@phnx-labs/agents-cli 1.20.3 → 1.20.5

package/dist/commands/repo.js

@@ -26,6 +26,30 @@ function resolveRepoPath(target) {
 import { ensureAgentsDir, getExtraRepoDir, getSystemAgentsDir, getUserAgentsDir, readMeta, resolveExtraRepoDir, updateMeta, } from '../lib/state.js';
 import { parseSource, pullRepo, commitAndPush, isGitRepo, isSystemRepoOrigin } from '../lib/git.js';
 import { DEFAULT_SYSTEM_REPO } from '../lib/types.js';
+import { ALL_AGENT_IDS, isAgentName, resolveAgentName } from '../lib/agents.js';
+import { refresh } from '../lib/refresh.js';
+import { capableAgents } from '../lib/capabilities.js';
+import { getGlobalDefault, getVersionHomePath, listInstalledVersions } from '../lib/versions.js';
+import { syncAllMarketplaces } from '../lib/plugin-marketplace.js';
+/**
+ * After a repo add/remove/enable/disable, reconcile each plugins-capable
+ * agent's default version against the new marketplace set. Re-synthesizes
+ * catalogs and known_marketplaces.json entries. Source-copy of plugins is
+ * out of scope here — full sync still goes through `agents repo refresh`.
+ */
+function syncMarketplacesForDefaults() {
+    for (const agent of capableAgents('plugins')) {
+        const def = getGlobalDefault(agent);
+        if (!def)
+            continue;
+        if (!listInstalledVersions(agent).includes(def))
+            continue;
+        try {
+            syncAllMarketplaces(agent, getVersionHomePath(agent, def));
+        }
+        catch { /* best-effort */ }
+    }
+}
 const ALIAS_PATTERN = /^[a-zA-Z0-9][a-zA-Z0-9_-]{0,63}$/;
 /** Derive a default alias from a source URL (e.g. gh:foo/.agents-work -> agents-work). */
 function deriveAlias(source) {
@@ -42,16 +66,97 @@ function deriveAlias(source) {
     // becomes ~/.agents-<alias>/ on disk (e.g. ".agents-work" -> "work").
     return base.replace(/^\.+/, '').replace(/^agents-/, '') || 'repo';
 }
-/** Get the last commit short hash for a repo, or null if unavailable. */
-async function getShortCommit(repoDir) {
+/**
+ * Categorized working-tree summary: `M:2 A:1 D:1 ?:3` — letters match the git
+ * porcelain shorthand (Modified / Added / Deleted / Renamed / Unmerged /
+ * Untracked). Zero counts are omitted so the column stays compact.
+ */
+function formatDirtyCounts(status) {
+    const parts = [];
+    if (status.modified.length)
+        parts.push(chalk.yellow(`M:${status.modified.length}`));
+    if (status.created.length)
+        parts.push(chalk.green(`A:${status.created.length}`));
+    if (status.deleted.length)
+        parts.push(chalk.red(`D:${status.deleted.length}`));
+    if (status.renamed.length)
+        parts.push(chalk.cyan(`R:${status.renamed.length}`));
+    if (status.conflicted.length)
+        parts.push(chalk.magenta(`U:${status.conflicted.length}`));
+    if (status.not_added.length)
+        parts.push(chalk.gray(`?:${status.not_added.length}`));
+    return parts.join(' ');
+}
+/** Visible character width of a string with embedded ANSI color codes. */
+function visibleWidth(s) {
+    return s.replace(/\[[0-9;]*m/g, '').length;
+}
+/** Pad string with trailing spaces to a target visible column width. */
+function padVisible(s, width) {
+    return s + ' '.repeat(Math.max(0, width - visibleWidth(s)));
+}
+/**
+ * Render one row of the unified repo table: alias / branch / ahead-behind /
+ * dirty counts / url+commit. Used by `agents repo list` and the hidden
+ * `agents repo status` alias.
+ */
+async function renderRepoRow(t) {
+    const aliasCol = chalk.cyan(t.alias.padEnd(12));
+    if (!fs.existsSync(t.dir)) {
+        return `  ${aliasCol} ${chalk.red('missing')} ${chalk.gray(t.dir)}`;
+    }
+    if (!isGitRepo(t.dir)) {
+        return `  ${aliasCol} ${chalk.gray('local (no git remote)')} ${chalk.gray(t.dir)}`;
+    }
     try {
-        const git = simpleGit(repoDir);
-        const log = await git.log({ maxCount: 1 });
