@cortexkit/aft 0.25.1 → 0.26.0

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;AAqIpB,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;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"}

package/dist/commands/doctor.d.ts

@@ -1,4 +1,5 @@
 import type { HarnessAdapter } from "../adapters/types.js";
+import { type DiagnosticReport } from "../lib/diagnostics.js";
 import { type ClearResult } from "../lib/lsp-cache.js";
 export type DoctorClearTarget = "plugin-cache" | "lsp-cache" | "binary-cache";
 export declare const DOCTOR_CLEAR_TARGET_OPTIONS: {
@@ -36,6 +37,7 @@ export interface CacheClearOptions {
     includePluginBytes?: boolean;
 }
 export declare function runDoctor(options: DoctorOptions): Promise<number>;
+export declare function hasDoctorProblems(report: DiagnosticReport): boolean;
 export declare function clearDoctorCaches(adapters: HarnessAdapter[], targets: readonly DoctorClearTarget[], options?: CacheClearOptions): Promise<CacheClearSummary>;
 /**
  * Clear cached `aft` binaries except the version this CLI ships with.
@@ -58,4 +60,5 @@ export interface BinaryCacheClearResult {
     keptVersion: string | null;
 }
 export declare function clearOldBinaries(): BinaryCacheClearResult;
+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;AAM3D,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,CAoGvE;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"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAE3D,OAAO,EAEL,KAAK,gBAAgB,EAGtB,MAAM,uBAAuB,CAAC;AAI/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,CAsGvE;AAED,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,gBAAgB,GAAG,OAAO,CAWnE;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;AAyFD,wBAAsB,gBAAgB,CAAC,QAAQ,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC,CAIhF"}

package/dist/index.js

@@ -8208,10 +8208,8 @@ function readPiExtensionIndex() {
     if (!existsSync4(path))
       continue;
     try {
-      const raw = readFileSync3(path, "utf-8");
-      const trimmed = raw.replace(/^\uFEFF/, "");
-      const value = JSON.parse(trimmed);
-      const extensions = value.extensions ?? value.plugins ?? [];
+      const { value } = readJsoncFile(path);
+      const extensions = value?.extensions ?? value?.plugins ?? [];
       if (Array.isArray(extensions)) {
         const installed = extensions.map((e) => typeof e === "string" ? e : typeof e?.name === "string" ? e.name : "").filter((name) => name.length > 0);
         return { installed, path };
@@ -10047,7 +10045,7 @@ var MAX_NOISE_LINES_IN_ERROR = 5;
 var init_aft_bridge = () => {};
 
