@cortexkit/aft 0.30.3 → 0.31.1

package/dist/adapters/opencode.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"opencode.d.ts","sourceRoot":"","sources":["../../src/adapters/opencode.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EACV,cAAc,EACd,kBAAkB,EAClB,eAAe,EACf,iBAAiB,EAClB,MAAM,YAAY,CAAC;AAoFpB,qBAAa,eAAgB,YAAW,cAAc;IACpD,QAAQ,CAAC,IAAI,EAAG,UAAU,CAAU;IACpC,QAAQ,CAAC,WAAW,cAAc;IAClC,QAAQ,CAAC,iBAAiB,6BAAe;IACzC,QAAQ,CAAC,sBAAsB,oCAAgB;IAE/C,WAAW,IAAI,OAAO;IAStB,cAAc,IAAI,MAAM,GAAG,IAAI;IAQ/B,iBAAiB,IAAI,kBAAkB;IAgBvC,cAAc,IAAI,OAAO;IAOnB,iBAAiB,IAAI,OAAO,CAAC,iBAAiB,CAAC;IAkDrD,kBAAkB,IAAI,eAAe;IA0BrC,aAAa,IAAI,MAAM;IAKvB,UAAU,IAAI,MAAM;IAIpB,cAAc,IAAI,MAAM;IAIlB,gBAAgB,CAAC,KAAK,EAAE,OAAO,GAAG,OAAO,CAAC;QAC9C,MAAM,EAAE,SAAS,GAAG,YAAY,GAAG,WAAW,GAAG,gBAAgB,GAAG,OAAO,CAAC;QAC5E,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,KAAK,CAAC,EAAE,MAAM,CAAC;KAChB,CAAC;IAgCF,qEAAqE;IACrE,mBAAmB,IAAI,MAAM;IAI7B,mEAAmE;IACnE,uBAAuB,IAAI,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC;CAUlD"}
+{"version":3,"file":"opencode.d.ts","sourceRoot":"","sources":["../../src/adapters/opencode.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EACV,cAAc,EACd,kBAAkB,EAClB,eAAe,EACf,iBAAiB,EAClB,MAAM,YAAY,CAAC;AAoFpB,qBAAa,eAAgB,YAAW,cAAc;IACpD,QAAQ,CAAC,IAAI,EAAG,UAAU,CAAU;IACpC,QAAQ,CAAC,WAAW,cAAc;IAClC,QAAQ,CAAC,iBAAiB,6BAAe;IACzC,QAAQ,CAAC,sBAAsB,oCAAgB;IAE/C,WAAW,IAAI,OAAO;IAStB,cAAc,IAAI,MAAM,GAAG,IAAI;IAQ/B,iBAAiB,IAAI,kBAAkB;IAgBvC,cAAc,IAAI,OAAO;IAOnB,iBAAiB,IAAI,OAAO,CAAC,iBAAiB,CAAC;IAkDrD,kBAAkB,IAAI,eAAe;IA0BrC,aAAa,IAAI,MAAM;IAIvB,UAAU,IAAI,MAAM;IAIpB,cAAc,IAAI,MAAM;IAIlB,gBAAgB,CAAC,KAAK,EAAE,OAAO,GAAG,OAAO,CAAC;QAC9C,MAAM,EAAE,SAAS,GAAG,YAAY,GAAG,WAAW,GAAG,gBAAgB,GAAG,OAAO,CAAC;QAC5E,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,KAAK,CAAC,EAAE,MAAM,CAAC;KAChB,CAAC;IAgCF,qEAAqE;IACrE,mBAAmB,IAAI,MAAM;IAI7B,mEAAmE;IACnE,uBAAuB,IAAI,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC;CAUlD"}

package/dist/adapters/pi.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pi.d.ts","sourceRoot":"","sources":["../../src/adapters/pi.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EACV,cAAc,EACd,kBAAkB,EAClB,eAAe,EACf,iBAAiB,EAClB,MAAM,YAAY,CAAC;AAmIpB,qBAAa,SAAU,YAAW,cAAc;IAC9C,QAAQ,CAAC,IAAI,EAAG,IAAI,CAAU;IAC9B,QAAQ,CAAC,WAAW,QAAQ;IAC5B,QAAQ,CAAC,iBAAiB,uBAAe;IACzC,QAAQ,CAAC,sBAAsB,2BAAgB;IAE/C,WAAW,IAAI,OAAO;IAStB,cAAc,IAAI,MAAM,GAAG,IAAI;IAuB/B,iBAAiB,IAAI,kBAAkB;IAevC,cAAc,IAAI,OAAO;IAInB,iBAAiB,IAAI,OAAO,CAAC,iBAAiB,CAAC;IAmCrD,kBAAkB,IAAI,eAAe;IA6BrC,aAAa,IAAI,MAAM;IAKvB,UAAU,IAAI,MAAM;IAIpB,cAAc,IAAI,MAAM;IAIlB,gBAAgB,CAAC,MAAM,EAAE,OAAO,GAAG,OAAO,CAAC;QAC/C,MAAM,EAAE,SAAS,GAAG,YAAY,GAAG,WAAW,GAAG,gBAAgB,GAAG,OAAO,CAAC;QAC5E,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,KAAK,CAAC,EAAE,MAAM,CAAC;KAChB,CAAC;IAUF,uBAAuB,IAAI,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC;CAUlD"}
+{"version":3,"file":"pi.d.ts","sourceRoot":"","sources":["../../src/adapters/pi.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EACV,cAAc,EACd,kBAAkB,EAClB,eAAe,EACf,iBAAiB,EAClB,MAAM,YAAY,CAAC;AAmIpB,qBAAa,SAAU,YAAW,cAAc;IAC9C,QAAQ,CAAC,IAAI,EAAG,IAAI,CAAU;IAC9B,QAAQ,CAAC,WAAW,QAAQ;IAC5B,QAAQ,CAAC,iBAAiB,uBAAe;IACzC,QAAQ,CAAC,sBAAsB,2BAAgB;IAE/C,WAAW,IAAI,OAAO;IAStB,cAAc,IAAI,MAAM,GAAG,IAAI;IAuB/B,iBAAiB,IAAI,kBAAkB;IAevC,cAAc,IAAI,OAAO;IAInB,iBAAiB,IAAI,OAAO,CAAC,iBAAiB,CAAC;IAmCrD,kBAAkB,IAAI,eAAe;IA6BrC,aAAa,IAAI,MAAM;IAIvB,UAAU,IAAI,MAAM;IAIpB,cAAc,IAAI,MAAM;IAIlB,gBAAgB,CAAC,MAAM,EAAE,OAAO,GAAG,OAAO,CAAC;QAC/C,MAAM,EAAE,SAAS,GAAG,YAAY,GAAG,WAAW,GAAG,gBAAgB,GAAG,OAAO,CAAC;QAC5E,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,MAAM,CAAC,EAAE,MAAM,CAAC;QAChB,KAAK,CAAC,EAAE,MAAM,CAAC;KAChB,CAAC;IAUF,uBAAuB,IAAI,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC;CAUlD"}