-        return log.latest?.hash.slice(0, 8) || null;
+        const git = simpleGit(t.dir);
+        const status = await git.status();
+        const branch = status.tracking || status.current || '(detached)';
+        const inSync = (status.ahead ?? 0) === 0 && (status.behind ?? 0) === 0;
+        const remoteRaw = inSync ? 'in sync' : `+${status.ahead ?? 0} -${status.behind ?? 0}`;
+        const remoteColored = inSync ? chalk.green(remoteRaw) : chalk.yellow(remoteRaw);
+        const remotePad = ' '.repeat(Math.max(0, 12 - remoteRaw.length));
+        const tree = status.isClean() ? chalk.green('clean') : formatDirtyCounts(status);
+        const remotes = await git.getRemotes(true);
+        const origin = remotes.find((r) => r.name === 'origin');
+        const url = origin?.refs?.fetch || '';
+        const commit = (await git.log({ maxCount: 1 })).latest?.hash.slice(0, 8) || '';
+        const tail = url
+            ? chalk.gray(`${url}${commit ? ` (${commit})` : ''}`)
+            : commit
+                ? chalk.gray(`(${commit})`)
+                : '';
+        return `  ${aliasCol} ${branch.padEnd(28)}  ${remoteColored}${remotePad}  ${padVisible(tree, 14)}  ${tail}`;
     }
-    catch {
-        return null;
+    catch (err) {
+        return `  ${aliasCol} ${chalk.red('error')} ${err.message}`;
+    }
+}
+/**
+ * Shared action body for `agents repo list` and the hidden `agents repo status`
+ * alias. Prints a unified table: alias, branch, ahead/behind, dirty counts,
+ * remote URL and short commit hash.
+ */
+async function listRepos(alias) {
+    const targets = collectRepoTargets(alias);
+    if (!targets) {
+        process.exitCode = 1;
+        return;
+    }
+    if (targets.length === 0) {
+        console.log(chalk.gray('No repos to show.'));
+        return;
+    }
+    console.log('');
+    console.log(`  ${chalk.gray('REPO'.padEnd(12))} ${chalk.gray('BRANCH'.padEnd(28))}  ${chalk.gray('REMOTE'.padEnd(12))}  ${chalk.gray('LOCAL'.padEnd(14))}  ${chalk.gray('URL')}`);
+    for (const t of targets) {
+        console.log(await renderRepoRow(t));
     }
+    const userDir = getUserAgentsDir();
+    if (!isGitRepo(userDir) && fs.existsSync(userDir)) {
+        console.log(chalk.gray('\n  user repo has no git remote — scaffold one with: agents repo init'));
+    }
+    console.log('');
 }
 /** Register the `agents repo` command tree. */
 export function registerRepoCommands(program) {
@@ -201,6 +306,7 @@ export function registerRepoCommands(program) {
         if (parsed.type === 'local') {
             extras[alias] = { url: parsed.url, path: parsed.url, enabled: true };
             updateMeta({ extraRepos: extras });
+            syncMarketplacesForDefaults();
             console.log(chalk.green(`Registered local repo "${alias}" -> ${parsed.url}`));
             return;
         }
@@ -236,78 +342,16 @@ export function registerRepoCommands(program) {
         }
         extras[alias] = { url: parsed.url, path: targetDir, enabled: true };
         updateMeta({ extraRepos: extras });
+        syncMarketplacesForDefaults();
         console.log(chalk.gray(`\nRegistered as "${alias}". Skills and commands from this repo will be`));
         console.log(chalk.gray(`picked up automatically the next time you launch any agent.`));
     });
     repoCmd
-        .command('list')
+        .command('list [alias]')
         .alias('ls')
-        .description('Show all repos: system, user, and any registered extras')
-        .action(async () => {
-        const meta = readMeta();
-        console.log('');
-        // System repo
-        const systemUrl = meta.source || DEFAULT_SYSTEM_REPO;
-        const systemDir = getSystemAgentsDir();
-        const systemOnDisk = fs.existsSync(systemDir);
-        const systemIsGit = systemOnDisk && isGitRepo(systemDir);
