@phnx-labs/agents-cli 1.20.58 → 1.20.60

package/dist/lib/routines.js

@@ -187,7 +187,52 @@ export function writeJob(config) {
     const devArr = output.devices;
     if (!devArr || devArr.length === 0)
         delete output.devices;
-    atomicWriteFileSync(filePath, yaml.stringify(output));
+    let existingText = null;
+    if (ymlExists || yamlExists) {
+        try {
+            existingText = fs.readFileSync(filePath, 'utf-8');
+        }
+        catch {
+            existingText = null;
+        }
+    }
+    atomicWriteFileSync(filePath, serializeJob(output, existingText));
+}
+/**
+ * Serialize a job config, preserving the on-disk formatting of an existing file.
+ *
+ * A full `yaml.stringify(config)` re-emits the whole document — restyling every
+ * scalar (unquoting `schedule`, re-wrapping the folded `prompt` block, reordering
+ * keys). When a routine is only being toggled (pause/resume) or re-pinned
+ * (`devices --set`), that rewrites the entire file, leaving the git-backed
+ * `~/.agents` tree perpetually dirty so `agents repo pull` refuses to sync across
+ * the fleet. To keep the diff to the field that actually changed, we edit the
+ * existing document in place and only re-render touched nodes; untouched nodes
+ * (notably the large `prompt` block) keep their byte-for-byte formatting.
+ *
+ * `existingText` is the current file contents, or null for a new file. New,
+ * unparseable, and non-mapping documents fall back to canonical `yaml.stringify`.
+ */
+export function serializeJob(output, existingText) {
+    if (existingText == null)
+        return yaml.stringify(output);
+    const doc = yaml.parseDocument(existingText);
+    if (doc.errors.length > 0 || !yaml.isMap(doc.contents))
+        return yaml.stringify(output);
+    const existing = (doc.toJS() ?? {});
+    // Update or add only the keys that actually changed; leave the rest untouched
+    // so their original formatting is preserved.
+    for (const [key, value] of Object.entries(output)) {
+        if (JSON.stringify(existing[key]) !== JSON.stringify(value))
+            doc.set(key, value);
+    }
+    // Drop keys that no longer belong (e.g. an omitted default, or `devices`
+    // cleared back to fleet-wide).
+    for (const key of Object.keys(existing)) {
+        if (!(key in output))
+            doc.delete(key);
+    }
+    return doc.toString();
 }
 /** Delete a job config file by name. Returns true if the file existed. */
 export function deleteJob(name) {

package/dist/lib/secrets/remote.d.ts

@@ -50,6 +50,7 @@ export declare function splitBundleRef(ref: string): {
 export declare function remoteSecretsRaw(target: string, args: string[], opts?: {
     tty?: boolean;
     input?: string;
+    osLookupName?: string;
 }): SshExecResult;
 /**
  * Run a remote `agents secrets <args>` FOREGROUND, with the local stdio wired
@@ -64,7 +65,9 @@ export declare function remoteSecretsRaw(target: string, args: string[], opts?:
  * bundle's passphrase at your own terminal. Output is NOT captured (it streams
  * to the terminal); only the exit code is returned.
  */
-export declare function remoteSecretsStream(target: string, args: string[]): number;
+export declare function remoteSecretsStream(target: string, args: string[], opts?: {
+    osLookupName?: string;
+}): number;
 /**
  * Resolve a remote bundle to a plaintext env map by driving the remote's
  * `agents secrets export <bundle> --plaintext --format json`. Values cross over
@@ -78,4 +81,6 @@ export declare function remoteSecretsStream(target: string, args: string[]): num
  * SSH will block on Touch-ID — use `view`/`exec` with a remote `file` bundle,
  * an already-unlocked remote secrets-agent, or an interactive `-tt` session.)
  */
-export declare function remoteResolveEnv(target: string, bundle: string): Promise<Record<string, string>>;
+export declare function remoteResolveEnv(target: string, bundle: string, opts?: {
+    osLookupName?: string;
+}): Promise<Record<string, string>>;

