@mycelish/cli 0.2.7 → 0.3.0

package/dist/commands/remove.js

@@ -1,18 +1,20 @@
 /**
- * Remove command — soft-delete items from mycelium sync.
+ * Remove command — delete items from mycelium sync.
  *
- * mycelium remove <name>              — Find item in manifest, set state: "deleted"
+ * mycelium remove <name>              — Remove item: delete from manifest + purge files/symlinks
  * mycelium remove <name> --type mcp   — Disambiguate when name exists in multiple sections
- * mycelium remove plugin <name>       — Mark all items from that source as deleted
- *
- * After removing, run `mycelium sync` to propagate to tool configs.
+ * mycelium remove <name> --soft       — Only mark as deleted (no file cleanup)
+ * mycelium remove plugin <name>       — Remove all items from a plugin + release takeover
  */
 import { Command } from "commander";
 import * as fs from "node:fs/promises";
 import * as path from "node:path";
-import { expandPath } from "@mycelish/core";
+import * as os from "node:os";
+import { expandPath, TOOL_REGISTRY, resolvePath } from "@mycelish/core";
 import { getTracer } from "../core/global-tracer.js";
+import { MYCELIUM_HOME } from "../core/fs-helpers.js";
 import { loadStateManifest, saveStateManifest, ITEM_SECTIONS, ALL_ITEM_TYPES, sectionForType, } from "../core/manifest-state.js";
+import { setPluginEnabled, syncPluginSymlinks, } from "../core/plugin-takeover.js";
 // ============================================================================
 // Manifest helpers
 // ============================================================================
@@ -53,7 +55,8 @@ function findItemInManifest(manifest, name) {
     return matches;
 }
 /**
- * Remove (soft-delete) an item by setting state: "deleted" in manifest.
+ * Remove an item: mark as deleted in manifest + purge files/symlinks.
+ * Use --soft to skip file cleanup (old behavior).
  */
 export async function removeItem(name, opts) {
     const log = getTracer().createTrace("remove");
@@ -75,6 +78,21 @@ export async function removeItem(name, opts) {
         matches = matches.filter((m) => m.section === section);
     }
     if (matches.length === 0) {
+        // Allow removing filesystem-only items not in manifest
+        if (opts?.type) {
+            const section = typeToSection(opts.type);
+            if (section) {
+                const sectionData = (manifest[section] ?? {});
+                sectionData[name] = { state: "deleted" };
+                manifest[section] = sectionData;
+                await saveStateManifest(manifestDir, manifest);
+                if (!opts?.soft)
+                    await purgeItemFiles(name, opts.type, log);
+                const msg = `${opts.type} '${name}' removed`;
+                log.info({ scope: "manifest", op: "remove", msg, item: name });
+                return { success: true, name, section: opts.type, message: msg };
+            }
+        }
         const error = `'${name}' not found in manifest`;
         log.error({ scope: "manifest", op: "remove", msg: error, item: name, error });
         return { success: false, name, error };
@@ -88,56 +106,242 @@ export async function removeItem(name, opts) {
         };
     }
     const match = matches[0];
+    const itemType = sectionToType(match.section);
+    // Check if item belongs to a taken-over plugin
+    const pluginOrigin = match.config.pluginOrigin;
+    // Mark as deleted
     match.config.state = "deleted";
-    // Write back
     const sectionData = manifest[match.section];
     sectionData[name] = match.config;
+    // If from a plugin, check if ALL components are now deleted → release plugin
+    if (pluginOrigin?.pluginId && manifest.takenOverPlugins) {
+        await releasePluginIfFullyDeleted(manifest, pluginOrigin.pluginId, manifestDir, log);
+    }
     await saveStateManifest(manifestDir, manifest);
-    const msg = `${sectionToType(match.section)} '${name}' marked as deleted`;
+    // Purge files/symlinks (default behavior)
+    if (!opts?.soft) {
+        await purgeItemFiles(name, itemType, log);
+        // Re-sync plugin symlinks to clean up
+        if (pluginOrigin) {
+            await syncPluginSymlinks(manifestDir);
+        }
+    }
+    const action = opts?.soft ? "marked as deleted" : "removed";
+    const msg = `${itemType} '${name}' ${action}`;
     log.info({ scope: "manifest", op: "remove", msg, item: name });
-    return { success: true, name, section: sectionToType(match.section), message: msg };
+    return { success: true, name, section: itemType, message: msg };
 }
 /**
- * Mark all items from a given source as deleted.
+ * Remove all items from a plugin — marks all components as deleted,
+ * releases plugin takeover, and purges files.
  */
-export async function removeBySource(source, opts) {
+export async function removePlugin(pluginName, opts) {
+    const log = getTracer().createTrace("remove");
     const manifestDir = opts?.manifestDir ?? await resolveManifestDir();
     const manifest = await loadStateManifest(manifestDir);
     if (!manifest) {
         return { removed: [], errors: [`Could not load manifest from ${manifestDir}`] };
     }
     const removed = [];
-    for (const { key: section } of ITEM_SECTIONS) {
-        const sectionData = manifest[section];
-        if (!sectionData || typeof sectionData !== "object" || Array.isArray(sectionData))
-            continue;
