@mycelish/cli 0.1.0 → 0.2.0

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

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

@@ -6,6 +6,6 @@
  */
 import { Command } from "commander";
 export type { DiagnosticResult, DoctorResult } from "./health-checks/index.js";
-export { checkGlobalMyceliumExists, checkManifestValid, checkToolPathExists, checkBrokenSymlinks, checkMcpConfigJson, checkMcpConfigYaml, checkOrphanedConfigs, checkMcpServerConnectivity, checkMemoryFilesExist, checkMemoryFileSize, checkToolVersions, runAllChecks, formatDoctorOutput, formatDoctorJson, } from "./health-checks/index.js";
+export { checkGlobalMyceliumExists, checkManifestValid, checkToolPathExists, checkBrokenSymlinks, checkMcpConfigJson, checkMcpConfigYaml, checkOrphanedConfigs, checkMcpServerConnectivity, checkMemoryFilesExist, checkMemoryFileSize, checkToolVersions, checkTakenOverPlugins, runAllChecks, formatDoctorOutput, formatDoctorJson, } from "./health-checks/index.js";
 export declare const doctorCommand: Command;
 //# sourceMappingURL=doctor.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAQpC,YAAY,EAAE,gBAAgB,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AAC/E,OAAO,EACL,yBAAyB,EACzB,kBAAkB,EAClB,mBAAmB,EACnB,mBAAmB,EACnB,kBAAkB,EAClB,kBAAkB,EAClB,oBAAoB,EACpB,0BAA0B,EAC1B,qBAAqB,EACrB,mBAAmB,EACnB,iBAAiB,EACjB,YAAY,EACZ,kBAAkB,EAClB,gBAAgB,GACjB,MAAM,0BAA0B,CAAC;AAElC,eAAO,MAAM,aAAa,SAyBtB,CAAC"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAQpC,YAAY,EAAE,gBAAgB,EAAE,YAAY,EAAE,MAAM,0BAA0B,CAAC;AAC/E,OAAO,EACL,yBAAyB,EACzB,kBAAkB,EAClB,mBAAmB,EACnB,mBAAmB,EACnB,kBAAkB,EAClB,kBAAkB,EAClB,oBAAoB,EACpB,0BAA0B,EAC1B,qBAAqB,EACrB,mBAAmB,EACnB,iBAAiB,EACjB,qBAAqB,EACrB,YAAY,EACZ,kBAAkB,EAClB,gBAAgB,GACjB,MAAM,0BAA0B,CAAC;AAElC,eAAO,MAAM,aAAa,SAyBtB,CAAC"}

package/dist/commands/doctor.js

@@ -6,7 +6,7 @@
  */
 import { Command } from "commander";
 import { runAllChecks, formatDoctorOutput, formatDoctorJson, } from "./health-checks/index.js";
-export { checkGlobalMyceliumExists, checkManifestValid, checkToolPathExists, checkBrokenSymlinks, checkMcpConfigJson, checkMcpConfigYaml, checkOrphanedConfigs, checkMcpServerConnectivity, checkMemoryFilesExist, checkMemoryFileSize, checkToolVersions, runAllChecks, formatDoctorOutput, formatDoctorJson, } from "./health-checks/index.js";
+export { checkGlobalMyceliumExists, checkManifestValid, checkToolPathExists, checkBrokenSymlinks, checkMcpConfigJson, checkMcpConfigYaml, checkOrphanedConfigs, checkMcpServerConnectivity, checkMemoryFilesExist, checkMemoryFileSize, checkToolVersions, checkTakenOverPlugins, runAllChecks, formatDoctorOutput, formatDoctorJson, } from "./health-checks/index.js";
 export const doctorCommand = new Command("doctor")
     .description("Check system health and diagnose issues")
     .option("-j, --json", "Output as JSON")