package/dist/lib/secrets/remote.js

@@ -22,11 +22,12 @@ import { sshTargetFor } from '../hosts/types.js';
 import { buildRemoteAgentsInvocation } from '../hosts/remote-cmd.js';
 import { resolveRemoteOsSync } from '../hosts/remote-os.js';
 const REMOTE_TIMEOUT_MS = 30_000;
-/** Remote OS for a target string (bare alias matches a device entry; a raw
- * `user@host` falls back to POSIX). Threaded into the command builder so a
- * Windows host gets PowerShell instead of `bash -lc`. */
-function osForTarget(target) {
-    return resolveRemoteOsSync(target.split('@').pop() ?? target);
+/** Remote OS for a host name or target string. Prefer the original host name
+ * because enrolled inline hosts resolve to `user@address`, while the OS
+ * registry is keyed by the host name. */
+function osForTarget(target, lookupName) {
+    const byName = lookupName ? resolveRemoteOsSync(lookupName) : undefined;
+    return byName ?? resolveRemoteOsSync(target.split('@').pop() ?? target);
 }
 /**
  * Resolve a `--host` value to an ssh target string. Tries the `agents hosts`
@@ -86,7 +87,7 @@ export function splitBundleRef(ref) {
  * remote Touch-ID / passphrase prompt can surface (e.g. `view --reveal`).
  */
 export function remoteSecretsRaw(target, args, opts = {}) {
-    const remoteCmd = buildRemoteAgentsInvocation(['secrets', ...args], undefined, osForTarget(target));
+    const remoteCmd = buildRemoteAgentsInvocation(['secrets', ...args], undefined, osForTarget(target, opts.osLookupName));
     return sshExec(target, remoteCmd, {
         timeoutMs: REMOTE_TIMEOUT_MS,
         input: opts.input,
@@ -107,8 +108,8 @@ export function remoteSecretsRaw(target, args, opts = {}) {
  * bundle's passphrase at your own terminal. Output is NOT captured (it streams
  * to the terminal); only the exit code is returned.
  */
-export function remoteSecretsStream(target, args) {
-    const remoteCmd = buildRemoteAgentsInvocation(['secrets', ...args], undefined, osForTarget(target));
+export function remoteSecretsStream(target, args, opts = {}) {
+    const remoteCmd = buildRemoteAgentsInvocation(['secrets', ...args], undefined, osForTarget(target, opts.osLookupName));
     return sshStream(target, remoteCmd, { tty: true });
 }
 /**
@@ -124,9 +125,9 @@ export function remoteSecretsStream(target, args) {
  * SSH will block on Touch-ID — use `view`/`exec` with a remote `file` bundle,
  * an already-unlocked remote secrets-agent, or an interactive `-tt` session.)
  */
-export async function remoteResolveEnv(target, bundle) {
+export async function remoteResolveEnv(target, bundle, opts = {}) {
     assertValidSshTarget(target);
-    const remoteCmd = buildRemoteAgentsInvocation(['secrets', 'export', bundle, '--plaintext', '--format', 'json'], undefined, osForTarget(target));
+    const remoteCmd = buildRemoteAgentsInvocation(['secrets', 'export', bundle, '--plaintext', '--format', 'json'], undefined, osForTarget(target, opts.osLookupName));
     const res = sshExec(target, remoteCmd, {
         timeoutMs: REMOTE_TIMEOUT_MS,
     });

package/dist/lib/session/db.d.ts

@@ -24,6 +24,7 @@ export interface SessionRow {
     label: string | null;
     message_count: number | null;
     token_count: number | null;
+    output_tokens: number | null;
     cost_usd: number | null;
     duration_ms: number | null;
     file_path: string;
@@ -184,6 +185,8 @@ export interface UsageRollupRow {
     durationMs: number;
     sessionCount: number;
     tokenCount: number;
+    /** Real generated (output) tokens — excludes cache-read/-write context. */
+    outputTokens: number;
 }
 /** What to group a usage rollup by. */
 export type UsageRollupGroup = 'agent' | 'project' | 'day';