-        for (const [name, config] of Object.entries(sectionData)) {
-            if (config.source === source) {
-                config.state = "deleted";
-                removed.push(`${sectionToType(section)}: ${name}`);
+    // Find matching plugin in takenOverPlugins
+    let matchedPluginId = null;
+    if (manifest.takenOverPlugins) {
+        for (const pluginId of Object.keys(manifest.takenOverPlugins)) {
+            if (pluginId.startsWith(pluginName + "@") || pluginId === pluginName) {
+                matchedPluginId = pluginId;
+                break;
+            }
+        }
+    }
+    // 1. Mark all items with this pluginOrigin as deleted
+    if (matchedPluginId) {
+        for (const { key: section } of ITEM_SECTIONS) {
+            const sectionData = manifest[section];
+            if (!sectionData || typeof sectionData !== "object" || Array.isArray(sectionData))
+                continue;
+            for (const [name, config] of Object.entries(sectionData)) {
+                if (config.pluginOrigin?.pluginId === matchedPluginId) {
+                    config.state = "deleted";
+                    removed.push(`${sectionToType(section)}: ${name}`);
+                    if (!opts?.soft) {
+                        await purgeItemFiles(name, sectionToType(section), log);
+                    }
+                }
+            }
+        }
+        // 2. Release plugin takeover
+        delete manifest.takenOverPlugins[matchedPluginId];
+        if (manifest.takenOverPlugins && Object.keys(manifest.takenOverPlugins).length === 0) {
+            delete manifest.takenOverPlugins;
+        }
+        // 3. Re-enable plugin in Claude Code settings
+        try {
+            await setPluginEnabled(matchedPluginId, true);
+        }
+        catch { /* best effort */ }
+        // 4. Remove from installed_plugins.json
+        try {
+            const ipPath = path.join(os.homedir(), ".claude", "plugins", "installed_plugins.json");
+            const raw = await fs.readFile(ipPath, "utf-8");
+            const data = JSON.parse(raw);
+            if (data.version === 2 && data.plugins && matchedPluginId in data.plugins) {
+                delete data.plugins[matchedPluginId];
+                await fs.writeFile(ipPath, JSON.stringify(data, null, 2) + "\n", "utf-8");
+                log.info({ scope: "plugin", op: "cleanup", msg: `Removed ${matchedPluginId} from installed_plugins.json`, item: matchedPluginId });
+            }
+        }
+        catch { /* best effort */ }
+        // 5. Delete plugin cache directory
+        try {
+            const atIdx = matchedPluginId.lastIndexOf("@");
+            if (atIdx > 0) {
+                const pluginPart = matchedPluginId.slice(0, atIdx);
+                const marketplacePart = matchedPluginId.slice(atIdx + 1);
+                const cacheDir = path.join(os.homedir(), ".claude", "plugins", "cache", marketplacePart, pluginPart);
+                await fs.rm(cacheDir, { recursive: true, force: true });
+                log.info({ scope: "plugin", op: "cleanup", msg: `Deleted cache: ${cacheDir}`, item: matchedPluginId });
+            }
+        }
+        catch { /* best effort */ }
+        log.info({ scope: "plugin", op: "release", msg: `Released plugin takeover: ${matchedPluginId}`, item: matchedPluginId });
+    }
+    // 2b. Also mark items by source name (for non-plugin items)
+    if (removed.length === 0) {
+        for (const { key: section } of ITEM_SECTIONS) {
+            const sectionData = manifest[section];
+            if (!sectionData || typeof sectionData !== "object" || Array.isArray(sectionData))
+                continue;
+            for (const [name, config] of Object.entries(sectionData)) {
+                if (config.source === pluginName) {
+                    config.state = "deleted";
+                    removed.push(`${sectionToType(section)}: ${name}`);
+                    if (!opts?.soft) {
+                        await purgeItemFiles(name, sectionToType(section), log);
+                    }
+                }
             }
         }
     }
     if (removed.length === 0) {
-        return { removed: [], errors: [`No items found with source '${source}'`] };
+        return { removed: [], errors: [`No items found for plugin '${pluginName}'`] };
     }
     await saveStateManifest(manifestDir, manifest);
+    // Sync plugin symlinks to clean up
+    if (matchedPluginId) {
+        await syncPluginSymlinks(manifestDir);
+    }
     return { removed, errors: [] };
 }
+/**
+ * Legacy: mark all items from a source as deleted (soft only).
+ */
+export async function removeBySource(source, opts) {
+    return removePlugin(source, { manifestDir: opts?.manifestDir });
+}
+// ============================================================================
+// Plugin release helper
+// ============================================================================
+/**
+ * If ALL components from a plugin are now deleted, release the plugin takeover.
+ */
+async function releasePluginIfFullyDeleted(manifest, pluginId, manifestDir, log) {
+    if (!manifest.takenOverPlugins?.[pluginId])
+        return;
+    // Check if any component from this plugin is still NOT deleted
+    for (const { key: section } of ITEM_SECTIONS) {
+        const sectionData = manifest[section];
+        if (!sectionData)
