@indy2kro/agentenv 1.1.3 → 1.2.0

package/dist/commands/doctor.d.ts

@@ -4,14 +4,17 @@ import { isAgentInstalled } from '../adapters/detect.js';
 import { loadConfig } from '../config/schema.js';
 import type { AgentKey } from '../config/schema.js';
 import { findConfigPath, userConfigDir } from '../config/scopes.js';
+import type { ScopeValue } from '../config/scopes.js';
 import { checkAgentShellConfiguration, detectShell } from '../shell/detector.js';
-import { getInstalledToolState, getMiseVersion, isMiseInstalled, miseGlobalConfigPath, shimsDir, shimsDirOnPath, toolAvailabilityClassification } from '../toolchain/mise.js';
+import { getInstalledToolState, getMiseVersion, isMiseInstalled, miseGlobalConfigPath, shimsDir, shimsDirOnPath, findShadowedShims, toolAvailabilityClassification } from '../toolchain/mise.js';
 import { checkRtkInstallation } from '../toolchain/rtk.js';
 export type DoctorStatus = 'ok' | 'warn' | 'fail';
 export interface DoctorItem {
     status: DoctorStatus;
     label: string;
     detail: string;
+    /** A command that fixes this item, for scripts and agents; absent when there isn't one. */
+    fix?: string;
 }
 export interface DoctorSection {
     title: string;
@@ -57,6 +60,9 @@ export interface GatherDoctorDeps {
     miseGlobalConfigPath?: typeof miseGlobalConfigPath;
     shimsDir?: typeof shimsDir;
     shimsDirOnPath?: typeof shimsDirOnPath;
+    findShadowedShims?: typeof findShadowedShims;
+    /** Whether `mise which <binary>` resolves, i.e. the install really provides an executable. */
+    miseProvidesExecutable?: (binary: string, cwd: string) => boolean;
     findConfigPath?: typeof findConfigPath;
     userConfigDir?: typeof userConfigDir;
     loadConfig?: typeof loadConfig;
@@ -80,6 +86,8 @@ export declare function agentShellItem(agent: AgentKey, info: {
     isConfigured: boolean;
     shell?: string;
 }, exists: (candidate: string) => boolean): DoctorItem;
+/** The deps that make `doctor --scope <scope>` inspect that scope; none without a scope. */
+export declare function scopedDoctorDeps(scope: ScopeValue | undefined): GatherDoctorDeps;
 export declare function gatherDoctor(sectionFilter?: string, deps?: GatherDoctorDeps): DoctorSection[];
 export declare const doctorCommand: Command;
 //# sourceMappingURL=doctor.d.ts.map

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

@@ -1 +1 @@
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package/dist/commands/doctor.js