package/dist/lib/session/db.js

@@ -13,7 +13,7 @@ import { getSessionsDir, getSessionsDbPath } from '../state.js';
 const SESSIONS_DIR = getSessionsDir();
 const DB_PATH = getSessionsDbPath();
 /** Current schema version; bumped when migrations are added. */
-const SCHEMA_VERSION = 11;
+const SCHEMA_VERSION = 12;
 /**
  * Canonicalize a file path for use as a scan_ledger key. The same physical
  * session file is reachable via multiple aliases — `~/.claude/projects/x.jsonl`
@@ -54,6 +54,7 @@ CREATE TABLE IF NOT EXISTS sessions (
   label TEXT,
   message_count INTEGER,
   token_count INTEGER,
+  output_tokens INTEGER,
   cost_usd REAL,
   duration_ms INTEGER,
   file_path TEXT NOT NULL,
@@ -224,6 +225,16 @@ function migrateSchema(db, fromVersion) {
             db.exec(`ALTER TABLE sessions ADD COLUMN plan TEXT`);
         db.exec(`DELETE FROM scan_ledger;`);
     }
+    if (fromVersion < 12) {
+        // v11 → v12: `output_tokens` — the real generated-token count, kept separate
+        // from `token_count` (which sums cache-read/-write and so is dominated by
+        // cheap re-counted context). This is the honest "output" metric powering
+        // `agents output`. Additive column; rescan to backfill from transcripts.
+        const cols = db.prepare(`PRAGMA table_info(sessions)`).all();
+        if (!cols.some(c => c.name === 'output_tokens'))
+            db.exec(`ALTER TABLE sessions ADD COLUMN output_tokens INTEGER`);
+        db.exec(`DELETE FROM scan_ledger;`);
+    }
 }
 /** Open (or return the cached) sessions database, applying migrations as needed. */
 export function getDB() {
@@ -438,13 +449,13 @@ const upsertSessionStmt = (db) => db.prepare(`
   INSERT INTO sessions (
     id, short_id, agent, version, account, timestamp, last_activity,
     project, cwd, git_branch, topic, label, message_count, token_count,
-    cost_usd, duration_ms,
+    output_tokens, cost_usd, duration_ms,
     file_path, file_mtime_ms, file_size, scanned_at, is_team_origin,
     pr_url, pr_number, worktree_slug, ticket_id, plan
   ) VALUES (
     @id, @short_id, @agent, @version, @account, @timestamp, @last_activity,
     @project, @cwd, @git_branch, @topic, @label, @message_count, @token_count,
-    @cost_usd, @duration_ms,
+    @output_tokens, @cost_usd, @duration_ms,
     @file_path, @file_mtime_ms, @file_size, @scanned_at, @is_team_origin,
     @pr_url, @pr_number, @worktree_slug, @ticket_id, @plan
   )
@@ -462,6 +473,7 @@ const upsertSessionStmt = (db) => db.prepare(`
     label = excluded.label,
     message_count = excluded.message_count,
     token_count = excluded.token_count,
+    output_tokens = excluded.output_tokens,
     cost_usd = excluded.cost_usd,
     duration_ms = excluded.duration_ms,
     file_path = excluded.file_path,
@@ -510,6 +522,7 @@ export function upsertSession(meta, content, scan) {
         label: meta.label ?? null,
         message_count: meta.messageCount ?? null,
         token_count: meta.tokenCount ?? null,
+        output_tokens: meta.outputTokens ?? null,
         cost_usd: meta.costUsd ?? null,
         duration_ms: meta.durationMs ?? null,
         file_path: meta.filePath,
@@ -599,6 +612,7 @@ export function upsertSessionsBatch(entries) {
                     label: meta.label ?? null,
                     message_count: meta.messageCount ?? null,
                     token_count: meta.tokenCount ?? null,
+                    output_tokens: meta.outputTokens ?? null,
                     cost_usd: meta.costUsd ?? null,
                     duration_ms: meta.durationMs ?? null,
                     file_path: meta.filePath,
@@ -772,6 +786,7 @@ function rowToMeta(row) {
         gitBranch: row.git_branch ?? undefined,
         messageCount: row.message_count ?? undefined,
         tokenCount: row.token_count ?? undefined,
+        outputTokens: row.output_tokens ?? undefined,
         costUsd: row.cost_usd ?? undefined,
         durationMs: row.duration_ms ?? undefined,
         version: row.version ?? undefined,
@@ -956,7 +971,8 @@ export function queryUsageRollup(options) {
       IFNULL(SUM(cost_usd), 0) AS costUsd,
       IFNULL(SUM(duration_ms), 0) AS durationMs,
       COUNT(*) AS sessionCount,
-      IFNULL(SUM(token_count), 0) AS tokenCount
+      IFNULL(SUM(token_count), 0) AS tokenCount,
+      IFNULL(SUM(output_tokens), 0) AS outputTokens
     FROM sessions
     ${clause}
     GROUP BY key