-        const systemCommit = systemIsGit ? await getShortCommit(systemDir) : null;
-        const systemStatus = !systemOnDisk
-            ? chalk.red('missing')
-            : !systemIsGit
-                ? chalk.yellow('not a git repo — run: agents setup')
-                : chalk.green('cloned');
-        const systemCommitLabel = systemCommit ? chalk.gray(`(${systemCommit})`) : '';
-        console.log(chalk.bold('System  (~/.agents-system/)'));
-        console.log(`  ${chalk.cyan('system'.padEnd(12))}  ${systemUrl}  ${systemStatus}  ${systemCommitLabel}`);
-        // User repo
-        const userDir = getUserAgentsDir();
-        const userOnDisk = fs.existsSync(userDir);
-        const userIsGit = userOnDisk && isGitRepo(userDir);
-        const userCommit = userIsGit ? await getShortCommit(userDir) : null;
-        let userRemoteUrl = '';
-        if (userIsGit) {
-            try {
-                const git = simpleGit(userDir);
-                const remotes = await git.getRemotes(true);
-                const origin = remotes.find(r => r.name === 'origin');
-                userRemoteUrl = origin?.refs?.fetch || '';
-            }
-            catch { /* no remote */ }
-        }
-        const userStatus = !userOnDisk
-            ? chalk.gray('not created')
-            : !userIsGit
-                ? chalk.gray('local (no remote)')
-                : chalk.green('cloned');
-        const userCommitLabel = userCommit ? chalk.gray(`(${userCommit})`) : '';
-        console.log(chalk.bold('\nUser  (~/.agents/)'));
-        console.log(`  ${chalk.cyan('user'.padEnd(12))}  ${userRemoteUrl || '~/.agents/'}  ${userStatus}  ${userCommitLabel}`);
-        if (!userIsGit) {
-            console.log(chalk.gray(`  ${''.padEnd(12)}  scaffold one with: agents repo init`));
-        }
-        // Extra repos
-        const extras = meta.extraRepos || {};
-        const aliases = Object.keys(extras);
-        console.log(chalk.bold('\nExtras:'));
-        if (aliases.length === 0) {
-            console.log(chalk.gray('  (none — add one with `agents repo add <source>`)\n'));
-            return;
-        }
-        for (const alias of aliases) {
-            const config = extras[alias];
-            const dir = resolveExtraRepoDir(alias, config);
-            const onDisk = fs.existsSync(dir);
-            const commit = onDisk ? await getShortCommit(dir) : null;
-            const status = !config.enabled
-                ? chalk.yellow('disabled')
-                : !onDisk
-                    ? chalk.red('missing')
-                    : chalk.green('enabled');
-            const commitLabel = commit ? chalk.gray(`(${commit})`) : '';
-            console.log(`  ${chalk.cyan(alias.padEnd(12))}  ${config.url}  ${status}  ${commitLabel}`);
-        }
-        console.log('');
+        .description('Show all repos: branch, ahead/behind, dirty counts, URL, commit.')
+        .action(async (alias) => {
+        await listRepos(alias);
     });
     repoCmd
         .command('remove <alias>')
@@ -335,6 +379,7 @@ export function registerRepoCommands(program) {
         }
         delete extras[alias];
         updateMeta({ extraRepos: extras });
+        syncMarketplacesForDefaults();
         console.log(chalk.green(`Removed "${alias}"`));
     });
     repoCmd
@@ -351,7 +396,7 @@ export function registerRepoCommands(program) {
     });
     repoCmd
         .command('pull [alias]')
-        .description('Pull updates. Aliases: "system" (~/.agents-system/), "user" (~/.agents/), or any registered extra. No arg pulls all.')
+        .description('Pull updates. Aliases: "system" (~/.agents/.system/), "user" (~/.agents/), or any registered extra. No arg pulls all.')
         .action(async (alias) => {
         const targets = collectRepoTargets(alias);
         if (!targets) {
@@ -483,46 +528,43 @@ export function registerRepoCommands(program) {
