@mycelish/cli 0.1.0 → 0.2.0

package/dist/commands/health-checks/plugin-takeover-check.js

@@ -0,0 +1,274 @@
+/**
+ * Health check for taken-over plugins.
+ * Verifies 8 invariants:
+ * 1. Every symlink in ~/.claude/{skills,agents,commands}/ has valid target
+ * 2. Every disabled item with pluginOrigin has NO symlink
+ * 3. Every enabled item with pluginOrigin HAS symlink pointing to plugin cache
+ * 4. Taken-over plugins have enabledPlugins[id] === false in settings.json
+ * 5. Released plugins have enabledPlugins[id] === true
+ * 6. Live cache components match takenOverPlugins entries
+ * 7. No phantom entries (skill name matches pluginId pattern)
+ * 8. No orphaned symlinks (symlinks pointing to non-existent targets)
+ */
+import * as fs from "node:fs/promises";
+import * as path from "node:path";
+import * as os from "node:os";
+import { expandPath } from "@mycelish/core";
+import { loadStateManifest, ITEM_SECTIONS } from "../../core/manifest-state.js";
+import { readFileIfExists } from "../../core/fs-helpers.js";
+import { scanPluginComponents } from "../../core/plugin-scanner.js";
+import { PLUGIN_COMPONENT_DIRS, getSymlinkPath } from "../../core/plugin-takeover.js";
+import { getTracer } from "../../core/global-tracer.js";
+const CLAUDE_HOME = path.join(os.homedir(), ".claude");
+const SETTINGS_PATH = path.join(CLAUDE_HOME, "settings.json");
+const PLUGIN_CACHE_DIR = path.join(CLAUDE_HOME, "plugins", "cache");
+export async function checkTakenOverPlugins() {
+    const results = [];
+    const manifest = await loadStateManifest(expandPath("~/.mycelium"));
+    if (!manifest) {
+        return results;
+    }
+    // Load Claude Code settings to verify plugin states
+    let enabledPlugins = {};
+    try {
+        const raw = await readFileIfExists(SETTINGS_PATH);
+        if (raw) {
+            const settings = JSON.parse(raw);
+            enabledPlugins = settings.enabledPlugins ?? {};
+        }
+    }
+    catch {
+        // settings unreadable
+    }
+    // Check 4: Taken-over plugins disabled + Check 6: Cache components match
+    if (manifest.takenOverPlugins && Object.keys(manifest.takenOverPlugins).length > 0) {
+        for (const [pluginId, info] of Object.entries(manifest.takenOverPlugins)) {
+            // Check cache dir exists
+            const cacheExists = await fs.access(info.cachePath).then(() => true, () => false);
+            if (!cacheExists) {
+                results.push({
+                    name: `plugin-takeover:${pluginId}`,
+                    status: "warn",
+                    message: `Taken-over plugin cache missing: ${info.cachePath}`,
+                    fix: `Run 'mycelium plugin release ${pluginId}' to release the plugin`,
+                });
+                continue;
+            }
+            // Check 4: Plugin is still disabled in settings
+            if (enabledPlugins[pluginId] === true) {
+                results.push({
+                    name: `plugin-takeover:${pluginId}`,
+                    status: "warn",
+                    message: `Plugin ${pluginId} was re-enabled in Claude Code settings but is still marked as taken over`,
+                    fix: `Run 'mycelium plugin release ${pluginId}' or disable it again in Claude Code`,
+                });
+                continue;
+            }
+            // Check 6: Live cache components match takenOverPlugins entries
+            try {
+                const components = await scanPluginComponents(info.cachePath);
+                const liveComponentNames = components.map(c => c.name);
+                const registeredComponents = info.allComponents ?? info.allSkills;
+                const missing = registeredComponents.filter(name => !liveComponentNames.includes(name));
+                const extra = liveComponentNames.filter(name => !registeredComponents.includes(name));
+                if (missing.length > 0 || extra.length > 0) {
+                    const issues = [];
+                    if (missing.length > 0)
+                        issues.push(`missing: ${missing.join(", ")}`);
+                    if (extra.length > 0)
+                        issues.push(`extra: ${extra.join(", ")}`);
+                    results.push({
+                        name: `plugin-takeover:${pluginId}:cache-mismatch`,
+                        status: "warn",
+                        message: `Plugin ${pluginId} cache components don't match manifest (${issues.join("; ")})`,