package/dist/lib/session/discover.d.ts

@@ -46,6 +46,8 @@ interface ClaudeSessionScan {
     topic?: string;
     messageCount: number;
     tokenCount?: number;
+    /** Real generated (output) tokens, excluding cache-read/-write context. */
+    outputTokens?: number;
     /** Total USD cost accumulated from per-(model, direction) token usage. */
     costUsd?: number;
     /** Wall-clock duration in ms between the first and last timestamped event. */

package/dist/lib/session/discover.js

@@ -508,6 +508,7 @@ async function readClaudeMeta(filePath, sessionId, account, label) {
             label,
             messageCount: scan.messageCount,
             tokenCount: scan.tokenCount,
+            outputTokens: scan.outputTokens,
             costUsd: scan.costUsd,
             durationMs: scan.durationMs,
             isTeamOrigin,
@@ -533,6 +534,7 @@ async function readClaudeMeta(filePath, sessionId, account, label) {
             label,
             messageCount: scan.messageCount,
             tokenCount: scan.tokenCount,
+            outputTokens: scan.outputTokens,
             costUsd: scan.costUsd,
             durationMs: scan.durationMs,
             topic: scan.topic,
@@ -748,6 +750,7 @@ export async function readCodexMeta(filePath, resolveAccount, currentVersion) {
         topic: scan.topic,
         messageCount: scan.messageCount,
         tokenCount: scan.tokenCount,
+        outputTokens: scan.outputTokens,
         costUsd: scan.costUsd,
         durationMs: scan.durationMs,
         account: resolveAccount?.(),
@@ -873,6 +876,7 @@ function readGeminiMeta(filePath, hashDir, projectMap, currentVersion) {
     let topic;
     let messageCount = 0;
     let tokenCount = 0;
+    let outputTokens = 0;
     let sawTokenCount = false;
     let costUsd = 0;
     let sawCost = false;
@@ -910,6 +914,16 @@ function readGeminiMeta(filePath, hashDir, projectMap, currentVersion) {
             tokenCount += total;
             sawTokenCount = true;
         }
+        // Output tokens: sum directional generation fields per message (output +
+        // thoughts + tool), mirroring the cost path — never `tokens.total`, which
+        // may be cumulative and would double-count when summed.
+        const gtk = message.tokens;
+        if (gtk && typeof gtk === 'object') {
+            outputTokens +=
+                (typeof gtk.output === 'number' ? gtk.output : 0) +
+                    (typeof gtk.thoughts === 'number' ? gtk.thoughts : 0) +
+                    (typeof gtk.tool === 'number' ? gtk.tool : 0);
+        }
         // Per-message cost: directional tokens × this message's model price.
         const msgModel = (typeof message.model === 'string' ? message.model : undefined) || sessionModel;
         const tk = message.tokens;
@@ -944,6 +958,7 @@ function readGeminiMeta(filePath, hashDir, projectMap, currentVersion) {
         topic,
         messageCount,
         tokenCount: sawTokenCount ? tokenCount : undefined,
+        outputTokens: sawTokenCount ? outputTokens : undefined,
         costUsd: sawCost ? costUsd : undefined,
         durationMs,
     };
@@ -1158,6 +1173,7 @@ async function scanOpenCodeIncremental() {
         s.time_updated AS time_updated,
         COALESCE(stats.message_count, 0) AS message_count,
         stats.token_count AS token_count,
+        stats.output_tokens AS output_tokens,
         COALESCE(stats.has_token_data, 0) AS has_token_data
       FROM session s
       LEFT JOIN (
@@ -1171,6 +1187,7 @@ async function scanOpenCodeIncremental() {
             COALESCE(json_extract(data, '$.tokens.cache.read'), 0) +
             COALESCE(json_extract(data, '$.tokens.cache.write'), 0)
           ) AS token_count,
+          SUM(COALESCE(json_extract(data, '$.tokens.output'), 0)) AS output_tokens,
           MAX(CASE WHEN json_type(data, '$.tokens') IS NOT NULL THEN 1 ELSE 0 END) AS has_token_data
         FROM message
         GROUP BY session_id
@@ -1194,6 +1211,7 @@ async function scanOpenCodeIncremental() {
             const timeUpdated = asInt(row.time_updated);
             const messageCount = asInt(row.message_count);
             const tokenCount = asInt(row.token_count);
+            const outputTokens = asInt(row.output_tokens);
             const hasTokenData = asInt(row.has_token_data) === 1;
             const timestamp = isNaN(timeCreated) ? new Date().toISOString() : new Date(timeCreated).toISOString();
             // OpenCode is one shared DB, not one file per session — its row carries a
@@ -1215,6 +1233,7 @@ async function scanOpenCodeIncremental() {
                 topic,
                 messageCount: Number.isNaN(messageCount) ? undefined : messageCount,
                 tokenCount: hasTokenData && !Number.isNaN(tokenCount) ? tokenCount : undefined,
+                outputTokens: hasTokenData && !Number.isNaN(outputTokens) ? outputTokens : undefined,