package/dist/commands/doctor.d.ts

@@ -61,10 +61,12 @@ export interface BinaryCacheClearResult {
 }
 export declare function clearOldBinaries(): BinaryCacheClearResult;
 export interface DoctorFixPlanItem {
-    kind: "plugin" | "binary" | "onnx";
+    kind: "plugin" | "binary" | "onnx" | "storage";
     message: string;
 }
 export declare function buildDoctorFixPlan(adapters: HarnessAdapter[], report: DiagnosticReport): DoctorFixPlanItem[];
 export declare function shouldSkipDoctorFixConfirmation(argv: string[]): boolean;
+export declare function doctorSkewBinaryDownloadDecision(argv: string[]): "prompt" | "proceed" | "skip";
+export declare function formatDoctorStorageStatus(h: DiagnosticReport["harnesses"][number]): string;
 export declare function fixPluginEntries(adapters: HarnessAdapter[]): Promise<void>;
 //# sourceMappingURL=doctor.d.ts.map

package/dist/commands/doctor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,EAEL,KAAK,gBAAgB,EAGtB,MAAM,uBAAuB,CAAC;AAK/B,OAAO,EAAE,KAAK,WAAW,EAAkB,MAAM,qBAAqB,CAAC;AAMvE,MAAM,MAAM,iBAAiB,GAAG,cAAc,GAAG,WAAW,GAAG,cAAc,CAAC;AAE9E,eAAO,MAAM,2BAA2B,EAAE;IAAE,KAAK,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,iBAAiB,CAAA;CAAE,EAapF,CAAC;AAEF,eAAO,MAAM,0BAA0B,EAAE,iBAAiB,EAAqB,CAAC;AAEhF,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,OAAO,CAAC;IACf,GAAG,EAAE,OAAO,CAAC;IACb,KAAK,EAAE,OAAO,CAAC;IACf,KAAK,EAAE,OAAO,CAAC;IACf,IAAI,EAAE,MAAM,EAAE,CAAC;CAChB;AAED,MAAM,WAAW,iBAAiB;IAChC,SAAS,EAAE,OAAO,CAAC;IACnB,WAAW,CAAC,EAAE;QACZ,OAAO,EAAE,MAAM,CAAC;QAChB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,CAAC;KAChB,CAAC;IACF,QAAQ,CAAC,EAAE;QACT,OAAO,EAAE,MAAM,CAAC;QAChB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,CAAC;KAChB,CAAC;IACF,WAAW,CAAC,EAAE;QACZ,OAAO,EAAE,MAAM,CAAC;QAChB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,CAAC;KAChB,CAAC;CACH;AAED,MAAM,WAAW,iBAAiB;IAChC,cAAc,CAAC,EAAE,MAAM,WAAW,CAAC;IACnC,kBAAkB,CAAC,EAAE,OAAO,CAAC;CAC9B;AAED,wBAAsB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,MAAM,CAAC,CA4GvE;AAED,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,gBAAgB,GAAG,OAAO,CAiBnE;AA4BD,wBAAsB,iBAAiB,CACrC,QAAQ,EAAE,cAAc,EAAE,EAC1B,OAAO,EAAE,SAAS,iBAAiB,EAAE,EACrC,OAAO,GAAE,iBAAsB,GAC9B,OAAO,CAAC,iBAAiB,CAAC,CAgD5B;AAED;;;;;;;;;;GAUG;AACH,MAAM,WAAW,sBAAsB;IACrC,OAAO,EAAE,MAAM,CAAC;IAChB,cAAc,EAAE,MAAM,CAAC;IACvB,MAAM,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,EAAE,CAAC;IAC1C,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;CAC5B;AAED,wBAAgB,gBAAgB,IAAI,sBAAsB,CAsDzD;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,QAAQ,GAAG,QAAQ,GAAG,MAAM,CAAC;IACnC,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,wBAAgB,kBAAkB,CAChC,QAAQ,EAAE,cAAc,EAAE,EAC1B,MAAM,EAAE,gBAAgB,GACvB,iBAAiB,EAAE,CA4CrB;AAED,wBAAgB,+BAA+B,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAIvE;AAoKD,wBAAsB,gBAAgB,CAAC,QAAQ,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAIhF"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAG3D,OAAO,EAEL,KAAK,gBAAgB,EAKtB,MAAM,uBAAuB,CAAC;AAK/B,OAAO,EAAE,KAAK,WAAW,EAAkB,MAAM,qBAAqB,CAAC;AAMvE,MAAM,MAAM,iBAAiB,GAAG,cAAc,GAAG,WAAW,GAAG,cAAc,CAAC;AAE9E,eAAO,MAAM,2BAA2B,EAAE;IAAE,KAAK,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,iBAAiB,CAAA;CAAE,EAapF,CAAC;AAEF,eAAO,MAAM,0BAA0B,EAAE,iBAAiB,EAAqB,CAAC;AAEhF,