@detergent-software/atk 9.0.0-dev.1 → 9.0.0-dev.3

package/CHANGELOG.md

@@ -1,3 +1,21 @@
+## [9.0.0-dev.3](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/branchCompare?baseVersion=GTv9.0.0-dev.2&targetVersion=GTv9.0.0-dev.3) (2026-10-21)
+
+### Features
+
+* **cli:** atk doctor runs real checks and offers --fix (ATK-617) ([1d026a9](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/commit/1d026a982365f4457d13617ae88f114dd327a06d))
+
+### Bug Fixes
+
+* **cli:** confirm doctor's sign-in repair and skip undeclared hooks (ATK-617) ([c665d71](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/commit/c665d717ea2052c6fd2d6c4795355a9e6807b14c))
+* **cli:** keep doctor --fix from signing out a working session (ATK-617) ([9f0513b](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/commit/9f0513b4037141681634c4a5b28fee5803203e21))
+
+## [9.0.0-dev.2](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/branchCompare?baseVersion=GTv9.0.0-dev.1&targetVersion=GTv9.0.0-dev.2) (2026-10-20)
+
+### Bug Fixes
+
+* **cli:** name the resolved asset in the --update README hint (ATK-678) ([2995d86](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/commit/2995d868246cd978073bd48f6cb7d5f1f34bd68d))
+* **cli:** point publish --update at atk checkout for a placeholder README (ATK-678) ([69f71fd](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/commit/69f71fd79d683ee19ffdad22b48e1bb6bcdd5889))
+
 ## [9.0.0-dev.1](https://emergentcode.visualstudio.com/Emergent%20Software/_git/Emergent.AgenticToolkit/branchCompare?baseVersion=GTv8.10.0-dev.3&targetVersion=GTv9.0.0-dev.1) (2026-10-20)
 
 ### ⚠ BREAKING CHANGES

package/build/command-manifest.json

@@ -272,6 +272,11 @@
         "description": "Check environment health and diagnose issues",
         "file": "doctor.js",
         "options": [
+            {
+                "flags": "--fix",
+                "description": "Repair what it can (a corrupt cache, missing files, an expired sign-in), asking first",
+                "defaultValue": false
+            },
             {
                 "flags": "-j, --json",
                 "description": "Output raw JSON (for scripting and CI)",
@@ -285,6 +290,11 @@
                 "flags": "--user",
                 "description": "Use the user scope (the user root, ~ by default) instead of the project",
                 "defaultValue": false
+            },
+            {
+                "flags": "-y, --yes",
+                "description": "With --fix, repair without asking",
+                "defaultValue": false
             }
         ]
     },

package/build/commands/doctor.d.ts

@@ -1,13 +1,15 @@
 import { z } from 'zod';
 export declare const description = "Check environment health and diagnose issues";
 export declare const options: z.ZodObject<{
+    fix: z.ZodDefault<z.ZodBoolean>;
     json: z.ZodDefault<z.ZodBoolean>;
     projectRoot: z.ZodOptional<z.ZodString>;
     user: z.ZodOptional<z.ZodBoolean>;
+    yes: z.ZodDefault<z.ZodBoolean>;
 }, z.core.$strip>;
 type Props = {
     options: z.infer<typeof options>;
 };
-export default function Doctor({ options: { json, projectRoot, user } }: Props): import("react/jsx-runtime").JSX.Element;
+export default function Doctor({ options: { fix, json, projectRoot, user, yes } }: Props): import("react/jsx-runtime").JSX.Element;
 export {};
 //# sourceMappingURL=doctor.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.tsx"],"names":[],"mappings":"AACA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AASxB,eAAO,MAAM,WAAW,iDAAiD,CAAC;AAE1E,eAAO,MAAM,OAAO;;;;iBA2BlB,CAAC;AAiBH,KAAK,KAAK,GAAG;IACX,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,OAAO,CAAC,CAAC;CAClC,CAAC;AAEF,MAAM,CAAC,OAAO,UAAU,MAAM,CAAC,EAAE,OAAO,EAAE,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,EAAE,EAAE,KAAK,2CA+C7E"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.tsx"],"names":[],"mappings":"AAEA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAexB,eAAO,MAAM,WAAW,iDAAiD,CAAC;AAE1E,eAAO,MAAM,OAAO;;;;;;iBA4ClB,CAAC;AA+BH,KAAK,KAAK,GAAG;IACX,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,OAAO,CAAC,CAAC;CAClC,CAAC;AAEF,MAAM,CAAC,OAAO,UAAU,MAAM,CAAC,EAAE,OAAO,EAAE,EAAE,GAAG,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE,EAAE,KAAK,2CAmJvF"}

