(s.name)&&m.add(s.name),u.add(s.name),s.forbiddenGlobals!==void 0&&(!Array.isArray(s.forbiddenGlobals)||s.forbiddenGlobals.some(f=>typeof f!="string"))&&a.push(I("CONFIG_INVALID_FORBIDDEN_GLOBALS",`Layer "${s.name}" has an invalid forbiddenGlobals value; expected an array of strings (e.g. ["fetch", "Date.now"]). 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+`).length,d={kind:"import",file:e.path,line:o,excerpt:i.excerpt},l=gt(e.path,a,t);n.push({from:e.path,specifier:a,to:l?.path??null,resolution:l?"resolved":"unresolved",fromLayer:e.layer,toLayer:l?.layer??null,evidence:d})}return{edges:n,capabilityUses:r}}function gt(e,t,n){let r=e.split("/");r.pop();for(let a of t.split("/"))a==="."||a===""||(a===".."?r.pop():r.push(a));let i=r.join("/");for(let a of[i,`${i}.ts`,`${i}.tsx`,`${i}.mts`,`${i}.cts`,`${i}/index.ts`,`${i}/index.tsx`]){let o=n.get(a);if(o)return o}}function je(e,t){let n=[];for(let r of e){if(!r.to||!r.fromLayer||!r.toLayer)continue;let i=G(t.rules,r.fromLayer,r.toLayer,{fromPath:r.from,toPath:r.to,layers:t.layers});i&&n.push({ruleId:`layer-dependency:${i.from}->${i.to}`,message:i.message??`${i.from} must not depend on ${i.to}.`,edge:r,evidence:r.evidence})}return n}function he(e,t){let n=typeof e=="string"?ve(e,t):me(e,t);return{...n,policyHash:$(x(n.config))}}function mt(e){let t=he(e.baseConfig,e.baseSource??"base ark.config.json"),n=he(e.candidateConfig,e.candidateSource??"candidate ark.config.json"),r=Me(t.config,n.config),i=r.findings.filter(d=>d.classification==="weakening"||d.classification==="judgment-required").map(d=>d.id).sort(),a=i.length>0,o=a&&Ne(e.acknowledgement,{basePolicyHash:t.policyHash,candidatePolicyHash:n.policyHash,findingIds:i});return{schemaVersion:r.schemaVersion,basePolicyHash:t.policyHash,candidatePolicyHash:n.policyHash,classification:r.classification,findings:r.findings,blockingFindingIds:i,requiresAcknowledgement:a,acknowledged:o,valid:!a||o}}function J(e){let t=e.files.map(l=>{let u=v(l.path);return{path:u,content:l.content,contentHash:$(l.content),layer:_(u,e.contract.config.layers)??null}}).sort((l,u)=>l.path.localeCompare(u.path)),n=new Map(t.map(l=>[l.path,l])),r=[],i=[];for(let l of t){let u=Fe(l,n);r.push(...u.edges),i.push(...u.capabilityUses)}let a=je(r,e.contract.config),o=new Map(e.contract.config.layers.map(l=>[l.name,l])),d=new Map(e.contract.config.layers.map(l=>[l.name,new Set(z(l))]));for(let l of i){let u=n.get(l.file)?.layer;if(!u)continue;let y=o.get(u),g=ue(l.symbol,y?.forbiddenGlobals??[]);if(g){a.push({ruleId:"FORBIDDEN_GLOBAL",message:`${u} must not use module "${l.symbol}" because it is the import form of forbidden global "${g}".`,symbol:l.symbol,evidence:l.evidence});continue}d.get(u)?.has(l.capability)&&a.push({ruleId:"CAPABILITY_VIOLATION",message:`${u} denies the ${l.capability} capability; found import of "${l.symbol}".`,capability:l.capability,symbol:l.symbol,evidence:l.evidence})}return{ir:{schemaVersion:"1.0",policyHash:e.contract.policyHash,compilerOptionsHash:$(x(e.compilerOptions??