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,OAAO,CAAC;IACf,GAAG,EAAE,OAAO,CAAC;IACb,KAAK,EAAE,OAAO,CAAC;IACf,KAAK,EAAE,OAAO,CAAC;IACf,IAAI,EAAE,MAAM,EAAE,CAAC;CAChB;AAED,MAAM,WAAW,iBAAiB;IAChC,SAAS,EAAE,OAAO,CAAC;IACnB,WAAW,CAAC,EAAE;QACZ,OAAO,EAAE,MAAM,CAAC;QAChB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,CAAC;KAChB,CAAC;IACF,QAAQ,CAAC,EAAE;QACT,OAAO,EAAE,MAAM,CAAC;QAChB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,CAAC;KAChB,CAAC;IACF,WAAW,CAAC,EAAE;QACZ,OAAO,EAAE,MAAM,CAAC;QAChB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,CAAC;KAChB,CAAC;CACH;AAED,MAAM,WAAW,iBAAiB;IAChC,cAAc,CAAC,EAAE,MAAM,WAAW,CAAC;IACnC,kBAAkB,CAAC,EAAE,OAAO,CAAC;CAC9B;AAED,wBAAsB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,MAAM,CAAC,CA4GvE;AAED,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,gBAAgB,GAAG,OAAO,CAOnE;AA4BD,wBAAsB,iBAAiB,CACrC,QAAQ,EAAE,cAAc,EAAE,EAC1B,OAAO,EAAE,SAAS,iBAAiB,EAAE,EACrC,OAAO,GAAE,iBAAsB,GAC9B,OAAO,CAAC,iBAAiB,CAAC,CAgD5B;AAED;;;;;;;;;;GAUG;AACH,MAAM,WAAW,sBAAsB;IACrC,OAAO,EAAE,MAAM,CAAC;IAChB,cAAc,EAAE,MAAM,CAAC;IACvB,MAAM,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,EAAE,CAAC;IAC1C,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;CAC5B;AAED,wBAAgB,gBAAgB,IAAI,sBAAsB,CAsDzD;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,QAAQ,GAAG,QAAQ,GAAG,MAAM,GAAG,SAAS,CAAC;IAC/C,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,wBAAgB,kBAAkB,CAChC,QAAQ,EAAE,cAAc,EAAE,EAC1B,MAAM,EAAE,gBAAgB,GACvB,iBAAiB,EAAE,CAwDrB;AAED,wBAAgB,+BAA+B,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,OAAO,CAIvE;AAED,wBAAgB,gCAAgC,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,QAAQ,GAAG,SAAS,GAAG,MAAM,CAK9F;AA4JD,wBAAgB,yBAAyB,CAAC,CAAC,EAAE,gBAAgB,CAAC,WAAW,CAAC,CAAC,MAAM,CAAC,GAAG,MAAM,CAK1F;AAsGD,wBAAsB,gBAAgB,CAAC,QAAQ,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAIhF"}

package/dist/index.js

@@ -7948,6 +7948,22 @@ function getAftLspBinariesDir() {
   const base = process.env.XDG_CACHE_HOME || join2(homedir(), ".cache");
   return join2(base, "aft", "lsp-binaries");
 }
+function homeDir() {
+  if (process.platform === "win32")
+    return process.env.USERPROFILE || process.env.HOME || homedir();
+  return process.env.HOME || homedir();
+}
+function dataHome() {
+  if (process.env.XDG_DATA_HOME)
+    return process.env.XDG_DATA_HOME;
+  if (process.platform === "win32") {
+    return process.env.LOCALAPPDATA || process.env.APPDATA || join2(homeDir(), "AppData", "Local");
+  }
+  return join2(homeDir(), ".local", "share");
+}
+function getCortexKitStorageRoot() {
+  return join2(dataHome(), "cortexkit", "aft");
+}
 function getTmpLogPath(filename) {
   return join2(tmpdir(), filename);
 }
@@ -8143,8 +8159,7 @@ class OpenCodeAdapter {
     };
   }
   getStorageDir() {
-    const xdg = process.env.XDG_DATA_HOME || join3(homedir2(), ".local", "share");
-    return join3(xdg, "opencode", "storage", "plugin", "aft");
+    return getCortexKitStorageRoot();
   }
   getLogFile() {
     return getTmpLogPath("aft-plugin.log");
@@ -8395,7 +8410,7 @@ class PiAdapter {
     };
   }
   getStorageDir() {
-    return join4(getPiAgentDir(), "aft");
+    return getCortexKitStorageRoot();
   }
   getLogFile() {
     return getTmpLogPath("aft-pi.log");
@@ -10914,7 +10929,7 @@ var init_lsp_cache = __esm(() => {
 