@@ -5,10 +5,12 @@ import { AGENT_COMMANDS, isAgentInstalled } from '../adapters/detect.js';
 import { isQuiet, LOGO, resolveResultLine, setQuietEnabled, shouldPrintBanner, } from '../ui/output.js';
 import { theme } from '../ui/theme.js';
 import { BINARY_MAP, getEnabledAgents, loadConfig, TOOL_KEYS, validateConfig, } from '../config/schema.js';
-import { findConfigPath, userConfigDir } from '../config/scopes.js';
+import { findConfigPath, findConfigPathInScope, parseScopeFlag, userConfigDir, } from '../config/scopes.js';
 import { bashExecutable, checkAgentShellConfiguration, detectShell, generateGitBashPathAddition, gitInstallRoot, NATIVE_UNIX_TOOLS, preferredGitBashLauncher, readPersistentWindowsPath, resolveOnWindowsPath, } from '../shell/detector.js';
-import { getInstalledToolState, getMiseVersion, getShimsDirValue, isMiseInstalled, miseGlobalConfigPath, miseInstallInstructions, PINNED_TOOL_VERSIONS, shimsDir, shimsDirOnPath, toolAvailabilityClassification, } from '../toolchain/mise.js';
+import { getInstalledToolState, getMiseVersion, getShimsDirValue, isMiseInstalled, MISE_TOOL_NAMES, miseGlobalConfigPath, miseTomlPathFor, runMiseCaptured, miseInstallInstructions, PINNED_TOOL_VERSIONS, shimsDir, shimsDirOnPath, findShadowedShims, toolAvailabilityClassification, } from '../toolchain/mise.js';
 import { checkRtkInstallation } from '../toolchain/rtk.js';
+import { requestedInstructionFiles } from '../generate/agentsmd.js';
+import { userScopeInstructionFiles } from './apply.js';
 const STATUS_COLOR = {
     ok: theme.ok,
     warn: theme.warn,
@@ -149,6 +151,10 @@ export function agentShellItem(agent, info, exists) {
     }
     return { status: 'ok', label, detail: info.shell };
 }
+/** The deps that make `doctor --scope <scope>` inspect that scope; none without a scope. */
+export function scopedDoctorDeps(scope) {
+    return scope ? { findConfigPath: () => findConfigPathInScope(scope) } : {};
+}
 export function gatherDoctor(sectionFilter, deps = {}) {
     const detectShellFn = deps.detectShell ?? detectShell;
     const existsSync = deps.existsSync ?? fs.existsSync;
@@ -158,6 +164,9 @@ export function gatherDoctor(sectionFilter, deps = {}) {
     const miseGlobalConfigPathFn = deps.miseGlobalConfigPath ?? miseGlobalConfigPath;
     const shimsDirFn = deps.shimsDir ?? shimsDir;
     const shimsDirOnPathFn = deps.shimsDirOnPath ?? shimsDirOnPath;
+    const findShadowedShimsFn = deps.findShadowedShims ?? findShadowedShims;
+    const miseProvidesExecutableFn = deps.miseProvidesExecutable ??
+        ((binary, cwd) => runMiseCaptured(['which', binary], { cwd }).status === 0);
     const findConfigPathFn = deps.findConfigPath ?? findConfigPath;
     const userConfigDirFn = deps.userConfigDir ?? userConfigDir;
     const loadConfigFn = deps.loadConfig ?? loadConfig;
@@ -227,6 +236,7 @@ export function gatherDoctor(sectionFilter, deps = {}) {
             status: 'fail',
             label: 'shims_dir',
             detail: `not set to ${shimsDirFn()} in ${globalConfigPath} — run \`agentenv apply\``,
+            fix: 'agentenv apply',
         });
     }
     miseItems.push({
@@ -300,18 +310,45 @@ export function gatherDoctor(sectionFilter, deps = {}) {
             const item = { status: 'ok', label: `${binary} (${key})`, detail: '' };
             if (status === 'needs-new-terminal') {
                 item.status = 'warn';
-                item.detail = 'installed via mise; open a new terminal';
+                if (miseProvidesExecutableFn(binary, path.dirname(configPath))) {
+                    item.detail = 'installed via mise; open a new terminal';
+                }
+                else {
+                    // mise lists it as installed but `mise which` finds nothing to run (e.g. an
+                    // upstream package whose Windows asset has no .exe), so a new terminal
+                    // would never fix it.
+                    const miseName = MISE_TOOL_NAMES[key] || key;
+                    item.detail = `mise lists it as installed but provides no executable (\`mise which ${binary}\` fails), so a new terminal will not help; reinstall with \`mise install --force ${miseName}\`, and if that fails too the package is broken for this platform: \`agentenv remove ${key}\``;
+                    item.fix = `mise install --force ${miseName}`;
+                }
             }
             else if (status === 'manual') {
-                item.status = 'warn';
-                item.detail = 'not managed by mise; install manually';
+                // Not actionable by agentenv (e.g. tokei, or rga/jless on Windows), so it
+                // must not keep the whole report at 'warn' forever.
+                item.detail = 'not managed by mise; install manually if you want it';
             }
             else if (status === 'missing') {
                 item.status = 'fail';
-                item.detail = 'not on PATH — run `mise install` in this project';
+                item.detail =
+                    scope === 'user'
+                        ? 'not on PATH — run `agentenv apply --scope user`'
+                        : 'not on PATH — run `mise install` in this project';
+                item.fix = scope === 'user' ? 'agentenv apply --scope user' : 'agentenv apply';
             }
             toolItems.push(item);
         }
+        // mise's own `doctor` warns about this; without it every tool above can read
+        // [ok] while the agent actually runs a different copy of it.
+        const shadowed = findShadowedShimsFn(enabledTools.map((key) => BINARY_MAP[key]), { pathEnv: process.env.PATH ?? '', shimsDir: shimsDirFn() });
+        if (shadowed.length > 0) {
+            const shown = shadowed.slice(0, 5).map((s) => `${s.binary} → ${s.shadowedBy}`);
+            const more = shadowed.length > shown.length ? `, +${shadowed.length - shown.length} more` : '';
+            toolItems.push({
+                status: 'warn',
+                label: 'PATH order',