 // src/lib/binary-probe.ts
-import { execSync as execSync3 } from "node:child_process";
+import { execSync as execSync3, spawnSync as spawnSync2 } from "node:child_process";
 import { existsSync as existsSync5 } from "node:fs";
 import { createRequire as createRequire2 } from "node:module";
 import { homedir as homedir4 } from "node:os";
@@ -10059,29 +10057,37 @@ function normalizeVersion(output) {
   return trimmed.replace(/^aft\s+/, "");
 }
 function probeBinaryVersion(preferredVersion) {
-  const candidates = [];
-  if (preferredVersion) {
-    const tag = preferredVersion.startsWith("v") ? preferredVersion : `v${preferredVersion}`;
-    candidates.push(join5(getAftBinaryCacheDir(), tag, getAftBinaryName()));
-  }
+  const candidate = findAftBinary(preferredVersion);
+  if (!candidate)
+    return null;
   try {
-    const lookup = process.platform === "win32" ? "where aft" : "which aft";
-    const resolved = execSync3(lookup, { stdio: "pipe", encoding: "utf-8" }).trim();
-    if (resolved) {
-      candidates.push(resolved.split(/\r?\n/)[0]);
-    }
-  } catch {}
+    if (!existsSync5(candidate))
+      return null;
+    const result = spawnSync2(candidate, ["--version"], {
+      stdio: ["ignore", "pipe", "pipe"],
+      encoding: "utf-8"
+    });
+    if (result.error || result.status !== 0)
+      return null;
+    const output = `${result.stdout ?? ""}
+${result.stderr ?? ""}`;
+    return normalizeVersion(output);
+  } catch {
+    return null;
+  }
+}
+function pushCandidate(candidates, candidate) {
+  if (!candidate)
+    return;
+  if (!candidates.includes(candidate))
+    candidates.push(candidate);
+}
+function firstExisting(candidates) {
   for (const candidate of candidates) {
     try {
       if (!existsSync5(candidate))
         continue;
-      const output = execSync3(`"${candidate}" --version`, {
-        stdio: "pipe",
-        encoding: "utf-8"
-      });
-      const version = normalizeVersion(output);
-      if (version)
-        return version;
+      return candidate;
     } catch {}
   }
   return null;
@@ -10098,28 +10104,24 @@ function findAftBinary(preferredVersion) {
   const candidates = [];
   if (preferredVersion) {
     const tag = preferredVersion.startsWith("v") ? preferredVersion : `v${preferredVersion}`;
-    candidates.push(join5(getAftBinaryCacheDir(), tag, getAftBinaryName()));
+    pushCandidate(candidates, join5(getAftBinaryCacheDir(), tag, getAftBinaryName()));
   }
   const key = platformKey();
   if (key) {
     try {
       const require2 = createRequire2(import.meta.url);
-      candidates.push(require2.resolve(`@cortexkit/aft-${key}/bin/${getAftBinaryName()}`));
+      pushCandidate(candidates, require2.resolve(`@cortexkit/aft-${key}/bin/${getAftBinaryName()}`));
     } catch {}
   }
   try {
     const lookup = process.platform === "win32" ? "where aft" : "which aft";
     const resolved = execSync3(lookup, { stdio: "pipe", encoding: "utf-8" }).trim();
     if (resolved) {
-      candidates.push(resolved.split(/\r?\n/)[0]);
+      pushCandidate(candidates, resolved.split(/\r?\n/)[0]);
     }
   } catch {}
-  candidates.push(join5(homedir4(), ".cargo", "bin", getAftBinaryName()));
-  for (const candidate of candidates) {
-    if (existsSync5(candidate))
-      return candidate;
-  }
-  return null;
+  pushCandidate(candidates, join5(homedir4(), ".cargo", "bin", getAftBinaryName()));
+  return firstExisting(candidates);
 }
 var init_binary_probe = __esm(() => {
   init_paths();
@@ -10874,7 +10876,7 @@ function sanitizeValue(value) {
 var init_sanitize = () => {};
 
 // src/lib/diagnostics.ts
-import { existsSync as existsSync11, readFileSync as readFileSync4, statSync as statSync7 } from "node:fs";
+import { closeSync, existsSync as existsSync11, openSync, readSync, statSync as statSync7 } from "node:fs";
 async function collectDiagnostics(adapters) {
   const cliVersion = getSelfVersion();
   const binaryVersion = probeBinaryVersion(cliVersion);
@@ -10901,7 +10903,7 @@ async function diagnoseHarness(adapter) {
   const storage = adapter.getStorageDir();
   const logPath = adapter.getLogFile();
   const describeStorage = "describeStorageSubtrees" in adapter && typeof adapter.describeStorageSubtrees === "function" ? adapter.describeStorageSubtrees() : {};
-  const semanticEnabled = aftConfigRead.value?.experimental_semantic_search === true;
+  const semanticEnabled = aftConfigRead.value?.semantic_search === true || aftConfigRead.value?.experimental_semantic_search === true;
   const systemOrtDir = findSystemOnnxRuntime();
   const cachedOrtDir = findCachedOnnxRuntime(storage);
   const systemVersion = systemOrtDir ? detectOrtVersion(systemOrtDir) : null;
@@ -11002,12 +11004,38 @@ function renderDiagnosticsMarkdown(report) {
 function tailLogFile(path, lines) {
   if (!existsSync11(path))
     return "";
+  if (lines <= 0)
+    return "";
+  const chunkSize = 64 * 1024;
+  let fd = null;
   try {
-    const raw = readFileSync4(path, "utf-8");
-    return raw.split(/\r?\n/).slice(-lines).join(`
+    const size = statSync7(path).size;
+    fd = openSync(path, "r");
+    const chunks = [];
+    let position = size;
+    let newlineCount = 0;
+    while (position > 0 && newlineCount <= lines) {
+      const readLength = Math.min(chunkSize, position);
+      position -= readLength;
+      const buffer = Buffer.allocUnsafe(readLength);
+      const bytesRead = readSync(fd, buffer, 0, readLength, position);
+      const chunk = bytesRead === readLength ? buffer : buffer.subarray(0, bytesRead);
+      chunks.unshift(chunk);
+      for (let i = chunk.length - 1;i >= 0; i -= 1) {
+        if (chunk[i] === 10)
+          newlineCount += 1;
+      }
+    }
+    return Buffer.concat(chunks).toString("utf-8").trimEnd().split(/\r?\n/).slice(-lines).join(`
 `).trim();
   } catch {
     return "";
+  } finally {
+    if (fd !== null) {
+      try {
+        closeSync(fd);
+      } catch {}
+    }
   }
 }
 var init_diagnostics = __esm(() => {
@@ -11021,7 +11049,7 @@ var init_diagnostics = __esm(() => {
 });
 