 // src/lib/onnx.ts
 import { existsSync as existsSync10, readdirSync as readdirSync5, readlinkSync, realpathSync, statSync as statSync6 } from "node:fs";
-import { join as join9 } from "node:path";
+import { isAbsolute, join as join9, win32 } from "node:path";
 function getOnnxLibraryName() {
   if (process.platform === "darwin")
     return "libonnxruntime.dylib";
@@ -10943,11 +10958,38 @@ function getManualInstallHint() {
   }
   return "ONNX Runtime must be installed manually for this platform";
 }
+function pathEnvValue() {
+  return process.env.PATH ?? process.env.Path ?? process.env.path ?? "";
+}
+function pathEntriesForPlatform() {
+  const delimiter = process.platform === "win32" ? ";" : ":";
+  return pathEnvValue().split(delimiter).map((entry) => entry.trim().replace(/^"|"$/g, "")).filter((entry) => {
+    if (!entry || entry === "." || entry.includes("\x00"))
+      return false;
+    return isAbsolute(entry) || win32.isAbsolute(entry);
+  });
+}
+function directoryContainsLibrary(dir, libName) {
+  try {
+    const entries = readdirSync5(dir);
+    if (process.platform === "win32") {
+      const expected = libName.toLowerCase();
+      return entries.some((entry) => entry.toLowerCase() === expected);
+    }
+    return entries.includes(libName);
+  } catch {
+    return false;
+  }
+}
 function findSystemOnnxRuntime() {
   const libName = getOnnxLibraryName();
-  const searchPaths = process.platform === "darwin" ? ["/opt/homebrew/lib", "/usr/local/lib"] : process.platform === "linux" ? ["/usr/lib", "/usr/lib/x86_64-linux-gnu", "/usr/lib/aarch64-linux-gnu", "/usr/local/lib"] : [];
+  const searchPaths = process.platform === "darwin" ? ["/opt/homebrew/lib", "/usr/local/lib"] : process.platform === "linux" ? ["/usr/lib", "/usr/lib/x86_64-linux-gnu", "/usr/lib/aarch64-linux-gnu", "/usr/local/lib"] : process.platform === "win32" ? pathEntriesForPlatform() : [];
+  const seen = new Set;
   for (const path of searchPaths) {
-    if (existsSync10(join9(path, libName)))
+    if (seen.has(path))
+      continue;
+    seen.add(path);
+    if (directoryContainsLibrary(path, libName))
       return path;
   }
   return null;
@@ -11061,6 +11103,7 @@ async function diagnoseHarness(adapter) {
   const aftFlags = sanitizeValue(aftConfigRead.value ?? {}) ?? {};
   const storage = adapter.getStorageDir();
   const logPath = adapter.getLogFile();
+  const pluginCache = adapter.getPluginCacheInfo();
   const describeStorage = "describeStorageSubtrees" in adapter && typeof adapter.describeStorageSubtrees === "function" ? adapter.describeStorageSubtrees() : {};
   const semanticEnabled = aftConfigRead.value?.semantic_search === true || aftConfigRead.value?.experimental_semantic_search === true;
   const systemOrtDir = findSystemOnnxRuntime();
@@ -11079,7 +11122,7 @@ async function diagnoseHarness(adapter) {
       ...aftConfigRead.error ? { parseError: aftConfigRead.error } : {},
       flags: aftFlags
     },
-    pluginCache: adapter.getPluginCacheInfo(),
+    pluginCache,
     storageDir: {
       path: storage,
       exists: existsSync11(storage),
@@ -11111,12 +11154,21 @@ function renderDiagnosticsMarkdown(report) {
   lines.push(`- AFT binary: ${report.binaryVersion ?? "unknown"}`);
   lines.push(`- OS: ${report.platform} ${report.arch}`);
   lines.push(`- Node: ${report.nodeVersion}`);
+  const issues = collectDiagnosticIssues(report);
+  if (issues.length > 0) {
+    lines.push("");
+    lines.push("### Issues found");
+    for (const issue of issues) {
+      lines.push(`- **${issue.severity.toUpperCase()}** ${issue.scope}: ${issue.message} Remediation: ${issue.remediation}`);
+    }
+  }
   for (const h of report.harnesses) {
     lines.push("");
     lines.push(`### ${h.displayName}`);
     lines.push(`- Host installed: ${h.hostInstalled}`);
     lines.push(`- Host version: ${h.hostVersion ?? "unknown"}`);
     lines.push(`- Plugin registered: ${h.pluginRegistered}`);
+    lines.push(`- Plugin version: ${h.pluginCache.cached ?? "not installed"}`);
     lines.push(`- AFT config parse error: ${h.aftConfig.parseError ?? "none"}`);
     lines.push("");
     lines.push("#### Config paths");
@@ -11160,6 +11212,130 @@ function renderDiagnosticsMarkdown(report) {
   return lines.join(`
 `);
 }
+function normalizeVersion(version) {
+  return version.trim().replace(/^v/, "");
+}
+function compareLooseSemver(a, b) {
+  const aParts = normalizeVersion(a).split(/[.-]/).slice(0, 3).map((part) => Number.parseInt(part, 10));
+  const bParts = normalizeVersion(b).split(/[.-]/).slice(0, 3).map((part) => Number.parseInt(part, 10));
+  for (let i = 0;i < 3; i += 1) {
+    const av = Number.isFinite(aParts[i]) ? aParts[i] : 0;
+    const bv = Number.isFinite(bParts[i]) ? bParts[i] : 0;
+    if (av !== bv)
+      return av - bv;
+  }
+  return 0;
+}
+function pluginPackageNameForHarness(kind) {
+  if (kind === "pi")
+    return "@cortexkit/aft-pi";
+  return "@cortexkit/aft-opencode";
+}
+function pluginVersionSkewIssue(harness, cliVersion) {