+                detail: `${shadowed.length} tool(s) resolve to another copy before the mise shims: ${shown.join('; ')}${more} — move ${shimsDirFn()} earlier in PATH`,
+            });
+        }
     }
     sections.push({
         title: `Tools (${enabledTools.length} configured)`,
@@ -333,11 +370,12 @@ export function gatherDoctor(sectionFilter, deps = {}) {
                     status: 'fail',
                     label: 'rtk',
                     detail: 'not found via `mise which rtk` or on PATH — run `agentenv apply`',
+                    fix: 'agentenv apply',
                 });
             }
             else {
                 rtkItems.push({ status: 'ok', label: 'rtk', detail: rtkInfo.resolvedPath });
-                const pinned = PINNED_TOOL_VERSIONS.rtk;
+                const pinned = config.tool_versions?.rtk ?? PINNED_TOOL_VERSIONS.rtk;
                 if (rtkInfo.version) {
                     const detail = pinned && !rtkInfo.version.includes(pinned)
                         ? `${rtkInfo.version} (agentenv pins ${pinned})`
@@ -373,6 +411,12 @@ export function gatherDoctor(sectionFilter, deps = {}) {
                 detail: installed
                     ? ''
                     : 'CLI not found on PATH — install it or disable the agent in config',
+                // Installing it is the other way out, but only disabling is a command agentenv owns.
+                ...(installed
+                    ? {}
+                    : {
+                        fix: `agentenv remove ${agent}${config.scope === 'user' ? ' --scope user' : ''}`,
+                    }),
             });
             if (platform === 'win32' && SHELL_MANAGED_AGENTS.includes(agent)) {
                 agentItems.push(agentShellItem(agent, checkAgentShellFn(agent), existsSync));
@@ -385,6 +429,71 @@ export function gatherDoctor(sectionFilter, deps = {}) {
             ? agentItems
             : [{ status: 'warn', label: 'none', detail: 'no agents enabled' }],
     });
+    // Generated files — what `apply` wrote and agents actually read. `status`
+    // reports the same drift; agents are pointed at `doctor --json`, so it has
+    // to see a stripped managed block or a missing custom binary too.
+    const baseDir = config.scope === 'user' ? userConfigDirFn() : path.dirname(configPath);
+    const applyFix = config.scope === 'user' ? 'agentenv apply --scope user' : 'agentenv apply';
+    const marker = config.generate?.marker_start ?? '<!-- agentenv-managed-start -->';
+    const generated = [
+        { label: 'mise.toml', file: miseTomlPathFor(config.scope, baseDir), managed: false },
+        ...requestedInstructionFiles(config).map((name) => ({
+            label: name,
+            file: path.join(baseDir, name),
+            managed: true,
+        })),
+        ...userScopeInstructionFiles(config, baseDir, {}).map((entry) => ({
+            label: entry.path,
+            file: entry.path,
+            managed: true,
+        })),
+    ];
+    sections.push({
+        title: `Generated files (${generated.length})`,
+        items: generated.map(({ label, file, managed }) => {
+            if (!existsSync(file)) {
+                return { status: 'warn', label, detail: `missing — run \`${applyFix}\``, fix: applyFix };
+            }
+            let content = '';
+            try {
+                content = String(readFileSync(file, 'utf-8'));
+            }
+            catch {
+                // Unreadable counts as having no managed block below.
+            }
+            if (managed && !content.includes(marker)) {
+                return {
+                    status: 'warn',
+                    label,
+                    detail: `present but has no agentenv managed block — run \`${applyFix}\``,
+                    fix: applyFix,
+                };
+            }
+            return { status: 'ok', label, detail: file };
+        }),
+    });
+    const installedCustom = (config.custom_tools ?? []).filter((tool) => tool.already_installed);
+    if (installedCustom.length > 0) {
+        sections.push({
+            title: `Custom tools (${installedCustom.length})`,
+            items: installedCustom.map((tool) => {
+                const where = platform === 'win32'
+                    ? tool.path_windows
+                    : platform === 'darwin'
+                        ? tool.path_macos
+                        : tool.path_linux;
+                return where && existsSync(where)
+                    ? { status: 'ok', label: tool.name, detail: where }
+                    : {
+                        status: 'warn',
+                        label: tool.name,
+                        detail: where
+                            ? `not found at ${where}`
+                            : `no path configured for ${platform}; set path_${platform === 'win32' ? 'windows' : platform === 'darwin' ? 'macos' : 'linux'}`,
+                    };
+            }),
+        });
+    }
     return sections;
 }
 function doctorSummary(payload) {
@@ -419,11 +528,17 @@ export const doctorCommand = new Command()
     .description('Diagnose the machine: mise, shims, config, tools and agents (read-only)')
     .option('--json', 'emit a machine-readable JSON document on stdout')
     .option('--section <index|name>', 'only run one report section (1-based section index or title prefix)')
+    .option('--scope <scope>', 'config scope to inspect: project|user (default: nearest config)')
     .action((options, command) => {
+    const scope = parseScopeFlag(options.scope);
+    if (scope.error) {
+        command.error(scope.error);
+        return;
+    }
     const json = options.json === true;
     if (json)
         setQuietEnabled(true);
-    const gathered = gatherDoctor(options.section);
+    const gathered = gatherDoctor(options.section, scopedDoctorDeps(scope.scope));
     const sections = options.section === undefined ? gathered : filterDoctorSections(gathered, options.section);
     if (sections === undefined) {
         // Invalid argument, not an operational failure — docs/guides/exit-codes.md