         }
     });
     repoCmd
-        .command('status [alias]')
-        .description('Per-repo summary: branch, ahead/behind upstream, working-tree state')
-        .action(async (alias) => {
-        const targets = collectRepoTargets(alias) || [];
-        if (targets.length === 0) {
-            console.log(chalk.gray('No git repos found.'));
-            return;
-        }
-        console.log('');
-        console.log(`  ${chalk.gray('REPO'.padEnd(12))} ${chalk.gray('BRANCH'.padEnd(28))}  ${chalk.gray('REMOTE'.padEnd(12))}  ${chalk.gray('LOCAL')}`);
-        for (const t of targets) {
-            if (!fs.existsSync(t.dir)) {
-                console.log(`  ${chalk.cyan(t.alias.padEnd(12))} ${chalk.red('missing')} ${chalk.gray(t.dir)}`);
-                continue;
-            }
-            if (!isGitRepo(t.dir)) {
-                console.log(`  ${chalk.cyan(t.alias.padEnd(12))} ${chalk.gray('not a git repo')} ${chalk.gray(t.dir)}`);
-                continue;
-            }
-            try {
-                const git = simpleGit(t.dir);
-                const status = await git.status();
-                const branch = status.tracking || status.current || '(detached)';
-                const remoteRaw = (status.ahead ?? 0) === 0 && (status.behind ?? 0) === 0
-                    ? 'in sync'
-                    : `+${status.ahead ?? 0} -${status.behind ?? 0}`;
-                const remoteColored = (status.ahead ?? 0) === 0 && (status.behind ?? 0) === 0
-                    ? chalk.green(remoteRaw)
-                    : chalk.yellow(remoteRaw);
-                const tree = status.isClean()
-                    ? chalk.green('clean')
-                    : chalk.yellow(`${status.files.length} uncommitted`);
-                const remotePad = ' '.repeat(Math.max(0, 12 - remoteRaw.length));
-                console.log(`  ${chalk.cyan(t.alias.padEnd(12))} ${branch.padEnd(28)}  ${remoteColored}${remotePad}  ${tree}`);
+        .command('refresh [agent]')
+        .description('Re-materialize resources into installed agent version homes. No git, no network.')
+        .option('-y, --yes', 'Auto-sync everything without prompting')
+        .option('--skip-clis', 'Skip CLI version install/upgrade from agents.yaml')
+        .action(async (arg, options) => {
+        let agentFilter;
+        if (arg) {
+            if (!isAgentName(arg)) {
+                console.log(chalk.red(`Unknown agent "${arg}".`));
+                console.log(chalk.gray(`Available: ${ALL_AGENT_IDS.join(', ')}`));
+                process.exitCode = 1;
+                return;
             }
-            catch (err) {
-                console.log(`  ${chalk.cyan(t.alias.padEnd(12))} ${chalk.red('error')} ${err.message}`);
+            agentFilter = resolveAgentName(arg);
+        }
+        try {
+            await refresh({
+                agentFilter,
+                skipPrompts: options.yes,
+                skipClis: options.skipClis,
+            });
+            console.log(chalk.green('\nRefresh complete'));
+        }
+        catch (err) {
+            if (isPromptCancelled(err)) {
+                console.log(chalk.yellow('\nCancelled'));
+                return;
             }
+            console.error(chalk.red(err.message));
+            process.exit(1);
         }
-        console.log('');
+    });
+    repoCmd
+        .command('status [alias]', { hidden: true })
+        .description('Alias of `list` (kept for muscle memory).')
+        .action(async (alias) => {
+        await listRepos(alias);
     });
 }
 /**
@@ -564,5 +606,6 @@ async function toggle(alias, enabled) {
     }
     extras[alias] = { ...extras[alias], enabled };
     updateMeta({ extraRepos: extras });
+    syncMarketplacesForDefaults();
     console.log(chalk.green(`${enabled ? 'Enabled' : 'Disabled'} "${alias}"`));
 }