package/build/commands/doctor.js

@@ -1,14 +1,25 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { Box, Text } from 'ink';
+import { Box, Text, useApp } from 'ink';
+import { useEffect, useMemo, useRef, useState } from 'react';
 import { z } from 'zod';
 import { DiagnosticList, ErrorView, Link, Spinner } from '../components/index.js';
 import { useCommand } from '../hooks/useCommand.js';
+import { useConfirmation } from '../hooks/useConfirmation.js';
+import { CONFIRMATION_REQUIRED_CODE } from '../lib/confirmation-required.js';
 import { runDiagnostics } from '../lib/diagnostics.js';
+import { applyFix, planFixes } from '../lib/doctor-fix.js';
+import { errorMessage } from '../lib/errors.js';
 import { renderJson, useNonInteractive } from '../lib/output.js';
 import { option } from '../lib/pastel/index.js';
 import { buildGettingStartedWebUrl } from '../lib/web-app.js';
 export const description = 'Check environment health and diagnose issues';
 export const options = z.object({
+    fix: z
+        .boolean()
+        .default(false)
+        .describe(option({
+        description: 'Repair what it can (a corrupt cache, missing files, an expired sign-in), asking first',
+    })),
     json: z
         .boolean()
         .default(false)
@@ -29,12 +40,66 @@ export const options = z.object({
         .describe(option({
         description: 'Use the user scope (the user root, ~ by default) instead of the project',
     })),
+    yes: z
+        .boolean()
+        .default(false)
+        .describe(option({
+        alias: 'y',
+        description: 'With --fix, repair without asking',
+    })),
 });
-export default function Doctor({ options: { json, projectRoot, user } }) {
+/** The registry writes' message names `--dry-run`, which doctor doesn't have: the plan is in `fixes`. */
+const FIX_CONFIRMATION_MESSAGE = "Confirmation required: this run can't prompt (--json, or no TTY on stdin). Use --yes (-y) to apply the repairs in fixes.";
+export default function Doctor({ options: { fix, json, projectRoot, user, yes } }) {
+    const { exit } = useApp();
     const { json: effectiveJson } = useNonInteractive(json);
     const state = useCommand(async (progress) => {
         return runDiagnostics(progress, { projectRoot, user });
     }, [projectRoot, user], 'Running diagnostics...');
+    const fixes = useMemo(() => (fix && state.status === 'done' ? planFixes(state.data) : []), [fix, state]);
+    // Without --yes, a run that can't prompt (--json, or no TTY) repairs nothing.
+    const needsConfirmation = fixes.length > 0 && !yes;
+    const confirmation = useConfirmation(needsConfirmation && !effectiveJson);
+    const go = fixes.length > 0 && (yes || confirmation.isConfirmed);
+    const [fixState, setFixState] = useState({ phase: 'idle' });
+    const started = useRef(false);
+    useEffect(() => {
+        if (!go || started.current)
+            return;
+        started.current = true;
+        const progress = (message) => setFixState({ message, phase: 'fixing' });
+        void (async () => {
+            try {
+                const results = [];
+                for (const planned of fixes) {
+                    results.push(await applyFix(planned, {
+                        interactive: !effectiveJson,
+                        onDeviceCode: (prompt) => setFixState({ message: 'Waiting for you to sign in', phase: 'fixing', prompt }),
+                        progress,
+                        projectRoot,
+                        user,
+                    }));
+                }
+                const checks = await runDiagnostics(progress, { projectRoot, user });
+                setFixState({ checks, phase: 'done', results });
+            }
+            catch (err) {
+                setFixState({ error: errorMessage(err), phase: 'error' });
+            }
+        })();
+    }, [go, fixes, effectiveJson, projectRoot, user]);
+    useEffect(() => {
+        if (confirmation.isCancelled)
+            setFixState({ phase: 'cancelled' });
+    }, [confirmation.isCancelled]);
+    // The prompt holds stdin, so leave once --fix has nothing more to do.
+    const finished = fixState.phase === 'done' || fixState.phase === 'cancelled' || fixState.phase === 'error';
+    useEffect(() => {
+        if (!finished)
+            return;
+        const timer = setTimeout(() => exit(), 100);
+        return () => clearTimeout(timer);
+    }, [finished, exit]);
     if (state.status === 'loading') {
         return _jsx(Spinner, { message: state.message });
     }
@@ -50,21 +115,54 @@ export default function Doctor({ options: { json, projectRoot, user } }) {
         }
         return (_jsxs(Box, { flexDirection: 'column', children: [_jsx(ErrorView, { command: state.command, hint: state.hint, message: state.message }), _jsx(TroubleshootingVideo, {})] }));