package/dist/commands/doctor.js.map

@@ -1 +1 @@
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package/dist/commands/setup.d.ts

@@ -2,6 +2,7 @@ import { Command } from 'commander';
 import type { AgentenvConfig } from '../config/schema.js';
 import type { ScopeValue } from '../config/scopes.js';
 import { applyConfiguration } from './apply.js';
+import type { ApplyResult } from './apply.js';
 interface MisePrereqCheckDeps {
     isInstalled?: () => boolean;
     version?: () => string;
@@ -29,6 +30,11 @@ export interface SaveAndApplyDeps {
     persistConfig?: AgentenvConfig | null;
     /** JSON mode: don't stream raw mise output onto stdout (it would corrupt the document). */
     json?: boolean;
+    /**
+     * JSON mode: receives apply's structured result (and the config file it ran
+     * against) instead of the human message list and result box being printed.
+     */
+    onApplied?: (result: ApplyResult, file: string) => void;
 }
 /** Save the config and apply it, mirroring the shared setup tail. */
 export declare function saveAndApply(config: AgentenvConfig, file: string, deps?: SaveAndApplyDeps): Promise<void>;
@@ -39,7 +45,7 @@ interface SetupCommandOptions {
     tier2?: boolean;
     rtk?: boolean;
     config?: string;
-    superpowers?: string | boolean;
+    superpowers?: boolean;
     json?: boolean;
 }
 export interface UnattendedSetupDeps extends SaveAndApplyDeps {