+  const pluginVersion = harness.pluginCache.cached;
+  if (!pluginVersion)
+    return null;
+  if (normalizeVersion(pluginVersion) === normalizeVersion(cliVersion))
+    return null;
+  const relation = compareLooseSemver(pluginVersion, cliVersion) < 0 ? "older than" : "different from";
+  const packageName = pluginPackageNameForHarness(harness.kind);
+  return {
+    code: "plugin_cli_version_skew",
+    severity: "high",
+    scope: harness.displayName,
+    message: relation === "older than" ? `Plugin version (${pluginVersion}) is older than CLI (${cliVersion}). New binary cache won't be used until you update the plugin.` : `Plugin version (${pluginVersion}) does not match CLI (${cliVersion}). New binary cache may not be used until the plugin and CLI match.`,
+    remediation: `Update \`${packageName}\` in your harness config to \`@latest\`.`
+  };
+}
+function collectDiagnosticIssues(report) {
+  const issues = [];
+  if (!report.binaryVersion) {
+    issues.push({
+      code: "binary_missing",
+      severity: "high",
+      scope: "AFT binary",
+      message: `No aft binary matching CLI ${report.cliVersion} was detected.`,
+      remediation: "Run `aft doctor --fix` to download the matching binary, or start an AFT-enabled session to trigger plugin-side install."
+    });
+  }
+  for (const h of report.harnesses) {
+    if (!h.hostInstalled) {
+      issues.push({
+        code: "host_missing",
+        severity: "high",
+        scope: h.displayName,
+        message: "Host CLI is not installed or is not on PATH.",
+        remediation: `Install ${h.displayName} and rerun \`aft doctor\`.`
+      });
+      continue;
+    }
+    if (!h.pluginRegistered) {
+      issues.push({
+        code: "plugin_missing",
+        severity: "medium",
+        scope: h.displayName,
+        message: "AFT plugin is not registered with this harness.",
+        remediation: "Run `aft setup` or `aft doctor --fix` to register the plugin."
+      });
+    }
+    if (h.aftConfig.parseError) {
+      issues.push({
+        code: "config_parse_error",
+        severity: "high",
+        scope: h.displayName,
+        message: `AFT config parse error: ${h.aftConfig.parseError}`,
+        remediation: `Fix JSON/JSONC syntax in ${h.configPaths.aftConfig}.`
+      });
+    }
+    const skewIssue = pluginVersionSkewIssue(h, report.cliVersion);
+    if (skewIssue)
+      issues.push(skewIssue);
+    if (h.onnxRuntime.required) {
+      if (!h.onnxRuntime.cachedPath && !h.onnxRuntime.systemPath) {
+        issues.push({
+          code: "onnx_missing",
+          severity: "medium",
+          scope: h.displayName,
+          message: "ONNX Runtime is required for semantic search but was not detected.",
+          remediation: `Run \`aft doctor --fix\` or install ONNX Runtime manually (${h.onnxRuntime.installHint}).`
+        });
+      }
+      if (h.onnxRuntime.cachedCompatible === false) {
+        issues.push({
+          code: "onnx_incompatible",
+          severity: "medium",
+          scope: h.displayName,
+          message: `Cached ONNX Runtime ${h.onnxRuntime.cachedVersion ?? "unknown"} is incompatible (requires ${h.onnxRuntime.requirement}).`,
+          remediation: "Run `aft doctor --fix` to refresh AFT-managed ONNX Runtime state."
+        });
+      }
+      if (h.onnxRuntime.systemCompatible === false) {
+        issues.push({
+          code: "onnx_incompatible",
+          severity: "medium",
+          scope: h.displayName,
+          message: `System ONNX Runtime ${h.onnxRuntime.systemVersion ?? "unknown"} is incompatible (requires ${h.onnxRuntime.requirement}).`,
+          remediation: "Install a compatible ONNX Runtime or let AFT use its managed runtime."
+        });
+      }
+    }
+  }
+  return issues;
+}
+function findPluginCliVersionSkews(report) {
+  return collectDiagnosticIssues(report).filter((issue) => issue.code === "plugin_cli_version_skew");
+}
+function formatDiagnosticIssuesSection(report) {
+  const issues = collectDiagnosticIssues(report);
+  if (issues.length === 0)
+    return [];
+  const lines = ["--- Issues found ---"];
+  for (const issue of issues) {
+    lines.push(`[${issue.severity.toUpperCase()}] ${issue.scope}: ${issue.message}`);
+    lines.push(`  Remediation: ${issue.remediation}`);
+  }
+  return lines;
+}
 function tailLogFile(path, lines) {
   if (!existsSync11(path))
     return "";
@@ -11428,14 +11604,16 @@ __export(exports_doctor, {
   shouldSkipDoctorFixConfirmation: () => shouldSkipDoctorFixConfirmation,
   runDoctor: () => runDoctor,
   hasDoctorProblems: () => hasDoctorProblems,
+  formatDoctorStorageStatus: () => formatDoctorStorageStatus,
   fixPluginEntries: () => fixPluginEntries,
+  doctorSkewBinaryDownloadDecision: () => doctorSkewBinaryDownloadDecision,
   clearOldBinaries: () => clearOldBinaries,
   clearDoctorCaches: () => clearDoctorCaches,
   buildDoctorFixPlan: () => buildDoctorFixPlan,
   DOCTOR_FORCE_CLEAR_TARGETS: () => DOCTOR_FORCE_CLEAR_TARGETS,