     }
+    if (fixState.phase === 'error') {
+        process.exitCode = 1;
+        return effectiveJson ? (renderJson({ message: fixState.error, outcome: 'error' })) : (_jsx(ErrorView, { message: fixState.error }));
+    }
+    if (fixState.phase === 'fixing') {
+        return _jsx(Fixing, { message: fixState.message, prompt: fixState.prompt });
+    }
+    if (fixState.phase === 'done') {
+        const output = buildJsonOutput(fixState.checks);
+        // Set both ways: the first diagnosis's fail, behind the y/n prompt, already set it to 1.
+        process.exitCode = output.summary.fail > 0 || fixState.results.some((r) => r.status === 'failed') ? 1 : 0;
+        if (effectiveJson) {
+            return renderJson({ ...output, fixes: fixState.results });
+        }
+        return (_jsxs(Box, { flexDirection: 'column', children: [_jsx(FixResults, { results: fixState.results }), _jsx(DiagnosticList, { checks: fixState.checks, title: 'Environment diagnostics after --fix' }), _jsx(TroubleshootingVideo, {})] }));
+    }
     const output = buildJsonOutput(state.data);
+    if (go) {
+        // The repairs start on the next effect.
+        return _jsx(Fixing, { message: 'Starting repairs...' });
+    }
+    if (needsConfirmation && effectiveJson) {
+        process.exitCode = 1;
+        return renderJson({
+            code: CONFIRMATION_REQUIRED_CODE,
+            command: confirmCommand(projectRoot, user),
+            ...output,
+            fixes,
+            message: FIX_CONFIRMATION_MESSAGE,
+            outcome: 'error',
+        });
+    }
     if (output.summary.fail > 0) {
         process.exitCode = 1;
     }
     if (effectiveJson) {
-        return renderJson(output);
+        return renderJson(fix ? { ...output, fixes: [] } : output);
     }
-    return (_jsxs(Box, { flexDirection: 'column', children: [_jsx(DiagnosticList, { checks: state.data, title: 'Environment diagnostics' }), _jsx(TroubleshootingVideo, {})] }));
+    return (_jsxs(Box, { flexDirection: 'column', children: [_jsx(DiagnosticList, { checks: state.data, title: 'Environment diagnostics' }), fix && fixes.length === 0 && (_jsx(Box, { marginTop: 1, children: _jsx(Text, { dimColor: true, children: "Nothing for --fix to repair." }) })), needsConfirmation && _jsx(FixPrompt, { cancelled: fixState.phase === 'cancelled', fixes: fixes }), _jsx(TroubleshootingVideo, {})] }));
 }
 function buildJsonOutput(checks) {
     const summary = { fail: 0, pass: 0, warn: 0 };
     const diagnostics = checks.map((check) => {
         summary[check.status] += 1;
         return {
+            ...(check.command !== undefined ? { command: check.command } : {}),
             ...(check.detail !== undefined ? { detail: check.detail } : {}),
+            id: check.id,
             message: check.message,
             name: check.name,
             status: check.status,
@@ -76,6 +174,25 @@ function buildJsonOutput(checks) {
         summary,
     };
 }
+/** `atk doctor --fix --yes` in the scope this run checked. */
+function confirmCommand(projectRoot, user) {
+    const scope = user ? ' --user' : projectRoot ? ` -P ${JSON.stringify(projectRoot)}` : '';
+    return `atk doctor --fix --yes${scope}`;
+}
+function Fixing({ message, prompt }) {
+    if (!prompt) {
+        return _jsx(Spinner, { message: message });
+    }
+    return (_jsxs(Box, { flexDirection: 'column', gap: 1, children: [_jsxs(Text, { children: ["To sign in, open ", _jsx(Link, { url: prompt.verificationUri, children: prompt.verificationUri }), " and enter the code", ' ', _jsx(Text, { bold: true, color: 'cyan', children: prompt.userCode })] }), _jsx(Spinner, { message: message })] }));
+}
+/** The planned repairs and the y/n question, or that the run was cancelled. */
+function FixPrompt({ cancelled, fixes }) {
+    return (_jsxs(Box, { flexDirection: 'column', marginTop: 1, children: [_jsx(Text, { bold: true, children: "--fix would:" }), fixes.map((f) => (_jsxs(Text, { children: ['  ', "\u2022 ", f.description, " (", _jsx(Text, { dimColor: true, children: f.command }), ")"] }, f.kind))), cancelled ? _jsx(Text, { color: 'yellow', children: "Cancelled; nothing changed." }) : _jsx(Text, { children: "Apply these repairs? (y/n)" })] }));
+}
+function FixResults({ results }) {
+    const color = { applied: 'green', failed: 'red', skipped: 'yellow' };
+    return (_jsxs(Box, { flexDirection: 'column', marginBottom: 1, children: [_jsx(Text, { bold: true, children: "Repairs" }), results.map((r) => (_jsxs(Text, { children: ['  ', _jsx(Text, { color: color[r.status], children: r.status }), " ", r.description, ": ", r.message] }, r.kind)))] }));
+}
 /** Human output only: the getting-started chapter on atk doctor and what to do next. */
 function TroubleshootingVideo() {
     const video = buildGettingStartedWebUrl('troubleshoot');