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

@@ -1 +1 @@
-{"version":3,"file":"setup.d.ts","sourceRoot":"","sources":["../../src/commands/setup.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAKpC,OAAO,KAAK,EAAY,cAAc,EAAE,MAAM,qBAAqB,CAAC;AAEpE,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AACtD,OAAO,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAoBhD,UAAU,mBAAmB;IAC3B,WAAW,CAAC,EAAE,MAAM,OAAO,CAAC;IAC5B,OAAO,CAAC,EAAE,MAAM,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,IAAI,GAAE,mBAAwB,GAAG,OAAO,CAavE;AAED,MAAM,WAAW,gBAAgB;IAC/B,iEAAiE;IACjE,kBAAkB,CAAC,EAAE,OAAO,kBAAkB,CAAC;IAC/C,wEAAwE;IACxE,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,0EAA0E;IAC1E,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,gEAAgE;IAChE,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B;;;;OAIG;IACH,aAAa,CAAC,EAAE,cAAc,GAAG,IAAI,CAAC;IACtC,2FAA2F;IAC3F,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,qEAAqE;AACrE,wBAAsB,YAAY,CAChC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,MAAM,EACZ,IAAI,GAAE,gBAAqB,GAC1B,OAAO,CAAC,IAAI,CAAC,CA2Cf;AAED,UAAU,mBAAmB;IAC3B,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,UAAU,CAAC;IACnB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IAC/B,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,MAAM,WAAW,mBAAoB,SAAQ,gBAAgB;IAC3D,mBAAmB,CAAC,EAAE,mBAAmB,CAAC;CAC3C;AA4BD;;;;;;;GAOG;AACH,wBAAsB,eAAe,CACnC,OAAO,EAAE,mBAAmB,EAC5B,IAAI,GAAE,mBAAwB,GAC7B,OAAO,CAAC,IAAI,CAAC,CAuHf;AAED;;;;GAIG;AACH,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,mBAAmB,EAC5B,IAAI,GAAE,mBAAwB,GAC7B,OAAO,CAAC,IAAI,CAAC,CA0Bf;AAED,eAAO,MAAM,YAAY,SAuCrB,CAAC"}
+{"version":3,"file":"setup.d.ts","sourceRoot":"","sources":["../../src/commands/setup.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAKpC,OAAO,KAAK,EAAY,cAAc,EAAE,MAAM,qBAAqB,CAAC;AAEpE,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AACtD,OAAO,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAChD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAoB9C,UAAU,mBAAmB;IAC3B,WAAW,CAAC,EAAE,MAAM,OAAO,CAAC;IAC5B,OAAO,CAAC,EAAE,MAAM,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,IAAI,GAAE,mBAAwB,GAAG,OAAO,CAavE;AAED,MAAM,WAAW,gBAAgB;IAC/B,iEAAiE;IACjE,kBAAkB,CAAC,EAAE,OAAO,kBAAkB,CAAC;IAC/C,wEAAwE;IACxE,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,0EAA0E;IAC1E,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,gEAAgE;IAChE,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B;;;;OAIG;IACH,aAAa,CAAC,EAAE,cAAc,GAAG,IAAI,CAAC;IACtC,2FAA2F;IAC3F,IAAI,CAAC,EAAE,OAAO,CAAC;IACf;;;OAGG;IACH,SAAS,CAAC,EAAE,CAAC,MAAM,EAAE,WAAW,EAAE,IAAI,EAAE,MAAM,KAAK,IAAI,CAAC;CACzD;AAgBD,qEAAqE;AACrE,wBAAsB,YAAY,CAChC,MAAM,EAAE,cAAc,EACtB,IAAI,EAAE,MAAM,EACZ,IAAI,GAAE,gBAAqB,GAC1B,OAAO,CAAC,IAAI,CAAC,CAiDf;AAED,UAAU,mBAAmB;IAC3B,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,UAAU,CAAC;IACnB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,IAAI,CAAC,EAAE,OAAO,CAAC;CAChB;AAED,MAAM,WAAW,mBAAoB,SAAQ,gBAAgB;IAC3D,mBAAmB,CAAC,EAAE,mBAAmB,CAAC;CAC3C;AA4BD;;;;;;;GAOG;AACH,wBAAsB,eAAe,CACnC,OAAO,EAAE,mBAAmB,EAC5B,IAAI,GAAE,mBAAwB,GAC7B,OAAO,CAAC,IAAI,CAAC,CAkHf;AAED;;;;GAIG;AACH,wBAAsB,mBAAmB,CACvC,OAAO,EAAE,mBAAmB,EAC5B,IAAI,GAAE,mBAAwB,GAC7B,OAAO,CAAC,IAAI,CAAC,CA8Cf;AAED,eAAO,MAAM,YAAY,SAuCrB,CAAC"}