package/dist/commands/resource-view.d.ts

@@ -18,6 +18,7 @@ export interface ResourceRow {
     name: string;
     description?: string;
     extra?: string;
+    extra2?: string;
     targets: SyncTarget[];
     buildDetail: () => string;
 }
@@ -25,6 +26,7 @@ export interface ResourceViewOptions {
     resourcePlural: string;
     resourceSingular: string;
     extraLabel?: string;
+    extra2Label?: string;
     rows: ResourceRow[];
     emptyMessage: string;
     centralPath?: string;

package/dist/commands/resource-view.js

@@ -68,10 +68,13 @@ function formatPickerRow(row, opts) {
     const extra = opts.extraLabel
         ? chalk.gray(padRight(row.extra ?? '-', 10))
         : '';
+    const extra2 = opts.extra2Label
+        ? chalk.gray(padRight(row.extra2 ?? '-', 16))
+        : '';
     const descRaw = row.description ? truncate(row.description, 40) : '';
     const desc = padRight(chalk.gray(descRaw), 42);
     const sync = formatSyncSummary(row.targets, opts);
-    return `${name} ${extra}${desc} ${sync}`;
+    return `${name} ${extra}${extra2}${desc} ${sync}`;
 }
 /** Render resources as a plain-text table (used when output is piped). */
 function printResourceTable(opts) {
@@ -83,10 +86,13 @@ function printResourceTable(opts) {
         const extra = opts.extraLabel
             ? padRight(row.extra ?? '-', 10)
             : '';
+        const extra2 = opts.extra2Label
+            ? padRight(row.extra2 ?? '-', 16)
+            : '';
         const descRaw = row.description ? truncate(row.description, 40) : '-';
         const desc = padRight(chalk.gray(descRaw), 42);
         const sync = formatSyncSummary(row.targets, opts);
-        console.log(`${name} ${extra}${desc} ${sync}`);
+        console.log(`${name} ${extra}${extra2}${desc} ${sync}`);
     }
     console.log();
     const summary = [
@@ -103,9 +109,12 @@ function buildTableHeader(opts) {
     const extra = opts.extraLabel
         ? chalk.bold(padRight(opts.extraLabel, 10))
         : '';
+    const extra2 = opts.extra2Label
+        ? chalk.bold(padRight(opts.extra2Label, 16))
+        : '';
     const desc = padRight(chalk.bold('Description'), 42);
     const sync = chalk.bold('Synced');
-    return `${name} ${extra}${desc} ${sync}`;
+    return `${name} ${extra}${extra2}${desc} ${sync}`;
 }
 /** Compact sync summary: "everywhere", "14 of 16 installs", or "not installed". */
 function formatSyncSummary(targets, opts) {