+            continue;
+        for (const [, config] of Object.entries(sectionData)) {
+            if (config.pluginOrigin?.pluginId === pluginId && config.state !== "deleted") {
+                return; // Still has active components — don't release
+            }
+        }
+    }
+    // All components deleted — release plugin
+    delete manifest.takenOverPlugins[pluginId];
+    if (manifest.takenOverPlugins && Object.keys(manifest.takenOverPlugins).length === 0) {
+        delete manifest.takenOverPlugins;
+    }
+    try {
+        await setPluginEnabled(pluginId, true);
+        log.info({ scope: "plugin", op: "release", msg: `Released plugin takeover: ${pluginId} (all components deleted)`, item: pluginId });
+    }
+    catch { /* best effort */ }
+}
+// ============================================================================
+// Purge helpers
+// ============================================================================
+/**
+ * Delete source files from mycelium dirs and remove symlinks from all tools.
+ */
+async function purgeItemFiles(name, type, log) {
+    const DIR_MAP = {
+        skill: "skills", mcp: "mcps", agent: "agents",
+        command: "commands", rule: "rules", hook: "hooks",
+    };
+    const dirName = DIR_MAP[type] || `${type}s`;
+    // 1. Delete source files from global dir
+    const sourceDir = path.join(MYCELIUM_HOME, "global", dirName, name);
+    try {
+        await fs.rm(sourceDir, { recursive: true, force: true });
+        log.info({ scope: "purge", op: "delete-source", msg: `Deleted ${sourceDir}`, item: name });
+    }
+    catch { /* doesn't exist, fine */ }
+    // Also try single-file items (e.g., rules/name.md)
+    for (const ext of [".md", ".yaml", ".yml"]) {
+        const filePath = path.join(MYCELIUM_HOME, "global", dirName, `${name}${ext}`);
+        try {
+            await fs.unlink(filePath);
+        }
+        catch { /* noop */ }
+    }
+    // 2. Remove symlinks/copies from all tool directories
+    const pathKey = type === "skill" ? "skills"
+        : type === "agent" ? "agents"
+            : type === "command" ? "commands"
+                : type === "rule" ? "rules"
+                    : null;
+    if (pathKey) {
+        for (const [, desc] of Object.entries(TOOL_REGISTRY)) {
+            const itemPath = desc.paths[pathKey];
+            if (!itemPath)
+                continue;
+            const resolved = resolvePath(itemPath);
+            if (!resolved)
+                continue;
+            for (const candidate of [name, `${name}.md`, `${name}.yaml`, `${name}.yml`]) {
+                const targetPath = path.join(resolved, candidate);
+                try {
+                    const stats = await fs.lstat(targetPath);
+                    if (stats.isSymbolicLink() || stats.isFile()) {
+                        await fs.unlink(targetPath);
+                        log.info({ scope: "purge", op: "delete-target", msg: `Removed ${targetPath}`, item: name });
+                    }
+                    else if (stats.isDirectory()) {
+                        await fs.rm(targetPath, { recursive: true, force: true });
+                        log.info({ scope: "purge", op: "delete-target", msg: `Removed ${targetPath}`, item: name });
+                    }
+                }
+                catch { /* doesn't exist */ }
+            }
+        }
+    }
+}
 // ============================================================================
 // Commander.js Commands
 // ============================================================================
 const pluginCmd = new Command("plugin")
-    .description("Remove all items from a plugin/source")
-    .argument("<name>", "Plugin/source name")
-    .action(async (name) => {
-    const result = await removeBySource(name);
+    .description("Remove all items from a plugin and release takeover")
+    .argument("<name>", "Plugin name (e.g., 'superpowers' or 'superpowers@marketplace')")
+    .option("--soft", "Only mark as deleted in manifest (no file cleanup)")
+    .action(async (name, options) => {
+    const result = await removePlugin(name, { soft: options.soft });
     if (result.removed.length > 0) {
-        console.log("Marked as deleted:");
+        console.log("Removed:");
         for (const r of result.removed) {
             console.log(`  - ${r}`);
         }
-        console.log("Run `mycelium sync` to propagate to all tools.");
     }
     if (result.errors.length > 0) {
         for (const e of result.errors) {
@@ -149,14 +353,14 @@ const pluginCmd = new Command("plugin")
     }
 });
 export const removeCommand = new Command("remove")
-    .description("Remove (soft-delete) an item from mycelium sync")
+    .description("Remove an item from mycelium sync (deletes files + symlinks)")
     .argument("<name>", "Name of the item to remove")
     .option("--type <type>", "Item type if name is ambiguous")
+    .option("--soft", "Only mark as deleted in manifest (no file cleanup)")
     .action(async (name, options) => {
-    const result = await removeItem(name, { type: options.type });
+    const result = await removeItem(name, { type: options.type, soft: options.soft });
     if (result.success) {
         console.log(`✓ ${result.message}`);
-        console.log("Run `mycelium sync` to propagate to all tools.");
     }
     else {
         console.error(`✗ Error: ${result.error}`);