+                        fix: `Run 'mycelium plugin release ${pluginId}' and re-take it over`,
+                    });
+                }
+            }
+            catch (err) {
+                results.push({
+                    name: `plugin-takeover:${pluginId}:scan-error`,
+                    status: "warn",
+                    message: `Failed to scan plugin cache: ${err.message}`,
+                });
+            }
+            results.push({
+                name: `plugin-takeover:${pluginId}`,
+                status: "pass",
+                message: `Plugin ${pluginId} taken over: ${info.allSkills?.length ?? info.allComponents?.length ?? 0} components managed`,
+            });
+        }
+    }
+    // Collect all items with pluginOrigin for checks 2 & 3
+    const itemsWithPluginOrigin = [];
+    for (const { key, type } of ITEM_SECTIONS) {
+        if (type !== "skill" && type !== "agent" && type !== "command")
+            continue;
+        const section = manifest[key];
+        if (!section || typeof section !== "object" || Array.isArray(section))
+            continue;
+        for (const [itemName, config] of Object.entries(section)) {
+            if (config.pluginOrigin) {
+                itemsWithPluginOrigin.push({
+                    name: itemName,
+                    type: type,
+                    state: config.state ?? "enabled",
+                    pluginOrigin: config.pluginOrigin,
+                });
+            }
+        }
+    }
+    // Check 2: Disabled items with pluginOrigin should have NO symlink
+    const disabledWithOrigin = itemsWithPluginOrigin.filter(item => item.state === "disabled" || item.state === "deleted");
+    for (const item of disabledWithOrigin) {
+        const symlinkPath = getSymlinkPath(item.type, item.name);
+        try {
+            await fs.lstat(symlinkPath);
+            // Symlink exists but item is disabled
+            results.push({
+                name: `plugin-origin:${item.name}:disabled-has-symlink`,
+                status: "fail",
+                message: `Disabled ${item.type} "${item.name}" still has symlink at ${symlinkPath}`,
+                fix: `Run 'mycelium sync' to clean up orphaned symlinks`,
+            });
+        }
+        catch {
+            // Symlink doesn't exist - this is correct
+        }
+    }
+    // Check 3: Enabled items with pluginOrigin should HAVE symlink
+    const enabledWithOrigin = itemsWithPluginOrigin.filter(item => item.state === "enabled");
+    for (const item of enabledWithOrigin) {
+        const symlinkPath = getSymlinkPath(item.type, item.name);
+        try {
+            const stats = await fs.lstat(symlinkPath);
+            if (!stats.isSymbolicLink()) {
+                results.push({
+                    name: `plugin-origin:${item.name}:not-symlink`,
+                    status: "warn",
+                    message: `Enabled ${item.type} "${item.name}" exists but is not a symlink`,
+                    fix: `Run 'mycelium sync' to fix`,
+                });
+                continue;
+            }
+            // Verify it points to the plugin cache
+            const target = await fs.readlink(symlinkPath);
+            const expectedCachePrefix = item.pluginOrigin.cachePath;
+            if (!target.startsWith(expectedCachePrefix)) {
+                results.push({
+                    name: `plugin-origin:${item.name}:wrong-target`,
+                    status: "warn",
+                    message: `Enabled ${item.type} "${item.name}" symlink points to wrong location: ${target}`,
+                    fix: `Run 'mycelium sync' to fix`,
+                });
+            }
+        }
+        catch {
+            // Symlink doesn't exist but item is enabled
+            results.push({
+                name: `plugin-origin:${item.name}:missing-symlink`,
+                status: "fail",
+                message: `Enabled ${item.type} "${item.name}" missing symlink at ${symlinkPath}`,
+                fix: `Run 'mycelium sync' to create symlink`,
+            });
+        }
+    }
+    // Check 1 & 8: Every symlink has valid target (combined check)
+    for (const [type, { dir }] of Object.entries(PLUGIN_COMPONENT_DIRS)) {
+        try {
+            const entries = await fs.readdir(dir, { withFileTypes: true });
+            for (const entry of entries) {
+                if (!entry.isSymbolicLink())
+                    continue;
+                const symlinkPath = path.join(dir, entry.name);
+                try {