   DOCTOR_CLEAR_TARGET_OPTIONS: () => DOCTOR_CLEAR_TARGET_OPTIONS
 });
-import { existsSync as existsSync13, rmSync as rmSync4, statSync as statSync8, writeFileSync as writeFileSync2 } from "node:fs";
+import { existsSync as existsSync13, mkdirSync as mkdirSync2, rmSync as rmSync4, statSync as statSync8, writeFileSync as writeFileSync2 } from "node:fs";
 import { join as join11 } from "node:path";
 async function runDoctor(options) {
   if (options.issue) {
@@ -11473,6 +11651,7 @@ async function runDoctor(options) {
     }
     O2.info(`  host: ${h.hostVersion ?? "unknown version"}`);
     O2.info(`  plugin registered: ${h.pluginRegistered ? "yes" : "no"}`);
+    O2.info(`  plugin version: ${h.pluginCache.cached ?? "not installed"}`);
     if (!h.pluginRegistered) {
       O2.warn("  plugin registration can be fixed with `aft setup` or `aft doctor --fix`");
     }
@@ -11480,7 +11659,7 @@ async function runDoctor(options) {
     if (h.aftConfig.parseError) {
       O2.error(`  aft config parse error: ${h.aftConfig.parseError}`);
     }
-    O2.info(`  storage: ${h.storageDir.exists ? h.storageDir.path : "(not created)"} (${formatStorageSizes(h.storageDir.sizesByKey)})`);
+    O2.info(`  storage: ${formatDoctorStorageStatus(h)}`);
     if (h.onnxRuntime.required) {
       const parts = [];
       parts.push(`required: yes (${h.onnxRuntime.platform})`);
@@ -11506,6 +11685,7 @@ async function runDoctor(options) {
     await clearDoctorCaches(adapters, DOCTOR_FORCE_CLEAR_TARGETS, { includePluginBytes: false });
   }
   if (hadProblems) {
+    logDoctorIssues(report);
     wt("Run `aft setup` or `aft doctor --fix` to register AFT with any harness showing `plugin registered: no`. Run `aft doctor --fix` for ONNX Runtime issues or to download a missing aft binary.", "Tips");
     gt("Done — some issues found.");
     return 1;
@@ -11514,25 +11694,7 @@ async function runDoctor(options) {
   return 0;
 }
 function hasDoctorProblems(report) {
-  if (!report.binaryVersion)
-    return true;
-  return report.harnesses.some((h) => {
-    if (!h.hostInstalled)
-      return true;
-    if (!h.pluginRegistered)
-      return true;
-    if (h.aftConfig.parseError)
-      return true;
-    if (!h.onnxRuntime.required)
-      return false;
-    if (!h.onnxRuntime.cachedPath && !h.onnxRuntime.systemPath)
-      return true;
-    if (h.onnxRuntime.cachedCompatible === false)
-      return true;
-    if (h.onnxRuntime.systemCompatible === false)
-      return true;
-    return false;
-  });
+  return formatDiagnosticIssuesSection(report).length > 0;
 }
 async function runClearFlow(argv) {
   const targets = await selectMany("What do you want to clear?", DOCTOR_CLEAR_TARGET_OPTIONS, undefined, false);
@@ -11655,9 +11817,18 @@ function buildDoctorFixPlan(adapters, report) {
     }
   }
   if (!report.binaryVersion) {
+    const skews = findPluginCliVersionSkews(report);
     items.push({
       kind: "binary",
-      message: `Will download/cache the aft binary matching CLI v${report.cliVersion}`
+      message: skews.length > 0 ? `Will ask before caching CLI v${report.cliVersion} because the installed plugin will not use it until updated` : `Will download/cache the aft binary matching CLI v${report.cliVersion}`
+    });
+  }
+  for (const harness of report.harnesses) {
+    if (!harness.hostInstalled || !harness.pluginRegistered || harness.storageDir.exists)
+      continue;
+    items.push({
+      kind: "storage",
+      message: `Will create AFT storage directory at ${harness.storageDir.path}`
     });
   }
   for (const candidate of findOnnxFixCandidates(report)) {
@@ -11682,6 +11853,15 @@ function shouldSkipDoctorFixConfirmation(argv) {
     return true;
   return process.stdin.isTTY !== true || process.stdout.isTTY !== true;
 }
+function doctorSkewBinaryDownloadDecision(argv) {
+  if (argv.includes("--yes") || argv.includes("-y"))
+    return "proceed";
+  if (argv.includes("--ci"))
+    return "skip";
+  if (process.stdin.isTTY !== true || process.stdout.isTTY !== true)
+    return "skip";
+  return "prompt";
+}
 async function confirmDoctorFixPlan(plan, argv) {
   if (plan.length === 0)
     return true;
@@ -11723,29 +11903,36 @@ async function runFixFlow(argv) {
     }
   }
   await fixPluginEntries(adapters);
+  const storageSummary = ensureStorageDirsForRegisteredPlugins(adapters);
   let binaryDownloaded = false;
+  let binaryDownloadSkipped = false;
   let binaryDownloadError = null;
   if (!report.binaryVersion) {
-    O2.info("AFT binary not found. Downloading…");
-    try {
-      const bridgePackageName = "@cortexkit/aft-bridge";
-      const { ensureBinary } = await import(bridgePackageName);
-      const path = await ensureBinary(`v${report.cliVersion}`);
-      if (path) {
-        O2.success(`AFT binary installed at ${path}`);
-        binaryDownloaded = true;
-      } else {
-        O2.error("AFT binary download failed — no matching release asset on GitHub. " + "Try opening any AFT-enabled session to trigger plugin-side download instead.");