{})),files:t,layers:e.contract.config.layers.map(l=>l.name),edges:r,capabilityUses:i,violations:a}}}function Ae(e){let t=new Map(e.files.map(n=>[v(n.path),n]));for(let n of e.changes){let r=v(n.path);"delete"in n&&n.delete?t.delete(r):"content"in n&&t.set(r,{path:r,content:n.content})}return J({contract:e.contract,files:[...t.values()],compilerOptions:e.compilerOptions})}function ht(e){let t=`${e.evidence.file}:${e.evidence.line}`;if(!e.edge)return`${e.ruleId} at ${t}: ${e.message}`;let n=e.edge.to??e.edge.specifier;return`${e.ruleId} at ${t}: ${e.edge.from} imports ${n}. ${e.message}`}function Ve(e){let t=0,n=new Map,r=new Map,i=new Set,a=[],o=[],d=l=>{n.set(l,t),r.set(l,t),t+=1,a.push(l),i.add(l);for(let g of[...e.get(l)??[]].sort())e.has(g)&&(n.has(g)?i.has(g)&&r.set(l,Math.min(r.get(l)??0,n.get(g)??0)):(d(g),r.set(l,Math.min(r.get(l)??0,r.get(g)??0))));if(r.get(l)!==n.get(l))return;let u=[],y;do{if(y=a.pop(),y===void 0)break;i.delete(y),u.push(y)}while(y!==l);u.length>1&&o.push(u.sort())};for(let l of[...e.keys()].sort())n.has(l)||d(l);return o.sort((l,u)=>l[0].localeCompare(u[0])).map(l=>({ruleId:"CIRCULAR_DEPENDENCY",file:l[0],line:1,target:l.join(" \u2192 "),message:`Circular dependency among ${l.length} files: ${l.join(" \u2192 ")} \u2192 ${l[0]}.`,cycleKind:"value"}))}function be(e){let t=e.contentViolations.map(a=>({...a})),n=(e.warnings??[]).map(a=>({...a})),r=new Map(e.files.map(a=>[a,new Set]));for(let a of e.edges){if(a.to&&a.to!==a.from&&!a.typeOnly&&r.has(a.from)&&r.get(a.from)?.add(a.to),!a.to||!a.toLayer)continue;let o=G(e.rules,a.fromLayer,a.toLayer,{fromPath:a.from,toPath:a.to,layers:e.config.layers});if(!o)continue;let d=!!o.peerIsolation;t.push({ruleId:"LAYER_IMPORT_VIOLATION",file:a.from,line:a.line,fromLayer:a.fromLayer,toLayer:a.toLayer,target:a.to,...a.typeOnly?{typeOnly:!0}:{},...a.targetTypeOnlyExports?{targetTypeOnlyExports:!0}:{},...a.sourcePureTypeModule?{sourcePureTypeModule:!0}:{},...a.namedBindingsTypeOnly?{namedBindingsTypeOnly:!0}:{},...!d&&a.portProofEligible?{portProofEligible:!0}:{},...a.kind?{edgeKind:a.kind}:{},...d?{peerIsolation:!0}:{},message:o.message??(d?`${a.fromLayer} must not ${a.kind} another slice of ${a.toLayer} (${a.from} \u2192 ${a.to}). Extract shared code or use events/ports across slices.`:`${a.fromLayer} must not ${a.kind} ${a.toLayer}.`)})}let i=String(e.config.cyclePolicy??"strict").toLowerCase();if(i!=="off"){let a=Ve(r);i==="soft"||i==="framework-soft"?n.push(...a.map(o=>({...o,message:`${o.message} (soft cycle policy \u2014 advisory only; set cyclePolicy: "strict" to fail the check)`,failsStrict:!1}))):t.push(...a)}return{violations:t,warnings:n,safety:e.safety}}function He(e){switch(e.ruleId){case"LAYER_IMPORT_VIOLATION":return e.typeOnly||e.targetTypeOnlyExports||e.namedBindingsTypeOnly?"Move the referenced type to a mutually allowed layer, use `import type`, then preflight again.":e.peerIsolation?"Extract the shared dependency to a shared layer, then preflight again.":`Define a port in ${e.fromLayer??"the source layer"}, inject the ${e.toLayer??"outer-layer"} implementation, then preflight again.`;case"FORBIDDEN_GLOBAL":return`Inject ${e.target??"the capability"} through a port, then preflight again.`;case"CAPABILITY_VIOLATION":return`Define a ${String(e.capability??"capability")} port in ${e.fromLayer??"the walled layer"}, bind the implementation outside it, then preflight again.