+                    // lstat checks the symlink itself
+                    await fs.lstat(symlinkPath);
+                    // stat follows the symlink to check the target
+                    await fs.stat(symlinkPath);
+                    // Both succeed - valid symlink
+                }
+                catch (err) {
+                    // Check 8: Orphaned symlink (target doesn't exist)
+                    try {
+                        const target = await fs.readlink(symlinkPath);
+                        results.push({
+                            name: `symlink:${type}:${entry.name}:orphaned`,
+                            status: "warn",
+                            message: `Orphaned ${type} symlink "${entry.name}" points to non-existent target: ${target}`,
+                            fix: `Run 'mycelium sync' to clean up`,
+                        });
+                    }
+                    catch {
+                        // Can't even read the symlink
+                        results.push({
+                            name: `symlink:${type}:${entry.name}:invalid`,
+                            status: "fail",
+                            message: `Invalid ${type} symlink "${entry.name}" - cannot read link`,
+                            fix: `Manually remove ${symlinkPath}`,
+                        });
+                    }
+                }
+            }
+        }
+        catch {
+            // Directory doesn't exist - not an error for health check
+        }
+    }
+    // Check 5: Released plugins should have enabledPlugins[id] === true
+    // We check this by finding plugins that are NOT in takenOverPlugins but have items with pluginOrigin
+    const takenOverIds = new Set(Object.keys(manifest.takenOverPlugins ?? {}));
+    const releasedPluginIds = new Set();
+    for (const item of itemsWithPluginOrigin) {
+        const pluginId = item.pluginOrigin.pluginId;
+        if (!takenOverIds.has(pluginId)) {
+            releasedPluginIds.add(pluginId);
+        }
+    }
+    for (const pluginId of releasedPluginIds) {
+        if (enabledPlugins[pluginId] === false) {
+            results.push({
+                name: `plugin-release:${pluginId}:still-disabled`,
+                status: "warn",
+                message: `Plugin ${pluginId} was released but is still disabled in Claude Code settings`,
+                fix: `Enable ${pluginId} in Claude Code or run 'mycelium plugin takeover ${pluginId}' again`,
+            });
+        }
+    }
+    // Check 7: No phantom entries (skill name matches pluginId pattern)
+    for (const { key, type } of ITEM_SECTIONS) {
+        if (type !== "skill")
+            continue; // Only check skills section for phantom entries
+        const section = manifest[key];
+        if (!section || typeof section !== "object" || Array.isArray(section))
+            continue;
+        for (const itemName of Object.keys(section)) {
+            // Check if name matches pattern "name@marketplace"
+            if (itemName.includes("@") && itemName.split("@").length === 2) {
+                const [plugin, marketplace] = itemName.split("@");
+                if (plugin && marketplace) {
+                    results.push({
+                        name: `phantom:${itemName}`,
+                        status: "fail",
+                        message: `Phantom entry detected: skill name "${itemName}" matches plugin ID pattern`,
+                        fix: `Remove "${itemName}" from manifest.yaml - plugin names should not be registered as skills`,
+                    });
+                }
+            }
+        }
+    }
+    // Log health check results to trace DB
+    if (results.length > 0) {
+        const log = getTracer().createTrace("doctor");
+        const fails = results.filter(r => r.status === "fail").length;
+        const warns = results.filter(r => r.status === "warn").length;
+        const passes = results.filter(r => r.status === "pass").length;
+        const level = fails > 0 ? "error" : warns > 0 ? "warn" : "info";
+        log[level]({ scope: "plugin", op: "health-check", msg: `Plugin takeover health: ${passes} pass, ${warns} warn, ${fails} fail` });
+        for (const r of results.filter(r => r.status === "fail" || r.status === "warn")) {
+            log[r.status === "fail" ? "error" : "warn"]({ scope: "plugin", op: "health-check", msg: r.message, item: r.name });
+        }
+    }
+    return results;
+}
+//# sourceMappingURL=plugin-takeover-check.js.map