 // src/lib/github.ts
-import { execSync as execSync4, spawnSync as spawnSync2 } from "node:child_process";
+import { execSync as execSync4, spawnSync as spawnSync3 } from "node:child_process";
 function isGhInstalled() {
   try {
     execSync4("gh --version", { stdio: "ignore" });
@@ -11030,18 +11058,21 @@ function isGhInstalled() {
     return false;
   }
 }
+function getOpenBrowserCommand(url, platform = process.platform) {
+  return platform === "darwin" ? ["open", [url]] : platform === "win32" ? ["explorer.exe", [url]] : ["xdg-open", [url]];
+}
 function openBrowser(url) {
-  const commands = process.platform === "darwin" ? ["open", [url]] : process.platform === "win32" ? ["cmd", ["/c", "start", "", url]] : ["xdg-open", [url]];
+  const commands = getOpenBrowserCommand(url);
   try {
     const [cmd, args] = commands;
-    spawnSync2(cmd, args, { stdio: "ignore" });
+    spawnSync3(cmd, args, { stdio: "ignore" });
   } catch {}
 }
 function createGitHubIssue(repo, title, body) {
   if (!isGhInstalled()) {
     return { url: null, stderr: "gh CLI not installed" };
   }
-  const result = spawnSync2("gh", ["issue", "create", "--repo", repo, "--title", title, "--body-file", "-"], {
+  const result = spawnSync3("gh", ["issue", "create", "--repo", repo, "--title", title, "--body-file", "-"], {
     input: body,
     encoding: "utf-8",
     stdio: ["pipe", "pipe", "pipe"]
@@ -11144,6 +11175,8 @@ var init_onnx_fix = __esm(() => {
 var exports_doctor = {};
 __export(exports_doctor, {
   runDoctor: () => runDoctor,
+  hasDoctorProblems: () => hasDoctorProblems,
+  fixPluginEntries: () => fixPluginEntries,
   clearOldBinaries: () => clearOldBinaries,
   clearDoctorCaches: () => clearDoctorCaches,
   DOCTOR_FORCE_CLEAR_TARGETS: () => DOCTOR_FORCE_CLEAR_TARGETS,
@@ -11174,22 +11207,21 @@ async function runDoctor(options) {
   if (npmCount + ghCount > 0) {
     O2.info(`LSP cache: ${npmCount} npm + ${ghCount} github install(s), ${formatBytes(report.lspCache.totalSize)} total`);
   }
-  let hadProblems = false;
+  const hadProblems = hasDoctorProblems(report);
   for (const h of report.harnesses) {
     O2.step(`${h.displayName}`);
     if (!h.hostInstalled) {
       O2.warn(`  host not installed — install from: ${describeAdapterInstallHint(h.kind)}`);
-      hadProblems = true;
       continue;
     }
     O2.info(`  host: ${h.hostVersion ?? "unknown version"}`);
     O2.info(`  plugin registered: ${h.pluginRegistered ? "yes" : "no"}`);
-    if (!h.pluginRegistered)
-      hadProblems = true;
+    if (!h.pluginRegistered) {
+      O2.warn("  plugin registration can be fixed with `aft setup` or `aft doctor --fix`");
+    }
     O2.info(`  aft config: ${h.aftConfig.exists ? h.configPaths.aftConfig : "(not set)"}`);
     if (h.aftConfig.parseError) {
       O2.error(`  aft config parse error: ${h.aftConfig.parseError}`);
-      hadProblems = true;
     }
     O2.info(`  storage: ${h.storageDir.exists ? h.storageDir.path : "(not created)"} (${formatStorageSizes(h.storageDir.sizesByKey)})`);
     if (h.onnxRuntime.required) {
@@ -11203,26 +11235,46 @@ async function runDoctor(options) {
       }