package/dist/commands/remove.js.map

@@ -1 +1 @@
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package/dist/commands/remove.test.js

@@ -6,6 +6,9 @@ vi.mock("node:fs/promises", () => ({
     writeFile: vi.fn(),
     access: vi.fn(),
     mkdir: vi.fn(),
+    rm: vi.fn().mockResolvedValue(undefined),
+    unlink: vi.fn().mockResolvedValue(undefined),
+    lstat: vi.fn().mockRejectedValue(new Error("ENOENT")),
 }));
 vi.mock("@mycelish/core", async (importOriginal) => {
     const actual = await importOriginal();
@@ -114,6 +117,21 @@ describe("remove command", () => {
             // Skill should be untouched
             expect(saved.skills["shared-name"].state).toBeUndefined();
         });
+        it("removes files by default (purge is now default)", async () => {
+            const yaml = await import("yaml");
+            const manifest = {
+                version: "1",
+                skills: { "my-skill": { state: "enabled", source: "anthropic-skills" } },
+            };
+            vi.mocked(fs.readFile).mockResolvedValue(yaml.stringify(manifest));
+            vi.mocked(fs.writeFile).mockResolvedValue(undefined);
+            const { removeItem } = await import("./remove.js");
+            const result = await removeItem("my-skill", { manifestDir: MANIFEST_DIR });
+            expect(result.success).toBe(true);
+            expect(result.message).toContain("removed");
+            // Verify fs.rm was called to delete source files
+            expect(fs.rm).toHaveBeenCalled();
+        });
         it("returns error for invalid --type", async () => {
             const yaml = await import("yaml");
             vi.mocked(fs.readFile).mockResolvedValue(yaml.stringify({ version: "1", skills: { x: {} } }));

package/dist/commands/remove.test.js.map

@@ -1 +1 @@
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package/dist/commands/status.test.js

@@ -6,9 +6,14 @@
  * - MCPs count
  * - Sync status (synced, pending, error, disabled)
  */
-import { describe, it, expect, beforeEach, afterEach } from "vitest";
+import { describe, it, expect, beforeEach, afterEach, vi } from "vitest";
 import * as fs from "node:fs/promises";
 import * as path from "node:path";
+// Mock resolvePath so tests don't scan real system directories (e.g. ~/.claude/agents/)
+vi.mock("@mycelish/core", async (importOriginal) => {
+    const actual = await importOriginal();
+    return { ...actual, resolvePath: () => null };
+});
 // Test directory for isolated tests
 const testDir = `/tmp/mycelium-status-test-${Date.now()}`;
 const mockMyceliumDir = `${testDir}/.mycelium`;