-        binaryDownloadError = "no matching release asset";
+    const shouldDownload = await confirmBinaryDownloadDespitePluginSkew(report, argv);
+    if (!shouldDownload) {
+      binaryDownloadSkipped = true;
+    } else {
+      O2.info("AFT binary not found. Downloading…");
+      try {
+        const bridgePackageName = "@cortexkit/aft-bridge";
+        const { ensureBinary } = await import(bridgePackageName);
+        const path = await ensureBinary(`v${report.cliVersion}`);
+        if (path) {
+          O2.success(`AFT binary installed at ${path}`);
+          binaryDownloaded = true;
+        } else {
+          O2.error("AFT binary download failed — no matching release asset on GitHub. " + "Try opening any AFT-enabled session to trigger plugin-side download instead.");
+          binaryDownloadError = "no matching release asset";
+        }
+      } catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        O2.error(`AFT binary download failed: ${message}`);
+        binaryDownloadError = message;
       }
-    } catch (err) {
-      const message = err instanceof Error ? err.message : String(err);
-      O2.error(`AFT binary download failed: ${message}`);
-      binaryDownloadError = message;
     }
   }
   const onnxResult = await runOnnxFix(adapters, report, { yes: true });
-  if (onnxResult === null && !binaryDownloaded && !binaryDownloadError) {
+  if (onnxResult === null && !binaryDownloaded && !binaryDownloadSkipped && !binaryDownloadError && storageSummary.created === 0 && storageSummary.errors === 0) {
     O2.info("No auto-fixable issues detected.");
     wt("If you're still seeing 'Semantic Index: failed' in the TUI sidebar, run `aft doctor` (without --fix) for a full diagnostic dump.", "Tip");
     const afterReport2 = await collectDiagnostics(adapters);
@@ -11753,12 +11940,73 @@ async function runFixFlow(argv) {
     gt(stillHasProblems2 ? "Done — some issues remain." : "Done.");
     return stillHasProblems2 ? 1 : 0;
   }
-  const hadErrors = (onnxResult?.errors.length ?? 0) > 0 || binaryDownloadError !== null;
+  const hadErrors = (onnxResult?.errors.length ?? 0) > 0 || binaryDownloadError !== null || storageSummary.errors > 0;
   const afterReport = await collectDiagnostics(adapters);
   const stillHasProblems = hasDoctorProblems(afterReport);
   gt(hadErrors ? "Done — some fixes failed." : stillHasProblems ? "Done — some issues remain." : "Done.");
   return hadErrors || stillHasProblems ? 1 : 0;
 }
+function logDoctorIssues(report) {
+  const lines = formatDiagnosticIssuesSection(report);
+  if (lines.length === 0)
+    return;
+  O2.warn(lines[0]);
+  for (let i = 1;i < lines.length; i += 2) {
+    const issue = lines[i];
+    const remediation = lines[i + 1];
+    if (issue.startsWith("[HIGH]")) {
+      O2.error(issue);
+    } else {
+      O2.warn(issue);
+    }
+    if (remediation)
+      O2.warn(remediation);
+  }
+}
+function formatDoctorStorageStatus(h) {
+  const state = h.storageDir.exists ? h.storageDir.path : `${h.storageDir.path} (${h.pluginRegistered ? "not yet created (lazy — created on first tool call)" : "not created"})`;
+  return `${state} (${formatStorageSizes(h.storageDir.sizesByKey)})`;
+}
+async function confirmBinaryDownloadDespitePluginSkew(report, argv) {
+  const skews = findPluginCliVersionSkews(report);
+  if (skews.length === 0)
+    return true;
+  O2.warn("Plugin/CLI version mismatch detected before binary download:");
+  for (const skew of skews) {
+    O2.warn(`  ${skew.scope}: ${skew.message}`);
+    O2.warn(`  ${skew.remediation}`);
+  }
+  O2.warn("A newly cached binary will not be used by the older plugin until the plugin is updated.");
+  const decision = doctorSkewBinaryDownloadDecision(argv);
+  if (decision === "proceed") {
+    O2.info("Proceeding because --yes/-y was provided.");
+    return true;
+  }
+  if (decision === "skip") {
+    O2.info("Skipped binary download. Update the plugin to @latest, then rerun `aft doctor --fix`.");
+    return false;
+  }
+  return confirm("Download/cache the CLI-matching binary anyway for after you update the plugin?", false);
+}
+function ensureStorageDirsForRegisteredPlugins(adapters) {
+  const summary = { created: 0, errors: 0 };
+  for (const adapter of adapters) {
+    try {
+      if (!adapter.isInstalled() || !adapter.hasPluginEntry())
+        continue;
+      const storageDir = adapter.getStorageDir();
+      if (existsSync13(storageDir))
+        continue;
+      mkdirSync2(storageDir, { recursive: true });
+      summary.created += 1;
+      O2.success(`${adapter.displayName}: created AFT storage directory at ${storageDir}`);
+    } catch (err) {
+      summary.errors += 1;
+      O2.error(`${adapter.displayName}: failed to create AFT storage directory: ${err instanceof Error ? err.message : String(err)}`);
+    }
+  }
+  return summary;
+}
 async function clearPluginCache(adapter, includeBytes) {
   const info = adapter.getPluginCacheInfo();
   const bytes = info.exists ? dirSize(info.path) : 0;