             };
             entries.push({ meta, content: topic || '', scan: currentScan });
         }
@@ -1653,6 +1672,7 @@ async function readDroidMeta(filePath, currentVersion) {
         topic: scan.topic,
         messageCount: scan.messageCount,
         tokenCount,
+        outputTokens: settings.usage?.outputTokens,
         costUsd: costUsd > 0 ? costUsd : undefined,
         durationMs: scan.durationMs,
     };
@@ -1801,6 +1821,7 @@ export async function scanClaudeSession(filePath) {
     let entrypoint;
     let messageCount = 0;
     let tokenCount = 0;
+    let outputTokens = 0;
     let sawTokenCount = false;
     let costUsd = 0;
     let sawCost = false;
@@ -1961,6 +1982,8 @@ export async function scanClaudeSession(filePath) {
                 tokenCount += usage;
                 sawTokenCount = true;
             }
+            if (typeof usageObj?.output_tokens === 'number')
+                outputTokens += usageObj.output_tokens;
             // Per-assistant-message cost: each event carries its own model, so we
             // multiply that event's raw token directions by that model's price.
             const model = parsed.message?.model;
@@ -2000,6 +2023,7 @@ export async function scanClaudeSession(filePath) {
         entrypoint,
         messageCount,
         tokenCount: sawTokenCount ? tokenCount : undefined,
+        outputTokens: sawTokenCount ? outputTokens : undefined,
         costUsd: sawCost ? costUsd : undefined,
         durationMs,
         lastActivity: lastTsMs !== undefined ? new Date(lastTsMs).toISOString() : undefined,
@@ -2167,6 +2191,9 @@ async function scanCodexSession(filePath) {
         topic,
         messageCount,
         tokenCount,
+        outputTokens: lastTotalTokenUsage
+            ? (lastTotalTokenUsage.output_tokens ?? 0) + (lastTotalTokenUsage.reasoning_output_tokens ?? 0)
+            : undefined,
         costUsd,
         durationMs,
         lastActivity: lastTsMs !== undefined ? new Date(lastTsMs).toISOString() : undefined,
@@ -2500,7 +2527,7 @@ export function readKimiMeta(filePath) {
         }
     }
     // Parse wire.jsonl to extract message count and token usage
-    const { messageCount, tokenCount } = parseKimiWireMetrics(sessionDir);
+    const { messageCount, tokenCount, outputTokens } = parseKimiWireMetrics(sessionDir);
     const meta = {
         id: sessionId,
         shortId,
@@ -2511,6 +2538,7 @@ export function readKimiMeta(filePath) {
         topic,
         messageCount,
         tokenCount: tokenCount > 0 ? tokenCount : undefined,
+        outputTokens: outputTokens > 0 ? outputTokens : undefined,
     };
     return { meta, content: lastPrompt || '' };
 }
@@ -2522,8 +2550,9 @@ function parseKimiWireMetrics(sessionDir) {
     const wirePath = path.join(sessionDir, 'agents', 'main', 'wire.jsonl');
     let messageCount = 0;
     let tokenCount = 0;
+    let outputTokens = 0;
     if (!fs.existsSync(wirePath)) {
-        return { messageCount: 0, tokenCount: 0 };
+        return { messageCount: 0, tokenCount: 0, outputTokens: 0 };
     }
     try {
         const lines = fs.readFileSync(wirePath, 'utf-8').split('\n');
@@ -2539,6 +2568,7 @@ function parseKimiWireMetrics(sessionDir) {
                     // Kimi usage structure: inputOther + output + inputCacheRead + inputCacheCreation
                     const u = event.usage;
                     tokenCount += (u.inputOther || 0) + (u.output || 0) + (u.inputCacheRead || 0) + (u.inputCacheCreation || 0);
+                    outputTokens += (u.output || 0);
                 }
             }
             catch {
@@ -2549,11 +2579,13 @@ function parseKimiWireMetrics(sessionDir) {
     catch {
         // If wire.jsonl can't be read, return 0s (graceful degradation)
     }
-    return { messageCount, tokenCount };
+    return { messageCount, tokenCount, outputTokens };
 }
 /** Parse a time filter string (relative like '7d' or ISO timestamp) into epoch milliseconds. */
 export function parseTimeFilter(input) {
-    const relativeMatch = input.match(/^(\d+)([mhdw])$/i);
+    // Units: m=minute, h=hour, d=day, w=week, mo=month(30d), y=year(365d). `mo`
+    // must precede the single-letter alternatives so "1mo" isn't read as "1m"+"o".
+    const relativeMatch = input.match(/^(\d+)(mo|[mhdwy])$/i);
     if (relativeMatch) {
         const value = parseInt(relativeMatch[1], 10);
         const unit = relativeMatch[2].toLowerCase();
@@ -2565,6 +2597,10 @@ export function parseTimeFilter(input) {
             return Date.now() - value * 86_400_000;
         if (unit === 'w')
             return Date.now() - value * 7 * 86_400_000;
+        if (unit === 'mo')
+            return Date.now() - value * 30 * 86_400_000;
+        if (unit === 'y')
+            return Date.now() - value * 365 * 86_400_000;
     }
     const ts = new Date(input).getTime();
     return Number.isNaN(ts) ? 0 : ts;