       if (!h.onnxRuntime.cachedPath && !h.onnxRuntime.systemPath) {
         parts.push(`not installed — ${h.onnxRuntime.installHint}`);
-        hadProblems = true;
+      }
+      if (h.onnxRuntime.cachedCompatible === false || h.onnxRuntime.systemCompatible === false) {
+        parts.push("needs reinstall — run `aft doctor --fix`");
       }
       O2.info(`  onnx runtime: ${parts.join(" · ")}`);
+    } else {
+      O2.info("  onnx runtime: not required (semantic search disabled; ignoring ONNX status)");
     }
     O2.info(`  log: ${h.logFile.exists ? `${h.logFile.path} (${h.logFile.sizeKb} KB)` : "(not written yet)"}`);
   }
   if (options.force) {
     await clearDoctorCaches(adapters, DOCTOR_FORCE_CLEAR_TARGETS, { includePluginBytes: false });
   }
-  for (const adapter of adapters) {
-    await maybeFixPlugin(adapter);
-  }
   if (hadProblems) {
-    wt("Run `aft setup` to register AFT with any harness showing `plugin registered: no`.", "Tips");
+    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.", "Tips");
     gt("Done — some issues found.");
     return 1;
   }
   gt("Everything looks good.");
   return 0;
 }
+function hasDoctorProblems(report) {
+  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;
+  });
+}
 async function runClearFlow(argv) {
   const targets = await selectMany("What do you want to clear?", DOCTOR_CLEAR_TARGET_OPTIONS, undefined, false);
   if (targets.length === 0) {
@@ -11331,16 +11383,21 @@ async function runFixFlow(argv) {
   });
   O2.info("Running diagnostics to identify auto-fixable issues…");
   const report = await collectDiagnostics(adapters);
+  await fixPluginEntries(adapters);
   const onnxResult = await runOnnxFix(adapters, report);
   if (onnxResult === null) {
     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");
-    gt("Done.");
-    return 0;
+    const afterReport2 = await collectDiagnostics(adapters);
+    const stillHasProblems2 = hasDoctorProblems(afterReport2);
+    gt(stillHasProblems2 ? "Done — some issues remain." : "Done.");
+    return stillHasProblems2 ? 1 : 0;
   }
   const hadErrors = onnxResult.errors.length > 0;
-  gt(hadErrors ? "Done — some fixes failed." : "Done.");
-  return hadErrors ? 1 : 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;
 }
 async function clearPluginCache(adapter, includeBytes) {
   const info = adapter.getPluginCacheInfo();
@@ -11375,6 +11432,11 @@ function reportLspCacheClear(cleanup) {
     O2.error(`LSP install cache: failed to remove ${err.path}: ${err.error}`);
   }
 }
+async function fixPluginEntries(adapters) {
+  for (const adapter of adapters) {
+    await maybeFixPlugin(adapter);
+  }
+}
 async function maybeFixPlugin(adapter) {
   if (!adapter.hasPluginEntry() && adapter.isInstalled()) {
     O2.info(`${adapter.displayName}: attempting to register plugin…`);
@@ -11438,7 +11500,7 @@ ${tail || "<no log output>"}
   ].join(`
 `);
   const body = sanitizeContent(rawBody);
-  const title = `AFT issue: ${description.slice(0, 72)}`;
+  const title = sanitizeContent(`AFT issue: ${description.slice(0, 72)}`);
   const outPath = join11(process.cwd(), `aft-issue-${Date.now()}.md`);
   writeFileSync2(outPath, `${body}
 `);