package/dist/commands/doctor.js.map

@@ -1 +1 @@
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+{"version":3,"file":"doctor.js","sourceRoot":"","sources":["../../src/commands/doctor.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EACL,YAAY,EACZ,kBAAkB,EAClB,gBAAgB,GACjB,MAAM,0BAA0B,CAAC;AAIlC,OAAO,EACL,yBAAyB,EACzB,kBAAkB,EAClB,mBAAmB,EACnB,mBAAmB,EACnB,kBAAkB,EAClB,kBAAkB,EAClB,oBAAoB,EACpB,0BAA0B,EAC1B,qBAAqB,EACrB,mBAAmB,EACnB,iBAAiB,EACjB,qBAAqB,EACrB,YAAY,EACZ,kBAAkB,EAClB,gBAAgB,GACjB,MAAM,0BAA0B,CAAC;AAElC,MAAM,CAAC,MAAM,aAAa,GAAG,IAAI,OAAO,CAAC,QAAQ,CAAC;KAC/C,WAAW,CAAC,yCAAyC,CAAC;KACtD,MAAM,CAAC,YAAY,EAAE,gBAAgB,CAAC;KACtC,MAAM,CAAC,WAAW,EAAE,qCAAqC,CAAC;KAC1D,MAAM,CAAC,KAAK,EAAE,OAAO,EAAE,EAAE;IACxB,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,MAAM,YAAY,EAAE,CAAC;QAEpC,IAAI,OAAO,CAAC,IAAI,EAAE,CAAC;YACjB,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,MAAM,CAAC,CAAC,CAAC;QACxC,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAC,CAAC;QAC1C,CAAC;QAED,sCAAsC;QACtC,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC;YACpB,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC;IACH,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CACX,uBAAuB,EACvB,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CACvD,CAAC;QACF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;AACH,CAAC,CAAC,CAAC"}

package/dist/commands/enable.d.ts

@@ -1,13 +1,14 @@
 /**
  * Enable Command Module
  *
- * Enable a skill or MCP globally or for a specific tool:
- * - mycelium enable <name>              # Enable skill/MCP at project level
- * - mycelium enable <name> --global     # Enable skill/MCP globally
- * - mycelium enable <name> --tool <id>  # Enable skill/MCP for specific tool only
+ * Enable a skill, MCP, hook, or memory scope globally or for a specific tool:
+ * - mycelium enable <name>              # Enable item at project level
+ * - mycelium enable <name> --global     # Enable item globally
+ * - mycelium enable <name> --tool <id>  # Enable item for specific tool only
  */
 import { Command } from "commander";
 import { type ToolId } from "@mycelish/core";
+import { type ItemType } from "../core/manifest-state.js";
 export interface EnableOptions {
     name: string;
     tool?: ToolId;
@@ -18,15 +19,16 @@ export interface EnableOptions {
 export interface EnableResult {
     success: boolean;
     name: string;
-    type?: "skill" | "mcp";
+    type?: ItemType;
     level?: "global" | "project";
     tool?: ToolId;
     alreadyEnabled?: boolean;
+    pluginReleased?: boolean;
     message?: string;
     error?: string;
 }
 /**
- * Enable a skill or MCP
+ * Enable a skill, MCP, hook, or memory scope
  */
 export declare function enableSkillOrMcp(options: EnableOptions): Promise<EnableResult>;
 export declare const enableCommand: Command;

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

@@ -1 +1 @@
-{"version":3,"file":"enable.d.ts","sourceRoot":"","sources":["../../src/commands/enable.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAIpC,OAAO,EAAE,KAAK,MAAM,EAA2C,MAAM,gBAAgB,CAAC;AAMtF,MAAM,WAAW,aAAa;IAC5B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,YAAY;IAC3B,OAAO,EAAE,OAAO,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,CAAC,EAAE,OAAO,GAAG,KAAK,CAAC;IACvB,KAAK,CAAC,EAAE,QAAQ,GAAG,SAAS,CAAC;IAC7B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AA+FD;;GAEG;AACH,wBAAsB,gBAAgB,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,YAAY,CAAC,CAqGpF;AAMD,eAAO,MAAM,aAAa,SAsBtB,CAAC"}
+{"version":3,"file":"enable.d.ts","sourceRoot":"","sources":["../../src/commands/enable.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,KAAK,MAAM,EAAgB,MAAM,gBAAgB,CAAC;AAE3D,OAAO,EASL,KAAK,QAAQ,EACd,MAAM,2BAA2B,CAAC;AAQnC,MAAM,WAAW,aAAa;IAC5B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,YAAY;IAC3B,OAAO,EAAE,OAAO,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,CAAC,EAAE,QAAQ,CAAC;IAChB,KAAK,CAAC,EAAE,QAAQ,GAAG,SAAS,CAAC;IAC7B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAMD;;GAEG;AACH,wBAAsB,gBAAgB,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,YAAY,CAAC,CAwIpF;AAaD,eAAO,MAAM,aAAa,SAyBtB,CAAC"}