`;case"CIRCULAR_DEPENDENCY":return"Extract the shared dependency into a third module, then preflight again.";case"RAW_EVENT_PUBLISH":return"Publish through a registered intent creator, then run Ark again.";case"PUBLISH_MISSING_SOURCE":return"Add metadata.source to the publish call, then run Ark again.";default:return`Resolve ${typeof e.ruleId=="string"&&e.ruleId.length>0?e.ruleId:"ARK_UNKNOWN"} without weakening ark.config.json, then run Ark again.`}}function Ge(e){return $(x(e.map(({path:t,contentHash:n})=>({path:t,contentHash:n}))))}function At(e){let t=J(e),n=new Map(t.ir.files.map(s=>[s.path,s])),r=[],i=new Set,a=[];for(let s of e.changes){let p=s.path.replace(/\\/g,"/"),f=v(s.path);if(!f||f===".."||f.startsWith("../")||p.startsWith("/")||/^[A-Za-z]:\//.test(p)||p.includes("\0")){a.push({ruleId:"INVALID_CHANGE_PATH",file:"<change-set>",line:1,message:"Every change requires a safe, non-empty project-relative path."});continue}if(i.has(f)){a.push({ruleId:"DUPLICATE_CHANGE_PATH",file:f,line:1,message:`The atomic change set contains more than one operation for ${f}.`});continue}i.add(f),"delete"in s&&s.delete&&!n.has(f)&&a.push({ruleId:"DELETE_TARGET_MISSING",file:f,line:1,message:`Cannot delete ${f} because it is not present in the supplied base tree.`}),r.push("delete"in s&&s.delete?{path:f,delete:!0}:{path:f,content:"content"in s?s.content:""})}e.changes.length===0&&a.push({ruleId:"CHANGE_SET_EMPTY",file:"<change-set>",line:1,message:"Atomic preflight requires at least one create, update, or delete."});let o=Ae({...e,changes:r}),d=new Map(o.ir.files.map(s=>[s.path,s])),l=o.ir.violations.filter(s=>s.ruleId==="CAPABILITY_VIOLATION"||s.ruleId==="FORBIDDEN_GLOBAL").map(s=>{let p=d.get(s.evidence.file)?.layer;return{ruleId:s.ruleId,file:s.evidence.file,line:s.evidence.line,target:s.symbol,...s.capability?{capability:s.capability}:{},...p?{fromLayer:p}:{},edgeKind:"import",message:s.message}}),u=be({config:e.contract.config,rules:e.contract.config.rules,files:o.ir.files.map(s=>s.path),contentViolations:l,edges:o.ir.edges.filter(s=>!!s.fromLayer).map(s=>({from:s.from,fromLayer:s.fromLayer,...s.to?{to:s.to}:{},...s.toLayer?{toLayer:s.toLayer}:{},line:s.evidence.line,kind:"import"}))}),y=r.map(s=>{let p=v(s.path),f=n.get(p),m=d.get(p);return{path:p,operation:"delete"in s&&s.delete?"delete":f?"update":"create",...f?{beforeContentHash:f.contentHash}:{},...m?{candidateContentHash:m.contentHash}:{}}}).sort((s,p)=>s.path.localeCompare(p.path)),g=[...a,...u.violations].map(s=>({...s,nextAction:He(s)})),c=e.changeMap?re({changeMap:e.changeMap,changes:y,baseDependencies:t.ir.edges.flatMap(s=>s.to?[{from:s.from,to:s.to}]:[]),candidateDependencies:o.ir.edges.flatMap(s=>s.to?[{from:s.from,to:s.to}]:[])}):void 0;return{schemaVersion:"1.0",valid:g.length===0&&(c?.structurallyConverged??!0),readOnly:!0,policyHash:e.contract.policyHash,compilerOptionsHash:o.ir.compilerOptionsHash,baseTreeHash:Ge(t.ir.files),candidateTreeHash:Ge(o.ir.files),...e.changeMap?{changeMapHash:e.changeMap.hash}:{},...c?{convergence:c}:{},changes:y,violations:g,warnings:u.warnings}}function I(e,t,n={}){return{ruleId:e,message:t,...n}}function bt(e){let{config:t,rules:n,files:r,manifest:i}=e,a=[];if(t.dynamicImportAllowlist!