package/dist/commands/health-checks/plugin-takeover-check.js.map

@@ -0,0 +1 @@
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package/dist/commands/health-checks/runner.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"runner.d.ts","sourceRoot":"","sources":["../../../src/commands/health-checks/runner.ts"],"names":[],"mappings":"AAAA;;GAEG;AAoBH,OAAO,KAAK,EAAoB,YAAY,EAAE,MAAM,YAAY,CAAC;AAEjE;;GAEG;AACH,wBAAsB,YAAY,IAAI,OAAO,CAAC,YAAY,CAAC,CAuE1D"}
+{"version":3,"file":"runner.d.ts","sourceRoot":"","sources":["../../../src/commands/health-checks/runner.ts"],"names":[],"mappings":"AAAA;;GAEG;AAoBH,OAAO,KAAK,EAAoB,YAAY,EAAE,MAAM,YAAY,CAAC;AAEjE;;GAEG;AACH,wBAAsB,YAAY,IAAI,OAAO,CAAC,YAAY,CAAC,CAyF1D"}

package/dist/commands/health-checks/runner.js

@@ -59,6 +59,24 @@ export async function runAllChecks() {
         const memoryPath = resolvePath(desc.paths.globalMemory) ?? "";
         checks.push(await checkMemoryFileSize(memoryPath, maxLines));
     }
+    // 8. Check taken-over plugins
+    try {
+        const { checkTakenOverPlugins } = await import("./plugin-takeover-check.js");
+        const pluginChecks = await checkTakenOverPlugins();
+        checks.push(...pluginChecks);
+    }
+    catch {
+        // plugin takeover check is optional
+    }
+    // 9. Check MCP self-registration
+    try {
+        const { checkSelfRegistration } = await import("./mcp-check.js");
+        const selfRegChecks = await checkSelfRegistration();
+        checks.push(...selfRegChecks);
+    }
+    catch {
+        // self-registration check is optional
+    }
     // Calculate summary
     const summary = {
         passed: checks.filter((c) => c.status === "pass").length,