package/dist/commands/enable.js

@@ -1,173 +1,165 @@
 /**
  * Enable Command Module
  *
- * Enable a skill or MCP globally or for a specific tool:
- * - mycelium enable <name>              # Enable skill/MCP at project level
- * - mycelium enable <name> --global     # Enable skill/MCP globally
- * - mycelium enable <name> --tool <id>  # Enable skill/MCP for specific tool only
+ * Enable a skill, MCP, hook, or memory scope globally or for a specific tool:
+ * - mycelium enable <name>              # Enable item at project level
+ * - mycelium enable <name> --global     # Enable item globally
+ * - mycelium enable <name> --tool <id>  # Enable item for specific tool only
  */
 import { Command } from "commander";
-import * as fs from "node:fs/promises";
-import * as path from "node:path";
-import { parse as yamlParse, stringify as yamlStringify } from "yaml";
-import { TOOL_REGISTRY, ALL_TOOL_IDS, expandPath } from "@mycelish/core";
-// ============================================================================
-// Helper Functions
-// ============================================================================
-/**
- * Load manifest from a path
- */
-async function loadManifest(manifestDir) {
-    const manifestPath = path.join(manifestDir, "manifest.yaml");
-    try {
-        const content = await fs.readFile(manifestPath, "utf-8");
-        return yamlParse(content);
-    }
-    catch {
-        return null;
-    }
-}
-/**
- * Save manifest to a path
- */
-async function saveManifest(manifestDir, manifest) {
-    const manifestPath = path.join(manifestDir, "manifest.yaml");
-    const content = yamlStringify(manifest);
-    await fs.writeFile(manifestPath, content, "utf-8");
-}
-/**
- * Check if a tool ID is valid
- */
-function isValidToolId(toolId) {
-    return toolId in TOOL_REGISTRY;
-}
-/**
- * Find what type an item is (skill or MCP)
- */
-function findItemType(manifest, name) {
-    if (manifest.skills && name in manifest.skills) {
-        return { type: "skill", config: manifest.skills[name] };
-    }
-    if (manifest.mcps && name in manifest.mcps) {
-        return { type: "mcp", config: manifest.mcps[name] };
-    }
-    return null;
-}
-/**
- * Check if item is already enabled (globally or for a specific tool)
- */
-function isAlreadyEnabled(config, tool) {
-    if (tool) {
-        // Check tool-specific enablement
-        if (config.enabledTools?.includes(tool) || config.tools?.includes(tool)) {
-            return true;
-        }
-        return false;
-    }
-    // Check global enablement
-    return config.enabled === true;
-}
+import { ALL_TOOL_IDS } from "@mycelish/core";
+import { getTracer } from "../core/global-tracer.js";
+import { loadStateManifest, saveStateManifest, ensureItem, findItemType, setItemInManifest, isValidToolId, resolveManifestDir, } from "../core/manifest-state.js";
+import { setPluginEnabled, syncPluginSymlinks } from "../core/plugin-takeover.js";
+import { scanPluginComponents } from "../core/plugin-scanner.js";
 // ============================================================================
 // Core Enable Function
 // ============================================================================
 /**
- * Enable a skill or MCP
+ * Enable a skill, MCP, hook, or memory scope
  */
 export async function enableSkillOrMcp(options) {
     const { name, tool, global: isGlobal } = options;
+    const tracer = getTracer();
+    const log = tracer.createTrace("enable");
+    log.info({ scope: "manifest", op: "enable", msg: `Enabling ${name}`, item: name, tool });
     // Validate tool if provided
     if (tool && !isValidToolId(tool)) {
-        return {
-            success: false,
-            name,
-            error: `Invalid tool: ${tool}. Supported tools: ${ALL_TOOL_IDS.join(", ")}`,
-        };
+        const error = `Invalid tool: ${tool}. Supported tools: ${ALL_TOOL_IDS.join(", ")}`;
+        log.error({ scope: "manifest", op: "enable", msg: error, item: name, error });
+        return { success: false, name, error };
     }
-    // Determine which manifest to use
-    const manifestDir = isGlobal
-        ? options.globalPath || expandPath("~/.mycelium")
-        : options.projectPath || path.join(process.cwd(), ".mycelium");
-    // Load manifest