==void 0&&(!Array.isArray(t.dynamicImportAllowlist)||t.dynamicImportAllowlist.some(s=>typeof s!="string"))&&a.push(I("CONFIG_INVALID_DYNAMIC_IMPORT_ALLOWLIST","dynamicImportAllowlist must be an array of file globs.")),t.safety!==void 0&&(t.safety===null||typeof t.safety!="object"||Array.isArray(t.safety)))a.push(I("CONFIG_INVALID_SAFETY","safety must be an object."));else if(t.safety)for(let s of["maxTsSuppressions","maxAnyCasts"]){let p=t.safety[s];p!==void 0&&(!Number.isInteger(p)||p<0)&&a.push(I("CONFIG_INVALID_SAFETY_THRESHOLD",`safety.${s} must be a non-negative integer.`))}let o=Array.isArray(t.layers)?t.layers:[],d=Array.isArray(i?.architecture?.layers)?i.architecture.layers:[],l=new Set([...o.map(s=>s.name).filter(Boolean),...d.map(s=>s.name).filter(s=>!!s)]);o.length===0&&a.push(I("CONFIG_NO_LAYERS","No file layers are configured; ark-check cannot classify files for import-boundary enforcement."));let u=new Set,y=new Set;for(let s of o){if(!s.name){a.push(I("CONFIG_LAYER_WITHOUT_NAME","A configured layer is missing a name."));continue}u.has(s.name)&&y.add(s.name),u.add(s.name),s.forbiddenGlobals!==void 0&&(!Array.isArray(s.forbiddenGlobals)||s.forbiddenGlobals.some(f=>typeof f!="string"))&&a.push(I("CONFIG_INVALID_FORBIDDEN_GLOBALS",`Layer "${s.name}" has an invalid forbiddenGlobals value; expected an array of strings (e.g. ["fetch", "Date.now"]). The entry is ignored.`,{layer:s.name}));let p=Array.isArray(s.patterns)?s.patterns:[];if(p.length===0){a.push(I("CONFIG_LAYER_WITHOUT_PATTERNS",`Layer "${s.name}" has no file patterns and will never classify files.`,{layer:s.name}));continue}for(let f of p){let m;try{m=D(f)}catch(h){a.push(I("CONFIG_INVALID_LAYER_PATTERN",`Layer "${s.name}" has an invalid pattern "${f}": ${h instanceof Error?h.message:String(h)}`,{layer:s.name,pattern:f}));continue}!r.some(h=>m.test(h))&&!s.optional&&a.push(I("CONFIG_LAYER_PATTERN_NO_MATCHES",`Layer "${s.name}" pattern "${f}" matched no included files.`,{layer:s.name,pattern:f,failsStrict:!1}))}}for(let s of y)a.push(I("CONFIG_DUPLICATE_LAYER",`Layer "${s}" is configured more than once.`,{layer:s}));if(l.size>0)for(let s of n??[])s.from&&!l.has(s.from)&&a.push(I("CONFIG_RULE_UNKNOWN_FROM_LAYER",`Rule references unknown source layer "${s.from}".`,{fromLayer:s.from,toLayer:s.to})),s.to&&!l.has(s.to)&&a.push(I("CONFIG_RULE_UNKNOWN_TO_LAYER",`Rule references unknown target layer "${s.to}".`,{fromLayer:s.from,toLayer:s.to}));let g=new Set;if(o.length>1)for(let s of r){let p=-1,f=[];for(let m of o)for(let h of m.patterns??[]){if(!D(h).test(s))continue;let A=Q(h);A>p?(p=A,f=[m.name]):A===p&&!f.includes(m.name)&&f.push(m.name)}f.length>1&&g.add([...f].sort().join(" + "))}g.size>0&&a.push(I("CONFIG_AMBIGUOUS_LAYERS",`Some files match multiple layers at equal specificity; classification falls back to declaration order. Disambiguate the overlapping patterns: ${[...g].join(", ")}.`,{pairs:[...g]}));let c=r.filter(s=>!_(s,o));return c.length>0&&a.push(I("CONFIG_UNCLASSIFIED_FILES",`${c.length} included source file(s) are not matched by any configured layer; ark-check will not enforce import rules for those source files.