package/dist/commands/routines.js

@@ -43,9 +43,19 @@ function isPromptCancelled(err) {
             err.name === 'ExitPromptError' ||
             err.code === 'ERR_USE_AFTER_CLOSE'));
 }
-/** Interactive job picker. Returns the selected job name or null on cancel/empty. */
-async function pickJob(message, filter, alternatives = []) {
-    let jobs = listAllJobs();
+/**
+ * Interactive job picker. Returns the selected job name or null on cancel/empty.
+ *
+ * `cwd` is opt-in: pass `process.cwd()` only for inspect-class commands
+ * (`view`) whose backing operation tolerates project-layer entries. Mutation
+ * (`remove`/`edit`/`pause`/`resume`) and execution (`run`) callers omit it,
+ * which limits the picker — and therefore the user — to user-layer routines
+ * only. Without that guard, a cloned public repo's `.agents/routines/<name>.yml`
+ * would surface in `agents routines run`'s picker and execute with an
+ * attacker-supplied prompt under the user's Claude session.
+ */
+async function pickJob(message, filter, alternatives = [], cwd) {
+    let jobs = listAllJobs(cwd);
     if (filter) {
         jobs = jobs.filter(filter);
     }
@@ -114,7 +124,7 @@ export function registerRoutinesCommands(program) {
         .command('list')
         .description('See all scheduled jobs, when they run next, and their last execution status')
         .action(() => {
-        const jobs = listAllJobs();
+        const jobs = listAllJobs(process.cwd());
         if (jobs.length === 0) {
             console.log(chalk.gray('No jobs configured'));
             console.log(chalk.gray('  Add a job: agents routines add <path-to-job.yml>'));
@@ -149,7 +159,14 @@ export function registerRoutinesCommands(program) {
         for (const job of jobs) {
             const nextRun = scheduler.getNextRun(job.name);
             const nextStr = humanizeNextRun(nextRun ?? null, now, job.timezone);
-            const schedStr = humanizeCron(job.schedule, job.timezone);
+            let schedStr = humanizeCron(job.schedule, job.timezone);
+            if (job.endAt) {
+                const end = new Date(job.endAt);
+                const endLabel = Number.isFinite(end.getTime())
+                    ? end.toLocaleDateString()
+                    : job.endAt;
+                schedStr = `${schedStr} (until ${endLabel})`;
+            }
             const latestRun = getLatestRun(job.name);
             const lastStatus = latestRun?.status || '-';
             const repoInfo = formatRepoLink(job.repo);
@@ -189,6 +206,7 @@ export function registerRoutinesCommands(program) {
         .option('-t, --timeout <timeout>', 'Kill the agent if it runs longer than this (e.g., 10m, 2h, 3d, 1w; max 1w)', '10m')
         .option('--timezone <tz>', 'Interpret schedule in this timezone (e.g., America/Los_Angeles)')
         .option('--at <time>', 'One-shot mode: run once at this time (e.g., "14:30" or "2026-02-24 09:00"), then disable')
+        .option('--end-at <iso>', 'Stop firing on or after this ISO 8601 timestamp (e.g., "2026-12-31T23:59:00Z"); routine auto-disables.')
         .option('--disabled', 'Create the routine but keep it paused (enable later with resume)')
         .action(async (nameOrPath, options) => {
         // Check if inline mode (has flags) or file mode
@@ -242,6 +260,7 @@ export function registerRoutinesCommands(program) {
                 prompt: options.prompt,
                 timezone: options.timezone,
                 ...(runOnce ? { runOnce: true } : {}),
+                ...(options.endAt ? { endAt: options.endAt } : {}),
             };
             const errors = validateJob(config);
             if (errors.length > 0) {
@@ -329,11 +348,11 @@ export function registerRoutinesCommands(program) {
         .description('Show the full YAML configuration for a routine')
         .action(async (name) => {
         if (!name) {
-            name = await pickJob('Select job to view', undefined, ['agents routines view <name>']) ?? undefined;
+            name = await pickJob('Select job to view', undefined, ['agents routines view <name>'], process.cwd()) ?? undefined;
             if (!name)
                 return;
         }
-        const job = readJob(name);
+        const job = readJob(name, process.cwd());
         if (!job) {
             console.log(chalk.red(`Job '${name}' not found`));
             process.exit(1);
@@ -430,6 +449,12 @@ export function registerRoutinesCommands(program) {
             if (!name)
                 return;
         }
+        // Execution is intentionally user-only: a routine spawns a full agent
+        // session with a YAML-supplied prompt, so a cloned public repo's
+        // `.agents/routines/<name>.yml` would be a prompt-injection vector if
+        // `run` honored the project layer. `list` / `view` stay project-aware
+        // for inspection; `run`, `remove`, `edit`, `pause`, `resume` stay on
+        // the trusted user layer.
         const job = readJob(name);
         if (!job) {
             console.log(chalk.red(`Job '${name}' not found`));

package/dist/commands/rules.js

@@ -556,7 +556,7 @@ Examples:
             }
             const presets = Array.from(presetSet).sort();
             if (presets.length === 0) {
-                console.log(chalk.red('No presets found. Define presets in ~/.agents-system/rules/rules.yaml or ~/.agents/rules/rules.yaml.'));
+                console.log(chalk.red('No presets found. Define presets in ~/.agents/.system/rules/rules.yaml or ~/.agents/rules/rules.yaml.'));
                 process.exit(1);
             }
             let chosen = options.preset;

package/dist/commands/sessions.js

@@ -738,6 +738,7 @@ export function buildResumeCommand(session) {
         case 'rush':
         case 'hermes':
         case 'grok':
+        case 'kimi':
             // Grok (and some others) sessions are captured artifacts, not resumable the same way.
             return null;
     }