package/build/commands/doctor.js.map

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package/build/components/DiagnosticList.d.ts

@@ -1,5 +1,9 @@
 export interface DiagnosticCheck {
+    /** The command that fixes the check, for `--json`; the human `detail` says it in words. */
+    command?: string;
     detail?: string;
+    /** A stable, machine-readable name for the check (`api`, `cache`, `user-lockfile`). */
+    id: string;
     message: string;
     name: string;
     status: 'fail' | 'pass' | 'warn';

package/build/components/DiagnosticList.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"DiagnosticList.d.ts","sourceRoot":"","sources":["../../src/components/DiagnosticList.tsx"],"names":[],"mappings":"AAIA,MAAM,WAAW,eAAe;IAC9B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,MAAM,CAAC;CAClC;AAED,UAAU,mBAAmB;IAC3B,4CAA4C;IAC5C,MAAM,EAAE,eAAe,EAAE,CAAC;IAC1B,uCAAuC;IACvC,KAAK,EAAE,MAAM,CAAC;CACf;AAED;;;GAGG;AACH,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE,mBAAmB,2CAuB5E"}
+{"version":3,"file":"DiagnosticList.d.ts","sourceRoot":"","sources":["../../src/components/DiagnosticList.tsx"],"names":[],"mappings":"AAIA,MAAM,WAAW,eAAe;IAC9B,2FAA2F;IAC3F,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,uFAAuF;IACvF,EAAE,EAAE,MAAM,CAAC;IACX,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,MAAM,CAAC;CAClC;AAED,UAAU,mBAAmB;IAC3B,4CAA4C;IAC5C,MAAM,EAAE,eAAe,EAAE,CAAC;IAC1B,uCAAuC;IACvC,KAAK,EAAE,MAAM,CAAC;CACf;AAED;;;GAGG;AACH,MAAM,CAAC,OAAO,UAAU,cAAc,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE,mBAAmB,2CAuB5E"}

package/build/components/DiagnosticList.js

@@ -9,7 +9,7 @@ export default function DiagnosticList({ checks, title }) {
     const passCount = checks.filter((c) => c.status === 'pass').length;
     const warnCount = checks.filter((c) => c.status === 'warn').length;
     const failCount = checks.filter((c) => c.status === 'fail').length;
-    return (_jsxs(Box, { flexDirection: 'column', children: [_jsx(Text, { bold: true, children: title }), _jsx(Text, { children: " " }), checks.map((check) => (_jsxs(Box, { flexDirection: 'column', children: [_jsxs(Text, { children: [_jsx(CheckIcon, { status: check.status }), " ", _jsx(Text, { bold: true, children: check.name }), ' — ', check.message] }), check.detail && _jsxs(Text, { dimColor: true, children: [" ", check.detail] })] }, check.name))), _jsx(Text, { children: " " }), _jsx(DiagnosticSummary, { failCount: failCount, passCount: passCount, warnCount: warnCount })] }));
+    return (_jsxs(Box, { flexDirection: 'column', children: [_jsx(Text, { bold: true, children: title }), _jsx(Text, { children: " " }), checks.map((check) => (_jsxs(Box, { flexDirection: 'column', children: [_jsxs(Text, { children: [_jsx(CheckIcon, { status: check.status }), " ", _jsx(Text, { bold: true, children: check.name }), ' — ', check.message] }), check.detail && _jsxs(Text, { dimColor: true, children: [" ", check.detail] })] }, check.id))), _jsx(Text, { children: " " }), _jsx(DiagnosticSummary, { failCount: failCount, passCount: passCount, warnCount: warnCount })] }));
 }
 function DiagnosticSummary({ failCount, passCount, warnCount, }) {
     return (_jsxs(Box, { flexDirection: 'column', children: [_jsxs(Text, { children: [_jsxs(Text, { color: 'green', children: [passCount, " passed"] }), warnCount > 0 && (_jsxs(Text, { children: [",", ' ', _jsxs(Text, { color: 'yellow', children: [warnCount, " ", warnCount === 1 ? 'warning' : 'warnings'] })] })), failCount > 0 && (_jsxs(Text, { children: [", ", _jsxs(Text, { color: 'red', children: [failCount, " failed"] })] }))] }), failCount > 0 && _jsx(Text, { dimColor: true, children: "Fix the failed checks above to ensure atk works correctly." })] }));