package/dist/commands/status.test.js.map

@@ -1 +1 @@
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package/dist/commands/sync.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../src/commands/sync.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAIH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EACL,KAAK,MAAM,EACX,KAAK,YAAY,EACjB,KAAK,UAAU,EACf,KAAK,cAAc,EAKpB,MAAM,gBAAgB,CAAC;AA6BxB,MAAM,WAAW,WAAW;IAC1B,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAMD;;GAEG;AACH,wBAAsB,WAAW,CAC/B,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAuCjC;AAMD;;GAEG;AACH,wBAAsB,QAAQ,CAC5B,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,YAAY,EAC1B,OAAO,GAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAM,GACnC,OAAO,CAAC,cAAc,CAAC,CAqFzB;AAED;;GAEG;AACH,wBAAsB,OAAO,CAC3B,WAAW,EAAE,MAAM,EACnB,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE;IAAE,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,EAClD,OAAO,GAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAM,EACpC,OAAO,GAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAA;CAAO,GACjC,OAAO,CAAC,UAAU,CAAC,CAgIrB;AAMD,eAAO,MAAM,WAAW,SAqIpB,CAAC"}
+{"version":3,"file":"sync.d.ts","sourceRoot":"","sources":["../../src/commands/sync.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAIH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EACL,KAAK,MAAM,EACX,KAAK,YAAY,EACjB,KAAK,UAAU,EACf,KAAK,cAAc,EAKpB,MAAM,gBAAgB,CAAC;AA8BxB,MAAM,WAAW,WAAW;IAC1B,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAMD;;GAEG;AACH,wBAAsB,WAAW,CAC/B,OAAO,EAAE,MAAM,GACd,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CAuCjC;AAMD;;GAEG;AACH,wBAAsB,QAAQ,CAC5B,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,YAAY,EAC1B,OAAO,GAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAM,GACnC,OAAO,CAAC,cAAc,CAAC,CAqFzB;AAED;;GAEG;AACH,wBAAsB,OAAO,CAC3B,WAAW,EAAE,MAAM,EACnB,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE;IAAE,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,EAClD,OAAO,GAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAM,EACpC,OAAO,GAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAA;CAAO,GACjC,OAAO,CAAC,UAAU,CAAC,CAuIrB;AAMD,eAAO,MAAM,WAAW,SAkJpB,CAAC"}

package/dist/commands/sync.js

@@ -22,7 +22,8 @@ import { getTracer, closeTracer } from "../core/global-tracer.js";
 import { loadMachineOverrides, applyMachineOverrides, rescanOverrides, } from "../core/machine-overrides.js";
 import { getDisabledItems, loadStateManifest } from "../core/manifest-state.js";
 import { scanPluginComponents } from "../core/plugin-scanner.js";
-import { PLUGIN_COMPONENT_DIRS } from "../core/plugin-takeover.js";
+import { PLUGIN_COMPONENT_DIRS, cleanOrphanedTakeovers } from "../core/plugin-takeover.js";
+import { extractSecretsFromMcps } from "../core/env-template.js";
 // ============================================================================
 // Helper Functions
 // ============================================================================
@@ -157,6 +158,12 @@ export async function syncAll(projectRoot, enabledTools, envVars = {}, options =
     };
     const tracer = getTracer();
     const log = tracer.createTrace("sync");
+    // Clean up orphaned plugin takeovers (plugins uninstalled from Claude Code)
+    const cleaned = await cleanOrphanedTakeovers();
+    if (cleaned.length > 0) {
+        result.warnings.push(`Cleaned orphaned plugin takeovers: ${cleaned.join(", ")}`);
+        log.info({ scope: "plugin", op: "cleanup", msg: `Cleaned ${cleaned.length} orphaned takeover(s)` });
+    }
     // Load and merge all configs
     const mergedConfig = await loadAndMergeAllConfigs(projectRoot);
     log.info({ scope: "config", op: "merge", msg: "Loaded and merged config", configLevel: "all" });
@@ -290,6 +297,18 @@ export const syncCommand = new Command("sync")
     const globalEnvVars = await loadEnvFile(globalEnvPath);
     const projectEnvVars = await loadEnvFile(projectEnvPath);
     const envVars = { ...globalEnvVars, ...projectEnvVars };
+    // Auto-extract hardcoded secrets before syncing
+    const { extracted } = await extractSecretsFromMcps();
+    if (extracted.length > 0) {
+        console.warn(`\u26A0 Auto-extracted ${extracted.length} hardcoded secret(s) to ~/.mycelium/.env.local:`);
+        for (const item of extracted) {
+            console.warn(`  \u2713 ${item}`);
+        }
+        console.warn("");
+        // Reload env vars since we just wrote new ones
+        const freshGlobal = await loadEnvFile(globalEnvPath);
+        Object.assign(envVars, freshGlobal);
+    }
     // Get enabled tools from manifest (default all enabled)
     const enabledTools = Object.fromEntries(ALL_TOOL_IDS.map(id => [id, { enabled: true }]));
     if (options.tool) {