package/dist/commands/setup.d.ts

@@ -2,10 +2,10 @@
  * First-run setup command.
  *
  * Registers the `agents setup` command which clones the system repo into
- * ~/.agents-system/ and installs agent CLIs with resource syncing.
+ * ~/.agents/.system/ and installs agent CLIs with resource syncing.
  */
 import type { Command } from 'commander';
-/** First-run setup. Clones ~/.agents-system/ from the system repo if needed. */
+/** First-run setup. Clones ~/.agents/.system/ from the system repo if needed. */
 export declare function runSetup(program: Command, options?: {
     force?: boolean;
     suppressFooter?: boolean;
@@ -13,7 +13,7 @@ export declare function runSetup(program: Command, options?: {
 }): Promise<void>;
 /**
  * Ensure the system repo exists before running a command that needs it.
- * If ~/.agents-system/ is not a git repo AND we're in an interactive TTY,
+ * If ~/.agents/.system/ is not a git repo AND we're in an interactive TTY,
  * prompt the user to run setup now. In non-interactive mode, print a clear
  * error and exit.
  */

package/dist/commands/setup.js

@@ -2,7 +2,7 @@
  * First-run setup command.
  *
  * Registers the `agents setup` command which clones the system repo into
- * ~/.agents-system/ and installs agent CLIs with resource syncing.
+ * ~/.agents/.system/ and installs agent CLIs with resource syncing.
  */
 import chalk from 'chalk';
 import ora from 'ora';
@@ -52,12 +52,12 @@ async function importAgent(agentId, version) {
         return { success: false, error: err.message };
     }
 }
-/** First-run setup. Clones ~/.agents-system/ from the system repo if needed. */
+/** First-run setup. Clones ~/.agents/.system/ from the system repo if needed. */
 export async function runSetup(program, options = {}) {
     const agentsDir = getAgentsDir();
     const alreadyConfigured = isGitRepo(agentsDir);
     if (alreadyConfigured && !options.force) {
-        console.log(chalk.gray('~/.agents-system/ is already set up.'));
+        console.log(chalk.gray('~/.agents/.system/ is already set up.'));
         console.log(chalk.gray('\nTo sync updates:      agents repo pull system'));
         console.log(chalk.gray('To re-run setup:      agents setup --force'));
         return;
@@ -73,10 +73,10 @@ export async function runSetup(program, options = {}) {
     if (options.systemRepo === false) {
         ensureAgentsDir();
         console.log(chalk.gray('Skipping system repo clone (--no-system-repo).'));
-        console.log(chalk.gray(`Populate ~/.agents-system/ yourself before running other commands that depend on it.\n`));
+        console.log(chalk.gray(`Populate ~/.agents/.system/ yourself before running other commands that depend on it.\n`));
     }
     else {
-        console.log(chalk.gray(`Cloning the system repo from ${systemRepoSlug(systemRepo)} into ~/.agents-system/.\n`));
+        console.log(chalk.gray(`Cloning the system repo from ${systemRepoSlug(systemRepo)} into ~/.agents/.system/.\n`));
         ensureAgentsDir();
         const spinner = ora('Cloning system repo...').start();
         if (isGitRepo(agentsDir)) {
@@ -93,7 +93,7 @@ export async function runSetup(program, options = {}) {
             // Check git is available
             try {
                 const { execSync } = await import('child_process');
-                execSync('which git', { stdio: 'ignore' });
+                execSync('git --version', { stdio: 'ignore' });
             }
             catch {
                 spinner.fail('git is not installed');
@@ -175,7 +175,7 @@ export async function runSetup(program, options = {}) {
 }
 /**
  * Ensure the system repo exists before running a command that needs it.
- * If ~/.agents-system/ is not a git repo AND we're in an interactive TTY,
+ * If ~/.agents/.system/ is not a git repo AND we're in an interactive TTY,
  * prompt the user to run setup now. In non-interactive mode, print a clear
  * error and exit.
  */
@@ -203,23 +203,23 @@ export function registerSetupCommand(program) {
     const setupCmd = program
         .command('setup')
         .description('First-time setup. Clones a config repo and installs agent CLIs.')
-        .option('-f, --force', 'Re-run setup even if ~/.agents-system/ already exists (use with caution)')
-        .option('--no-system-repo', 'Skip cloning the system repo (you must populate ~/.agents-system/ yourself)');
+        .option('-f, --force', 'Re-run setup even if ~/.agents/.system/ already exists (use with caution)')
+        .option('--no-system-repo', 'Skip cloning the system repo (you must populate ~/.agents/.system/ yourself)');
     setHelpSections(setupCmd, {
         examples: `
-      # First-time setup (clones the system repo into ~/.agents-system/)
+      # First-time setup (clones the system repo into ~/.agents/.system/)
       agents setup
 