`,{count:c.length,samples:c.slice(0,5)})),a}export{fe as AMBIENT_CAPABILITY_ENTRIES,de as CAPABILITY_IDS,ce as SOURCE_POLICY_MESSAGES,Ze as ambientCoveredByForbiddenGlobals,re as analyzeArchitectureConvergence,Ae as analyzeChange,mt as analyzePolicyDelta,J as analyzeProject,V as capabilityForAmbientName,j as capabilityForModuleSpecifier,Je as classifyPublishFacts,bt as collectAnalysisConfigWarnings,Qe as collectCapabilityUses,oe as collectForbiddenCapabilityUses,Ve as detectArchitectureCycles,z as effectiveCapabilityDeny,be as evaluateArchitectureGraph,ht as explainViolation,se as extractSemanticDependencies,ue as forbiddenGlobalForModuleSpecifier,Ke as loadArchitectureChangeMap,he as loadContract,$e as looksLikeArkIntent,Xe as lowerForbiddenGlobal,q as loweredLayerCoverage,At as preflightChange};

package/bin/lib/architecture-scan.mjs

@@ -22,6 +22,7 @@ import {
   typeOnlyExportNames,
 } from './ast-scan.mjs';
 import { provePortProofInject } from './port-proof.mjs';
+import { summarizeParseHealth } from './parse-health.mjs';
 import {
   intentLayersFromManifest,
   layerForIntent,
@@ -35,6 +36,7 @@ import {
   effectiveCapabilityDeny,
   evaluateArchitectureGraph,
   extractSemanticDependencies,
+  forbiddenGlobalForModuleSpecifier,
 } from './analysis-engine.mjs';
 import { normalize } from './scan-files.mjs';
 import { collectSafetyDiagnostics } from './safety-diagnostics.mjs';
@@ -80,8 +82,10 @@ export function scanSourceFile(ts, root, config, rules, manifestIntentLayers, fi
     for (const use of collectCapabilityUses(ts, sourceFile)) {
       if (!capabilityDeny.has(use.capability)) continue;
       if (
-        use.source === 'ambient-global' &&
-        ambientCoveredByForbiddenGlobals(use.symbol, forbiddenGlobals)
+        (use.source === 'ambient-global' &&
+          ambientCoveredByForbiddenGlobals(use.symbol, forbiddenGlobals)) ||
+        (use.source === 'import-based' &&
+          forbiddenGlobalForModuleSpecifier(use.symbol, forbiddenGlobals))
       ) {
         continue;
       }
@@ -192,6 +196,7 @@ export function scanSourceFile(ts, root, config, rules, manifestIntentLayers, fi
   return {
     contentViolations: violations,
     edges,
+    parseDiagnosticCount: sourceFile.parseDiagnostics?.length ?? 0,
     exportsOnlyTypes: sourceFileExportsOnlyTypes(ts, sourceFile),
     typeOnlyExportNames: typeOnlyExportNames(ts, sourceFile),
     hasTopLevelSideEffects: sourceFileHasTopLevelSideEffects(ts, sourceFile),
@@ -210,7 +215,7 @@ export function runArchitectureScan({ root, config, manifest, rules, files, ts,
   const warnings = collectConfigWarnings(root, config, files, rules, manifest);
   const safety = collectSafetyDiagnostics(ts, root, config, files);
   warnings.push(...safety.warnings);
-  const cacheKey = args.noCache ? undefined : scanCacheKey(root, args);
+  const cacheKey = args.noCache ? undefined : scanCacheKey(root, args, ts.version);
   const cachedFiles = cacheKey ? loadScanCache(root, cacheKey) : undefined;
   const nextCacheFiles = {};
 
@@ -223,7 +228,10 @@ export function runArchitectureScan({ root, config, manifest, rules, files, ts,
     const fileKey = `${stat.mtimeMs}:${stat.size}`;
     const cached = cachedFiles?.[relFile];
     const entry =
-      cached && cached.fileKey === fileKey
+      cached &&
+      cached.fileKey === fileKey &&