-    const manifest = await loadManifest(manifestDir);
+    const manifestDir = resolveManifestDir(options);
+    const manifest = await loadStateManifest(manifestDir);
     if (!manifest) {
-        return {
-            success: false,
-            name,
-            error: `Could not load manifest from ${manifestDir}`,
-        };
+        const error = `Could not load manifest from ${manifestDir}`;
+        log.error({ scope: "manifest", op: "enable", msg: error, item: name, error });
+        return { success: false, name, error };
     }
-    // Find the item (skill or MCP)
-    const item = findItemType(manifest, name);
-    if (!item) {
-        return {
-            success: false,
-            name,
-            error: `'${name}' not found in manifest (checked skills and mcps)`,
-        };
+    // Load global config once (used for MCP type detection and later for re-adding)
+    const { loadGlobalConfig } = await import("../core/config-merger.js");
+    const globalConfig = await loadGlobalConfig();
+    // Detect MCP type from config files (mcps.yaml)
+    let typeHint;
+    if (globalConfig.mcps?.[name])
+        typeHint = "mcp";
+    // Detect type from plugin cache if available
+    if (!typeHint && !tool && manifest.takenOverPlugins) {
+        for (const [, info] of Object.entries(manifest.takenOverPlugins)) {
+            try {
+                const components = await scanPluginComponents(info.cachePath);
+                const match = components.find(c => c.name === name);
+                if (match) {
+                    typeHint = match.type;
+                    break;
+                }
+            }
+            catch { /* cache may not exist */ }
+        }
+    }
+    // Find or auto-register item
+    const { type, config, autoRegistered } = ensureItem(manifest, name, "disabled", typeHint);
+    if (autoRegistered) {
+        log.info({ scope: "manifest", op: "enable", msg: `Auto-registered '${name}' as ${type} in manifest`, item: name });
     }
-    const { type, config } = item;
     const level = isGlobal ? "global" : "project";
     // Check if already enabled
     if (isAlreadyEnabled(config, tool)) {
         const toolMsg = tool ? ` for ${tool}` : "";
-        return {
-            success: true,
-            name,
-            type,
-            level,
-            tool,
-            alreadyEnabled: true,
-            message: `${type} '${name}' is already enabled${toolMsg}`,
-        };
+        return { success: true, name, type, level, tool, alreadyEnabled: true, message: `${type} '${name}' is already enabled${toolMsg}` };
     }
-    // Enable the item
+    // Apply enable
     if (tool) {
-        // Enable for specific tool
-        if (!config.enabledTools) {
+        if (!config.enabledTools)
             config.enabledTools = [];
-        }
-        if (!config.enabledTools.includes(tool)) {
+        if (!config.enabledTools.includes(tool))
             config.enabledTools.push(tool);
-        }
-        // Also add to tools array if it exists
-        if (!config.tools) {
+        if (!config.tools)
             config.tools = [];
-        }
-        if (!config.tools.includes(tool)) {
+        if (!config.tools.includes(tool))
             config.tools.push(tool);
-        }
-        // Remove from excludeTools if present
         if (config.excludeTools) {
             config.excludeTools = config.excludeTools.filter((t) => t !== tool);
         }
     }
     else {
-        // Enable globally
-        config.enabled = true;
+        config.state = "enabled";
     }
-    // Update manifest
-    if (type === "skill") {
-        if (!manifest.skills)
-            manifest.skills = {};
-        manifest.skills[name] = config;
+    setItemInManifest(manifest, name, type, config);
+    await saveStateManifest(manifestDir, manifest);
+    // Add MCP back to tool configs immediately
+    if (type === "mcp") {
+        const { getAdapter } = await import("../core/tool-adapter.js");
+        const mcpConfig = globalConfig.mcps?.[name];
+        if (mcpConfig) {
+            const toolIds = tool ? [tool] : ALL_TOOL_IDS.filter(tid => {
+                if (config.excludeTools?.includes(tid))
+                    return false;