-      # Re-run after corruption or to repair ~/.agents-system/
+      # Re-run after corruption or to repair ~/.agents/.system/
       agents setup --force
     `,
         notes: `
       What it does:
-        1. Clones the system repo into ~/.agents-system/
-        2. Installs agent CLIs based on agents.yaml in that repo
-        3. Syncs commands, skills, hooks, and MCP servers to each version
+        1. Clones the system repo into ~/.agents/.system/
+        2. Imports any unmanaged agent installations it finds
 
-      Non-interactive alternative: agents pull
+      To install CLIs from agents.yaml and sync resources into version homes:
+        agents repo refresh -y
     `,
     });
     setupCmd.action(async (options) => {

package/dist/commands/skills.js

@@ -4,7 +4,8 @@ import * as fs from 'fs';
 import * as os from 'os';
 import * as path from 'path';
 import { select, checkbox } from '@inquirer/prompts';
-import { AGENTS, SKILLS_CAPABLE_AGENTS, resolveAgentName, formatAgentError, agentLabel, } from '../lib/agents.js';
+import { AGENTS, resolveAgentName, formatAgentError, agentLabel, } from '../lib/agents.js';
+import { capableAgents } from '../lib/capabilities.js';
 import { cloneRepo } from '../lib/git.js';
 import { discoverSkillsFromRepo, installSkillCentrally, listInstalledSkills, listInstalledSkillsWithScope, getSkillInfo, getSkillRules, getSkillsDir, countSkillFiles, tryParseSkillMetadata, diffVersionSkills, iterSkillsCapableVersions, removeSkillFromVersion, } from '../lib/skills.js';
 import { getGlobalDefault, resolveVersionAlias, syncResourcesToVersion, promptAgentVersionSelection, getVersionHomePath, } from '../lib/versions.js';
@@ -54,7 +55,7 @@ When to use:
             const resolved = resolveAgentName(parts[0]);
             if (!resolved) {
                 spinner.stop();
-                console.log(chalk.red(formatAgentError(parts[0], SKILLS_CAPABLE_AGENTS)));
+                console.log(chalk.red(formatAgentError(parts[0], capableAgents('skills'))));
                 process.exit(1);
             }
             filterAgent = resolved;
@@ -251,7 +252,7 @@ Examples:
             let selectedAgents;
             let versionSelections;
             if (options.agents) {
-                const result = await resolveAgentTargetsAutoInstalling(options.agents, SKILLS_CAPABLE_AGENTS, { yes: options.yes });
+                const result = await resolveAgentTargetsAutoInstalling(options.agents, capableAgents('skills'), { yes: options.yes });
                 if (!result) {
                     console.log(chalk.gray('Cancelled.'));
                     return;
@@ -260,7 +261,7 @@ Examples:
                 versionSelections = result.versionSelections;
             }
             else {
-                const result = await promptAgentVersionSelection(SKILLS_CAPABLE_AGENTS, {
+                const result = await promptAgentVersionSelection(capableAgents('skills'), {
                     skipPrompts: options.yes,
                 });
                 selectedAgents = result.selectedAgents;
@@ -441,7 +442,7 @@ Examples:
             const cwd = process.cwd();
             const allSkills = [];
             const seenNames = new Set();
-            for (const agentId of SKILLS_CAPABLE_AGENTS) {
+            for (const agentId of capableAgents('skills')) {
                 const skills = listInstalledSkillsWithScope(agentId, cwd);
                 for (const skill of skills) {
                     if (!seenNames.has(skill.name)) {