package/dist/lib/session/types.d.ts

@@ -66,6 +66,8 @@ export interface SessionMeta {
     gitBranch?: string;
     messageCount?: number;
     tokenCount?: number;
+    /** Real generated (output) tokens — excludes cache-read/-write context (issue: `agents output`). */
+    outputTokens?: number;
     /** Total USD cost, computed at scan time from per-model token usage (issue #323). */
     costUsd?: number;
     /** Wall-clock duration in ms (lastTs − firstTs), persisted at scan time. */

package/dist/lib/shims.js

@@ -2024,18 +2024,28 @@ export function releaseAdoptedLauncher(agent, overrides) {
     // records written before this format existed.
     const launcher = lines[1] || getPathShadowingExecutable(agent) || original;
     const shimReal = canonical(path.join(shimsDir, AGENTS[agent].cliCommand));
+    const shimPath = path.resolve(path.join(shimsDir, AGENTS[agent].cliCommand));
     try {
         // Only rewrite the launcher if it currently points at our shim (i.e. we own
         // it). If the user has since replaced it themselves, leave it alone.
         let pointsAtShim = false;
         try {
-            pointsAtShim = fs.lstatSync(launcher).isSymbolicLink()
-                && canonical(launcher) === shimReal;
+            const stat = fs.lstatSync(launcher);
+            if (stat.isSymbolicLink()) {
+                const target = fs.readlinkSync(launcher);
+                const absoluteTarget = path.resolve(path.dirname(launcher), target);
+                pointsAtShim = canonicalOrNull(launcher) === shimReal || absoluteTarget === shimPath;
+            }
         }
         catch { /* launcher gone — recreate below */ }
         if (pointsAtShim || !fs.existsSync(launcher)) {
             try {
-                fs.rmSync(launcher);
+                if (fs.lstatSync(launcher).isSymbolicLink()) {
+                    fs.unlinkSync(launcher);
+                }
+                else {
+                    fs.rmSync(launcher, { force: true });
+                }
             }
             catch { /* may not exist */ }
             fs.symlinkSync(original, launcher);