+      Number.isSafeInteger(cached.parseDiagnosticCount) &&
+      cached.parseDiagnosticCount >= 0
         ? cached
         : {
             fileKey,
@@ -242,8 +250,36 @@ export function runArchitectureScan({ root, config, manifest, rules, files, ts,
   }
 
   const engineEdges = [];
+  // Y08 derives exact forbidden-global module duals from dependency facts
+  // already stored in every current cache entry. This stays downstream of the
+  // cache: no second AST scan, no cache-shape/version bump, and warm pre-Y08
+  // entries gain the verdict immediately.
+  const forbiddenModuleDualViolations = [];
+  const forbiddenModuleDualKeys = new Set();
   for (const { file, sourceLayer, relFile, entry } of scanned) {
+    const layerConfig = config.layers.find((layer) => layer.name === sourceLayer);
+    const forbiddenGlobals = Array.isArray(layerConfig?.forbiddenGlobals)
+      ? layerConfig.forbiddenGlobals.filter((item) => typeof item === 'string')
+      : [];
     for (const edge of entry.edges) {
+      if (!edge.typeOnly) {
+        const forbiddenGlobal = forbiddenGlobalForModuleSpecifier(
+          edge.specifier,
+          forbiddenGlobals
+        );
+        if (forbiddenGlobal) {
+          forbiddenModuleDualKeys.add(`${relFile}\0${edge.specifier}`);
+          forbiddenModuleDualViolations.push({
+            ruleId: 'FORBIDDEN_GLOBAL',
+            file: relFile,
+            line: edge.line,
+            fromLayer: sourceLayer,
+            target: edge.specifier,
+            edgeKind: edge.kind,
+            message: `${sourceLayer} must not use module "${edge.specifier}" because it is the import form of forbidden global "${forbiddenGlobal}".`,
+          });
+        }
+      }
       const target = resolveImport(
         ts,
         edge.specifier,
@@ -309,13 +345,30 @@ export function runArchitectureScan({ root, config, manifest, rules, files, ts,
 
   if (cacheKey) saveScanCache(root, cacheKey, nextCacheFiles);
 
-  return evaluateArchitectureGraph({
-    config,
-    rules,
-    files: scanned.map(({ relFile }) => relFile),
-    contentViolations: scanned.flatMap(({ entry }) => entry.contentViolations),
-    edges: engineEdges,
-    warnings,
-    safety: safety.report,
-  });
+  // A cache written before Y08 can retain the overlapping capability-wall
+  // finding for this import. Filter by file+specifier (not line: D7 explicitly
+  // does not depend on cross-engine line anchors), then let FORBIDDEN_GLOBAL be
+  // the one declared-policy voice.
+  const contentViolations = scanned
+    .flatMap(({ entry }) => entry.contentViolations)
+    .filter(
+      (violation) =>
+        !(
+          violation.ruleId === 'CAPABILITY_VIOLATION' &&
+          forbiddenModuleDualKeys.has(`${violation.file}\0${violation.target}`)
+        )
+    );
+
+  return {
+    ...evaluateArchitectureGraph({
+      config,
+      rules,
+      files: scanned.map(({ relFile }) => relFile),
+      contentViolations: [...contentViolations, ...forbiddenModuleDualViolations],
+      edges: engineEdges,
+      warnings,
+      safety: safety.report,
+    }),
+    parseHealth: summarizeParseHealth(scanned),
+  };
 }

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}]