package/build/components/DiagnosticList.js.map

@@ -1 +1 @@
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package/build/lib/diagnostics.d.ts

@@ -3,6 +3,15 @@ import type { ProjectConfig } from './schemas/config.js';
 import type { Registry } from './schemas/index.js';
 import type { InstalledAsset } from './schemas/lockfile.js';
 import { type Scope } from './scope.js';
+import { type VersionStatus } from './update-check.js';
+/** How long the `/health` probe waits for the ATK API before it fails the check. */
+export declare const HEALTH_TIMEOUT_MS = 5000;
+/**
+ * Call the ATK API's anonymous `GET /health` once, with no bearer and no retries, so a down API
+ * fails the check in {@link HEALTH_TIMEOUT_MS} at most. It doesn't go through the process-wide
+ * client, whose connection-failure latch would then fail the registry check too.
+ */
+export declare function checkApiHealth(apiUrl: string, source?: string): Promise<DiagnosticCheck>;
 /**
  * Check for assets installed both in the project and at the user scope, with the version at each and
  * which copy each tool that has both uses. A copy uninstalled for every tool of its scope doesn't
@@ -16,6 +25,17 @@ export declare function checkBothScopes(project: {
     root: string;
     tools: string[];
 }): Promise<DiagnosticCheck | undefined>;
+/**
+ * Compare this CLI with its release channel on npm: `dev` for a prerelease, `latest` otherwise.
+ * A CLI ahead of npm (a local build) passes. `offline` (`--offline`): npm isn't asked, so only
+ * a cached version is compared.
+ */
+export declare function checkCliVersion(status: VersionStatus, offline?: boolean): DiagnosticCheck;
+/**
+ * Check for installed assets the registry deprecates, with each one's reason and replacement.
+ * Returns undefined when there are none.
+ */
+export declare function checkDeprecated(registry: Registry, assets: InstalledAsset[]): DiagnosticCheck | undefined;
 /**
  * Check that the hook scripts a configured tool runs directly are executable. Returns
  * undefined when there is nothing to check: on Windows, which has no exec bit, or when
@@ -29,6 +49,14 @@ export declare function checkHookScripts(projectDir: string, tools: string[], as
  * undefined when there are none. The sync command it suggests runs in `scope`.
  */
 export declare function checkLiftedHooks(projectConfig: ProjectConfig, assets: InstalledAsset[], registry: Registry, scope?: Scope): DiagnosticCheck | undefined;
+/**
+ * Check that each installed asset's placed files are on disk for every configured tool, as the
+ * scope's adapter places them. Frozen assets, those uninstalled for a tool and hooks whose locked
+ * version doesn't declare the tool (with `registry`) are left out, as `atk audit` and `atk sync`
+ * leave them. Only presence is checked; `atk audit` verifies content. Returns undefined when there
+ * is nothing to check. The sync command it suggests runs in `scope`.
+ */
+export declare function checkMissingFiles(root: string, tools: string[], assets: InstalledAsset[], projectConfig: null | ProjectConfig, scope?: Scope, registry?: Registry): Promise<DiagnosticCheck | undefined>;
 /**
  * Check whether the given Node.js version string meets the project requirements.
  *
@@ -36,6 +64,12 @@ export declare function checkLiftedHooks(projectConfig: ProjectConfig, assets: I
  * @returns a `DiagnosticCheck` with status pass / warn / fail
  */
 export declare function checkNodeVersion(version: string): DiagnosticCheck;
+/**
+ * Check the registry cache file: its age against the TTL, and whether it parses. An expired cache
+ * passes (the next read refreshes it); one that doesn't parse fails, with `atk cache clear` to
+ * remove it. Run after the registry check, which replaces an unreadable cache when it can fetch.
+ */
+export declare function checkRegistryCache(): Promise<DiagnosticCheck>;
 /**
  * Run all environment diagnostic checks and return the results.
  * Extracted from the `doctor` command so it can be tested independently.

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

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