package/dist/commands/setup.js

@@ -34,6 +34,21 @@ export function misePrereqCheck(deps = {}) {
     console.error('\nInstall mise first, then re-run `agentenv setup`.');
     return false;
 }
+/**
+ * The project file's own settings, for generating committed files without the
+ * user layer (see ApplyOptions.fileConfig). Undefined in user scope, or when
+ * the file can't be read back.
+ */
+function projectFileConfig(config, file) {
+    if (config.scope !== 'project')
+        return undefined;
+    try {
+        return loadConfig(file);
+    }
+    catch {
+        return undefined;
+    }
+}
 /** Save the config and apply it, mirroring the shared setup tail. */
 export async function saveAndApply(config, file, deps = {}) {
     const toSave = deps.persistConfig === undefined ? config : deps.persistConfig;
@@ -59,6 +74,7 @@ export async function saveAndApply(config, file, deps = {}) {
     // setup already printed the prereq line above, so tell apply not to repeat it.
     apply(config, path.dirname(file), {
         skipPrereqMessage: true,
+        fileConfig: projectFileConfig(config, file),
         skipMiseInstall: deps.skipMiseInstall,
         onMiseInstall: deps.json
             ? undefined
@@ -71,6 +87,12 @@ export async function saveAndApply(config, file, deps = {}) {
                 onEnd: () => spinner.start(),
             },
     }));
+    if (deps.json) {
+        deps.onApplied?.(result, file);
+        if (!result.success)
+            process.exitCode = 1;
+        return;
+    }
     printMessages(result.messages, result.errors, result.timeline);
     const elapsedMs = deps.startedAt === undefined ? result.elapsedMs : Date.now() - deps.startedAt;
     if (!result.success) {
@@ -212,13 +234,9 @@ export async function unattendedSetup(options, deps = {}) {
             }
             const includeTier2 = options.tier2 !== false;
             const rtkEnabled = options.rtk !== false;
-            const superpowersRef = options.superpowers === undefined
-                ? undefined
-                : typeof options.superpowers === 'string'
-                    ? options.superpowers
-                    : undefined;
-            config = buildDefaultSimpleConfig(agents, includeTier2, rtkEnabled, scope, superpowersRef);
-            console.log(`Defaults: agents ${agents.join(', ')}, Tier 2 tools ${includeTier2 ? 'on' : 'off'}, rtk ${rtkEnabled ? 'on' : 'off'}, Superpowers ${superpowersRef === undefined ? 'off' : `on (ref ${superpowersRef || 'default'})`}`);
+            const superpowers = options.superpowers === true;
+            config = buildDefaultSimpleConfig(agents, includeTier2, rtkEnabled, scope, superpowers);
+            console.log(`Defaults: agents ${agents.join(', ')}, Tier 2 tools ${includeTier2 ? 'on' : 'off'}, rtk ${rtkEnabled ? 'on' : 'off'}, Superpowers ${superpowers ? 'on' : 'off'}`);
         }
     }
     await saveAndApply(config, file, {
@@ -235,8 +253,12 @@ export async function unattendedSetup(options, deps = {}) {
 export async function unattendedSetupJson(options, deps = {}) {
     setQuietEnabled(true);
     setColorEnabled(false);
-    const messages = [];
-    const errors = [];
+    // Notes the flow prints before/around apply, warnings (e.g. ignored flags),
+    // and errors from steps that stop before apply ever runs (bad config, no
+    // agents). Apply's own messages/errors come from its structured result.
+    const notes = [];
+    const warnings = [];
+    const earlyErrors = [];
     const original = { log: console.log, warn: console.warn, error: console.error };
     const capture = (sink) => (message) => {
         for (const line of String(message ?? '').split(/\r?\n/)) {
@@ -244,13 +266,21 @@ export async function unattendedSetupJson(options, deps = {}) {
                 sink.push(line);
         }
     };
-    console.log = capture(messages);
-    console.warn = capture(messages);
-    console.error = capture(errors);
+    console.log = capture(notes);
+    console.warn = capture(warnings);
+    console.error = capture(earlyErrors);
     const priorExitCode = process.exitCode;
     process.exitCode = undefined;
+    let applied;
     try {
-        await unattendedSetup(options, { ...deps, json: true });
+        await unattendedSetup(options, {
+            ...deps,
+            json: true,
+            onApplied: (result, file) => {
+                applied = { result, file };
+                deps.onApplied?.(result, file);
+            },
+        });
     }
     finally {
         console.log = original.log;
@@ -258,7 +288,15 @@ export async function unattendedSetupJson(options, deps = {}) {
         console.error = original.error;
     }
     const failed = process.exitCode !== undefined && process.exitCode !== 0;
-    printJson({ success: !failed, messages, errors });
+    printJson({
+        success: !failed,
+        configPath: applied?.file ?? null,
+        baseDir: applied ? path.dirname(applied.file) : null,
+        messages: [...notes, ...(applied?.result.messages ?? [])],
+        errors: [...earlyErrors, ...(applied?.result.errors ?? [])],
+        warnings,
+        ...(applied?.result.elapsedMs === undefined ? {} : { elapsedMs: applied.result.elapsedMs }),
+    });
     if (!failed)
         process.exitCode = priorExitCode;
 }
@@ -271,7 +309,7 @@ export const setupCommand = new Command()
     .option('--scope <scope>', 'configuration scope: project|user (default: project; preselects the wizard prompt without --yes)')
     .option('--no-tier2', 'skip Tier 2 tools (unattended)')
     .option('--no-rtk', 'disable rtk command rewriting (unattended)')
-    .option('--superpowers [ref]', 'enable the Superpowers integration (unattended); optional github tag/branch/commit ref')
+    .option('--superpowers', 'enable the Superpowers integration (unattended); installed from the official Claude Code marketplace')
     .option('--config <path>', 'path to an existing agentenv.toml to apply (unattended)')
     .option('--json', 'emit one machine-readable JSON document on stdout (requires --yes)')
     .action(async (options, command) => {