package/dist/lib/binary-probe.d.ts

@@ -1,7 +1,6 @@
 /**
- * Probe `aft --version` from a prioritized list of candidate paths:
- *   1. Versioned cache for the given plugin version (if any)
- *   2. PATH (via `which`/`where`)
+ * Probe `aft --version` from the same prioritized candidate locations used by
+ * `findAftBinary()` (cache, npm platform package, PATH, cargo fallback).
  *
  * Returns the first successfully reported version, or null if nothing
  * resolves. Errors and missing files are swallowed — callers get a signal,

package/dist/lib/binary-probe.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"binary-probe.d.ts","sourceRoot":"","sources":["../../src/lib/binary-probe.ts"],"names":[],"mappings":"AAaA;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAAC,gBAAgB,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAgB3E;AAmBD,wBAAgB,WAAW,CACzB,QAAQ,GAAE,MAAyB,EACnC,IAAI,GAAE,MAAqB,GAC1B,MAAM,GAAG,IAAI,CAOf;AAED,wBAAgB,aAAa,CAAC,gBAAgB,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CA8BtE"}

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

@@ -1 +1 @@
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+{"version":3,"file":"diagnostics.d.ts","sourceRoot":"","sources":["../../src/lib/diagnostics.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAC3D,OAAO,EAAE,KAAK,eAAe,EAAsB,MAAM,mBAAmB,CAAC;AAG7E,OAAO,EAAqB,KAAK,cAAc,EAAE,MAAM,gBAAgB,CAAC;AAaxE,MAAM,WAAW,gBAAgB;IAC/B,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;IAC7B,SAAS,EAAE,iBAAiB,EAAE,CAAC;IAC/B,WAAW,EAAE,eAAe,CAAC;IAC7B,sEAAsE;IACtE,QAAQ,EAAE,cAAc,CAAC;CAC1B;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,aAAa,EAAE,OAAO,CAAC;IACvB,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,gBAAgB,EAAE,OAAO,CAAC;IAC1B,WAAW,EAAE,UAAU,CAAC,cAAc,CAAC,mBAAmB,CAAC,CAAC,CAAC;IAC7D,SAAS,EAAE;QACT,MAAM,EAAE,OAAO,CAAC;QAChB,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;KAChC,CAAC;IACF,WAAW,EAAE,UAAU,CAAC,cAAc,CAAC,oBAAoB,CAAC,CAAC,CAAC;IAC9D,UAAU,EAAE;QACV,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,EAAE,OAAO,CAAC;QAChB,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;KACpC,CAAC;IACF,WAAW,EAAE;QACX,QAAQ,EAAE,OAAO,CAAC;QAClB,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;QAC1B,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;QAC7B,gBAAgB,EAAE,OAAO,GAAG,IAAI,CAAC;QACjC,UAAU,EAAE,MAAM,GAAG,IAAI,CAAC;QAC1B,aAAa,EAAE,MAAM,GAAG,IAAI,CAAC;QAC7B,gBAAgB,EAAE,OAAO,GAAG,IAAI,CAAC;QACjC,QAAQ,EAAE,MAAM,CAAC;QACjB,WAAW,EAAE,MAAM,CAAC;QACpB,WAAW,EAAE,MAAM,CAAC;KACrB,CAAC;IACF,OAAO,EAAE;QACP,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,EAAE,OAAO,CAAC;QAChB,MAAM,EAAE,MAAM,CAAC;KAChB,CAAC;CACH;AAED,wBAAsB,kBAAkB,CAAC,QAAQ,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC,gBAAgB,CAAC,CAoB9F;AAiED,wBAAgB,yBAAyB,CAAC,MAAM,EAAE,gBAAgB,GAAG,MAAM,CAkE1E;AAED,yDAAyD;AACzD,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,CA0C/D"}

package/dist/lib/github.d.ts

@@ -1,4 +1,5 @@
 export declare function isGhInstalled(): boolean;
+export declare function getOpenBrowserCommand(url: string, platform?: NodeJS.Platform): [string, string[]];
 export declare function openBrowser(url: string): void;
 /**
  * Create a GitHub issue via `gh issue create`. Returns the issue URL on

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

@@ -1 +1 @@
-{"version":3,"file":"github.d.ts","sourceRoot":"","sources":["../../src/lib/github.ts"],"names":[],"mappings":"AAEA,wBAAgB,aAAa,IAAI,OAAO,CAOvC;AAED,wBAAgB,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAc7C;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,iBAAiB,CAC/B,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,MAAM,GACX;IAAE,GAAG,EAAE,MAAM,GAAG,IAAI,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,CAAA;CAAE,CAqBzC"}
+{"version":3,"file":"github.d.ts","sourceRoot":"","sources":["../../src/lib/github.ts"],"names":[],"mappings":"AAEA,wBAAgB,aAAa,IAAI,OAAO,CAOvC;AAED,wBAAgB,qBAAqB,CACnC,GAAG,EAAE,MAAM,EACX,QAAQ,GAAE,MAAM,CAAC,QAA2B,GAC3C,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,CAMpB;AAED,wBAAgB,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,IAAI,CAS7C;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,iBAAiB,CAC/B,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,MAAM,GACX;IAAE,GAAG,EAAE,MAAM,GAAG,IAAI,CAAC;IAAC,MAAM,CAAC,EAAE,MAAM,CAAA;CAAE,CAqBzC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cortexkit/aft",
-  "version": "0.25.1",
+  "version": "0.26.0",
   "type": "module",
   "description": "Unified CLI for Agent File Tools (AFT) — setup, doctor, and diagnostics across supported agent harnesses (OpenCode, Pi)",
   "license": "MIT",