package/dist/lib/diagnostics.d.ts

@@ -13,6 +13,14 @@ export interface DiagnosticReport {
     /** LSP package and binary caches populated by plugin auto-install. */
     lspCache: LspCacheReport;
 }
+export type DiagnosticIssueSeverity = "high" | "medium" | "low";
+export interface DiagnosticIssue {
+    code: "binary_missing" | "host_missing" | "plugin_missing" | "config_parse_error" | "plugin_cli_version_skew" | "onnx_missing" | "onnx_incompatible";
+    severity: DiagnosticIssueSeverity;
+    scope: string;
+    message: string;
+    remediation: string;
+}
 export interface HarnessDiagnostic {
     kind: string;
     displayName: string;
@@ -51,6 +59,9 @@ export interface HarnessDiagnostic {
 }
 export declare function collectDiagnostics(adapters: HarnessAdapter[]): Promise<DiagnosticReport>;
 export declare function renderDiagnosticsMarkdown(report: DiagnosticReport): string;
+export declare function collectDiagnosticIssues(report: DiagnosticReport): DiagnosticIssue[];
+export declare function findPluginCliVersionSkews(report: DiagnosticReport): DiagnosticIssue[];
+export declare function formatDiagnosticIssuesSection(report: DiagnosticReport): string[];
 /** Utility: read the tail of a log file, best-effort. */
 export declare function tailLogFile(path: string, lines: number): string;
 //# sourceMappingURL=diagnostics.d.ts.map

package/dist/lib/diagnostics.d.ts.map

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package/dist/lib/onnx.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"onnx.d.ts","sourceRoot":"","sources":["../../src/lib/onnx.ts"],"names":[],"mappings":"AAGA,eAAO,MAAM,oBAAoB,WAAW,CAAC;AAE7C,wBAAgB,kBAAkB,IAAI,MAAM,CAI3C;AAED,wBAAgB,oBAAoB,IAAI,MAAM,CAkB7C;AAED,wBAAgB,qBAAqB,IAAI,MAAM,GAAG,IAAI,CAarD;AAED,wBAAgB,qBAAqB,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAGvE;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAmC9D;AAED,+DAA+D;AAC/D,eAAO,MAAM,kBAAkB,IAAI,CAAC;AACpC,eAAO,MAAM,sBAAsB,KAAK,CAAC;AAEzC,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAM/D;AAED,uEAAuE;AACvE,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG;IAC9C,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,EAAE,OAAO,CAAC;IACf,MAAM,EAAE,OAAO,CAAC;CACjB,CAQA"}
+{"version":3,"file":"onnx.d.ts","sourceRoot":"","sources":["../../src/lib/onnx.ts"],"names":[],"mappings":"AAGA,eAAO,MAAM,oBAAoB,WAAW,CAAC;AAE7C,wBAAgB,kBAAkB,IAAI,MAAM,CAI3C;AAED,wBAAgB,oBAAoB,IAAI,MAAM,CAkB7C;AA8BD,wBAAgB,qBAAqB,IAAI,MAAM,GAAG,IAAI,CAoBrD;AAED,wBAAgB,qBAAqB,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAGvE;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAmC9D;AAED,+DAA+D;AAC/D,eAAO,MAAM,kBAAkB,IAAI,CAAC;AACpC,eAAO,MAAM,sBAAsB,KAAK,CAAC;AAEzC,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAM/D;AAED,uEAAuE;AACvE,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG;IAC9C,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,EAAE,OAAO,CAAC;IACf,MAAM,EAAE,OAAO,CAAC;CACjB,CAQA"}

package/dist/lib/paths.d.ts

@@ -15,6 +15,7 @@ export declare function getAftLspPackagesDir(): string;
  * servers (clangd, lua-ls, zls, tinymist, texlab).
  */
 export declare function getAftLspBinariesDir(): string;
+export declare function getCortexKitStorageRoot(): string;
 /** Resolve the plugin log file path. Shared with the plugin's logger. */
 export declare function getTmpLogPath(filename: string): string;
 //# sourceMappingURL=paths.d.ts.map

package/dist/lib/paths.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"paths.d.ts","sourceRoot":"","sources":["../../src/lib/paths.ts"],"names":[],"mappings":"AAGA,yFAAyF;AACzF,wBAAgB,oBAAoB,IAAI,MAAM,CAW7C;AAED,wBAAgB,gBAAgB,IAAI,MAAM,CAEzC;AAED;;;;;GAKG;AACH,wBAAgB,oBAAoB,IAAI,MAAM,CAW7C;AAED;;;;;GAKG;AACH,wBAAgB,oBAAoB,IAAI,MAAM,CAW7C;AAED,yEAAyE;AACzE,wBAAgB,aAAa,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAEtD"}
+{"version":3,"file":"paths.d.ts","sourceRoot":"","sources":["../../src/lib/paths.ts"],"names":[],"mappings":"AAGA,yFAAyF;AACzF,wBAAgB,oBAAoB,IAAI,MAAM,CAW7C;AAED,wBAAgB,gBAAgB,IAAI,MAAM,CAEzC;AAED;;;;;GAKG;AACH,wBAAgB,oBAAoB,IAAI,MAAM,CAW7C;AAED;;;;;GAKG;AACH,wBAAgB,oBAAoB,IAAI,MAAM,CAW7C;AAeD,wBAAgB,uBAAuB,IAAI,MAAM,CAEhD;AAED,yEAAyE;AACzE,wBAAgB,aAAa,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAEtD"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cortexkit/aft",
-  "version": "0.30.3",
+  "version": "0.31.1",
   "type": "module",
   "description": "Unified CLI for Agent File Tools (AFT) — setup, doctor, and diagnostics across supported agent harnesses (OpenCode, Pi)",
   "license": "MIT",
@@ -23,7 +23,7 @@
   },
   "dependencies": {
     "@clack/prompts": "^1.2.0",
-    "@cortexkit/aft-bridge": "0.30.3",
+    "@cortexkit/aft-bridge": "0.31.1",
     "comment-json": "^4.6.2"
   },
   "devDependencies": {