package/dist/lib/skills.js

@@ -10,7 +10,7 @@ import * as fs from 'fs';
 import * as path from 'path';
 import * as os from 'os';
 import * as yaml from 'yaml';
-import { ensureSkillsDir, agentConfigDirName } from './agents.js';
+import { AGENTS, ensureSkillsDir, agentConfigDirName } from './agents.js';
 import { capableAgents, isCapable } from './capabilities.js';
 import { getUserSkillsDir, getSkillsDir as getSystemSkillsDir, getProjectAgentsDir, getEnabledExtraRepos, getTrashSkillsDir } from './state.js';
 import { getEffectiveHome, getVersionHomePath, listInstalledVersions } from './versions.js';
@@ -432,6 +432,19 @@ function versionSkillMatches(agent, version, skillName) {
  */
 export function diffVersionSkills(agent, version) {
     const available = new Set(listAllSkills());
+    // Goose and other native ~/.agents/skills consumers read central storage
+    // directly. They intentionally have no per-version copy to diff, so every
+    // available central skill is already current for every supported version.
+    if (AGENTS[agent].nativeAgentsSkillsDir) {
+        return {
+            agent,
+            version,
+            toAdd: [],
+            toUpdate: [],
+            matched: Array.from(available).sort(),
+            orphans: [],
+        };
+    }
     const installed = new Set(listSkillsInVersionHome(agent, version));
     const toAdd = [];
     const toUpdate = [];

package/dist/lib/staleness/detectors/permissions.js

@@ -84,7 +84,7 @@ function buildOpenCodeDetector() {
         kind: 'permissions',
         agent: 'opencode',
         list({ versionHome }) {
-            const opencodeConfigPath = path.join(versionHome, '.opencode', 'opencode.jsonc');
+            const opencodeConfigPath = path.join(versionHome, '.config', 'opencode', 'opencode.jsonc');
             if (!fs.existsSync(opencodeConfigPath))
                 return [];
             try {
@@ -110,8 +110,11 @@ function buildGeminiDetector() {
                 return [];
             try {
                 const settings = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
-                const allowed = settings?.tools?.allowed;
-                if (Array.isArray(allowed) && allowed.length > 0) {
+                const core = settings?.tools?.core;
+                const exclude = settings?.tools?.exclude;
+                const hasCore = Array.isArray(core) && core.length > 0;
+                const hasExclude = Array.isArray(exclude) && exclude.length > 0;
+                if (hasCore || hasExclude) {
                     return discoverPermissionGroups().map(g => g.name);
                 }
             }
@@ -162,6 +165,28 @@ function buildGrokDetector() {
         },
     };
 }
+function buildGooseDetector() {
+    return {
+        kind: 'permissions',
+        agent: 'goose',
+        list({ versionHome }) {
+            const permissionsPath = path.join(versionHome, '.config', 'goose', 'permission.yaml');
+            if (!fs.existsSync(permissionsPath))
+                return [];
+            try {
+                const config = yaml.parse(fs.readFileSync(permissionsPath, 'utf-8'));
+                const user = config?.user;
+                const count = (Array.isArray(user?.always_allow) ? user.always_allow.length : 0) +
+                    (Array.isArray(user?.ask_before) ? user.ask_before.length : 0) +
+                    (Array.isArray(user?.never_allow) ? user.never_allow.length : 0);
+                if (count > 0)
+                    return discoverPermissionGroups().map(g => g.name);
+            }
+            catch { /* parse fail */ }
+            return [];
+        },
+    };
+}
 function buildKimiDetector() {
     return {
         kind: 'permissions',
@@ -202,6 +227,26 @@ function buildCursorDetector() {
         },
     };
 }
+function buildDroidDetector() {
+    return {
+        kind: 'permissions',
+        agent: 'droid',
+        list({ versionHome }) {
+            const settingsPath = path.join(versionHome, '.factory', 'settings.json');
+            if (!fs.existsSync(settingsPath))
+                return [];
+            try {
+                const settings = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
+                const hasAllow = Array.isArray(settings.commandAllowlist) && settings.commandAllowlist.length > 0;
+                const hasDeny = Array.isArray(settings.commandDenylist) && settings.commandDenylist.length > 0;
+                if (hasAllow || hasDeny)
+                    return discoverPermissionGroups().map(g => g.name);
+            }
+            catch { /* parse fail */ }
+            return [];
+        },
+    };
+}
 function buildKiroDetector() {
     return {
         kind: 'permissions',
@@ -228,8 +273,10 @@ const handlers = {
     gemini: buildGeminiDetector,
     antigravity: buildAntigravityDetector,
     grok: buildGrokDetector,
+    goose: buildGooseDetector,
     kimi: buildKimiDetector,
     cursor: buildCursorDetector,
+    droid: buildDroidDetector,
     kiro: buildKiroDetector,
 };
 export const permissionsDetectors = lazyAgentMap(() => {