+                if (config.tools?.length && !config.tools.includes(tid))
+                    return false;
+                return true;
+            });
+            for (const tid of toolIds) {
+                try {
+                    await getAdapter(tid).add(name, mcpConfig);
+                }
+                catch { /* tool may not be installed */ }
+            }
+        }
     }
-    else {
-        if (!manifest.mcps)
-            manifest.mcps = {};
-        manifest.mcps[name] = config;
+    // Plugin release: check ALL taken-over plugins that contain this item.
+    // An item can exist in multiple plugins — release each one whose items are all enabled.
+    let pluginReleased = false;
+    if (!tool && manifest.takenOverPlugins) {
+        let manifestDirty = false;
+        for (const [pluginId, pluginEntry] of Object.entries(manifest.takenOverPlugins)) {
+            // Check if this item belongs to this plugin (check both allSkills and allComponents)
+            const allItems = [...(pluginEntry.allSkills ?? []), ...(pluginEntry.allComponents ?? [])];
+            if (!allItems.includes(name))
+                continue;
+            // Check ALL components are enabled (not just skills)
+            const allEnabled = allItems.every((itemName) => {
+                const found = findItemType(manifest, itemName);
+                if (!found)
+                    return true; // not registered = enabled by default
+                return found.config.state === "enabled" || found.config.state === undefined;
+            });
+            if (allEnabled) {
+                // Re-enable plugin in Claude Code settings and remove symlinks
+                await setPluginEnabled(pluginId, true);
+                delete manifest.takenOverPlugins[pluginId];
+                // Clean up pluginOrigin from ALL sections
+                for (const itemName of new Set(allItems)) {
+                    for (const sectionName of ["skills", "agents", "commands", "hooks"]) {
+                        const section = manifest[sectionName];
+                        if (section && typeof section === "object" && itemName in section) {
+                            delete section[itemName].pluginOrigin;
+                        }
+                    }
+                }
+                pluginReleased = true;
+                manifestDirty = true;
+                log.info({ scope: "plugin", op: "release", msg: `Released plugin: ${pluginId}`, item: pluginId, itemType: typeHint });
+            }
+        }
+        if (manifestDirty) {
+            if (Object.keys(manifest.takenOverPlugins).length === 0)
+                delete manifest.takenOverPlugins;
+            await saveStateManifest(manifestDir, manifest);
+        }
+        // Sync symlinks declaratively — handles both re-symlinking (partial release)
+        // and orphan cleanup (full release)
+        await syncPluginSymlinks(manifestDir);
     }
-    // Save manifest
-    await saveManifest(manifestDir, manifest);
-    // Build success message
     const toolMsg = tool ? ` for ${tool}` : "";
-    return {
-        success: true,
-        name,
-        type,
-        level,
-        tool,
-        message: `${type} '${name}' enabled${toolMsg}`,
-    };
+    log.info({ scope: "manifest", op: "enable", msg: `${type} '${name}' enabled${toolMsg}`, item: name, tool });
+    return { success: true, name, type, level, tool, pluginReleased, message: `${type} '${name}' enabled${toolMsg}` };
+}
+function isAlreadyEnabled(config, tool) {
+    if (tool) {
+        return !!(config.enabledTools?.includes(tool) || config.tools?.includes(tool));
+    }
+    return config.state === "enabled" || config.state === undefined;
 }
 // ============================================================================
 // Commander.js Command
@@ -189,6 +181,9 @@ export const enableCommand = new Command("enable")
         }
         else {
             console.log(`\u2713 ${result.message}`);
+            if (result.pluginReleased) {
+                console.log(`  [experimental] Plugin released: all skills re-enabled, plugin restored in Claude Code`);
+            }
         }
     }
     else {

package/dist/commands/enable.js.map

@@ -1 +1 @@
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