package/dist/commands/setup.js.map

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package/dist/commands/status.d.ts

@@ -1,18 +1,14 @@
 import { Command } from 'commander';
 import { isAgentInstalled, resolveBinary } from '../adapters/detect.js';
 import { getEnabledAgents, loadConfig, validateConfig } from '../config/schema.js';
-import type { AgentKey, AgentenvConfig } from '../config/schema.js';
+import type { AgentenvConfig } from '../config/schema.js';
 import { findConfigPath, resolveScopeDir } from '../config/scopes.js';
 import { checkAgentShellConfiguration, detectShell } from '../shell/detector.js';
+import { AGENT_CONFIG_FILES } from './agent-files.js';
 import type { IntegrationResult, IntegrationState } from '../integrations/base.js';
 import { resolveGhAuthProbe } from '../toolchain/gh.js';
 import { getInstalledToolState, getMiseVersion, shimExists } from '../toolchain/mise.js';
 import type { ToolResolvability } from '../toolchain/mise.js';
-declare const AGENT_CONFIG_FILES: Record<AgentKey, {
-    label: string;
-    check: (baseDir: string) => string;
-    contains?: string;
-}>;
 export { AGENT_CONFIG_FILES };
 export interface StatusAgent {
     key: string;
@@ -20,6 +16,8 @@ export interface StatusAgent {
     installed: boolean;
     configured: boolean;
     drift: boolean;
+    /** The command that fixes this drift; present only when `drift` is true. */
+    fix?: string;
 }
 export interface StatusTool {
     key: string;
@@ -33,6 +31,8 @@ export interface StatusTool {
     pinned: string | null;
     /** Best-match installed version from `mise ls --json`, or `null` when moot/unknown. */
     installed: string | null;
+    /** The command that fixes this drift; present only when `drift` is true. */
+    fix?: string;
 }
 export interface StatusCustomTool {
     name: string;
@@ -43,6 +43,8 @@ export interface StatusGenerated {
     label: string;
     exists: boolean;
     managed: boolean;
+    /** The command that regenerates it; present only when it is missing or unmanaged. */
+    fix?: string;
 }
 export interface StatusIntegrationAgent {
     agent: string;
@@ -53,7 +55,6 @@ export interface StatusIntegration {
     key: string;
     enabled: boolean;
     source: string | null;
-    ref: string | null;
     scope: string | null;
     agents: string[];
     states: StatusIntegrationAgent[];