package/dist/commands/health-checks/runner.js.map

@@ -1 +1 @@
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+{"version":3,"file":"runner.js","sourceRoot":"","sources":["../../../src/commands/health-checks/runner.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAEL,aAAa,EACb,WAAW,EACX,UAAU,GACX,MAAM,gBAAgB,CAAC;AACxB,OAAO,EACL,yBAAyB,EACzB,kBAAkB,EAClB,mBAAmB,EACnB,mBAAmB,EACnB,kBAAkB,EAClB,kBAAkB,EAClB,oBAAoB,GACrB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EAAE,qBAAqB,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AAC/E,OAAO,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAC1D,OAAO,EAAE,iBAAiB,EAAE,MAAM,yBAAyB,CAAC;AAG5D;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,YAAY;IAChC,MAAM,MAAM,GAAuB,EAAE,CAAC;IAEtC,qCAAqC;IACrC,MAAM,CAAC,IAAI,CAAC,MAAM,yBAAyB,EAAE,CAAC,CAAC;IAE/C,iEAAiE;IACjE,iDAAiD;IACjD,MAAM,YAAY,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC;IAEjD,6BAA6B;IAC7B,IAAI,YAAY,EAAE,CAAC;QACjB,MAAM,CAAC,IAAI,CAAC,MAAM,kBAAkB,EAAE,CAAC,CAAC;IAC1C,CAAC;IAED,wBAAwB;IACxB,IAAI,YAAY,EAAE,CAAC;QACjB,MAAM,CAAC,IAAI,CAAC,MAAM,qBAAqB,EAAE,CAAC,CAAC;IAC7C,CAAC;IAED,yCAAyC;IACzC,KAAK,MAAM,CAAC,MAAM,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,CAAC;QAC3D,oBAAoB;QACpB,MAAM,CAAC,IAAI,CAAC,MAAM,mBAAmB,CAAC,MAAgB,CAAC,CAAC,CAAC;QAEzD,gDAAgD;QAChD,MAAM,UAAU,GAAG,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAClD,IAAI,UAAU,IAAI,MAAM,UAAU,CAAC,UAAU,CAAC,EAAE,CAAC;YAC/C,MAAM,CAAC,IAAI,CAAC,MAAM,mBAAmB,CAAC,UAAU,CAAC,CAAC,CAAC;QACrD,CAAC;QAED,4CAA4C;QAC5C,MAAM,aAAa,GAAG,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAClD,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,KAAK,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC;QACnE,IAAI,aAAa,EAAE,CAAC;YAClB,IAAI,GAAG,KAAK,MAAM,EAAE,CAAC;gBACnB,MAAM,CAAC,IAAI,CAAC,MAAM,kBAAkB,CAAC,aAAa,CAAC,CAAC,CAAC;YACvD,CAAC;iBAAM,IAAI,GAAG,KAAK,MAAM,EAAE,CAAC;gBAC1B,MAAM,CAAC,IAAI,CAAC,MAAM,kBAAkB,CAAC,aAAa,CAAC,CAAC,CAAC;YACvD,CAAC;QACH,CAAC;IACH,CAAC;IAED,gCAAgC;IAChC,IAAI,YAAY,EAAE,CAAC;QACjB,MAAM,CAAC,IAAI,CAAC,MAAM,oBAAoB,EAAE,CAAC,CAAC;IAC5C,CAAC;IAED,yBAAyB;IACzB,MAAM,CAAC,IAAI,CAAC,MAAM,iBAAiB,EAAE,CAAC,CAAC;IAEvC,mDAAmD;IACnD,KAAK,MAAM,CAAC,MAAM,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,cAAc,CAAC,EAAE,CAAC;QAChE,IAAI,QAAQ,IAAI,IAAI;YAAE,SAAS;QAC/B,MAAM,IAAI,GAAG,aAAa,CAAC,MAAM,CAAC,CAAC;QACnC,MAAM,UAAU,GAAG,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC;QAC9D,MAAM,CAAC,IAAI,CAAC,MAAM,mBAAmB,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC,CAAC;IAC/D,CAAC;IAED,8BAA8B;IAC9B,IAAI,CAAC;QACH,MAAM,EAAE,qBAAqB,EAAE,GAAG,MAAM,MAAM,CAAC,4BAA4B,CAAC,CAAC;QAC7E,MAAM,YAAY,GAAG,MAAM,qBAAqB,EAAE,CAAC;QACnD,MAAM,CAAC,IAAI,CAAC,GAAG,YAAY,CAAC,CAAC;IAC/B,CAAC;IAAC,MAAM,CAAC;QACP,oCAAoC;IACtC,CAAC;IAED,iCAAiC;IACjC,IAAI,CAAC;QACH,MAAM,EAAE,qBAAqB,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAC;QACjE,MAAM,aAAa,GAAG,MAAM,qBAAqB,EAAE,CAAC;QACpD,MAAM,CAAC,IAAI,CAAC,GAAG,aAAa,CAAC,CAAC;IAChC,CAAC;IAAC,MAAM,CAAC;QACP,sCAAsC;IACxC,CAAC;IAED,oBAAoB;IACpB,MAAM,OAAO,GAAG;QACd,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,MAAM;QACxD,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,MAAM;QACxD,QAAQ,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC,CAAC,MAAM;KAC3D,CAAC;IAEF,OAAO;QACL,OAAO,EAAE,OAAO,CAAC,MAAM,KAAK,CAAC;QAC7B,MAAM;QACN,OAAO;KACR,CAAC;AACJ,CAAC"}

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

@@ -1 +1 @@
-{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/commands/init.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAUpC,+EAA+E;AAC/E,eAAO,MAAM,iBAAiB,oBAAoB,CAAC;AAEnD;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB,OAAO,EAAE,OAAO,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,KAAK,EAAE,OAAO,CAAC;CAChB;AAED;;GAEG;AACH,MAAM,WAAW,kBAAkB;IACjC,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,KAAK,EAAE,OAAO,CAAC;CAChB;AAED;;GAEG;AACH,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA+BnC,CAAC;AAqDF;;GAEG;AACH,wBAAsB,UAAU,CAAC,OAAO,EAAE,iBAAiB,GAAG,OAAO,CAAC,UAAU,CAAC,CAyChF;AAED;;GAEG;AACH,wBAAsB,WAAW,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,UAAU,CAAC,CA4BlF;AAMD,qDAAqD;AACrD,wBAAgB,aAAa,IAAI,OAAO,CAOvC;AAED,oCAAoC;AACpC,wBAAgB,YAAY,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAOtD;AAED,8BAA8B;AAC9B,wBAAgB,aAAa,IAAI,MAAM,CAEtC;AAED,4DAA4D;AAC5D,wBAAsB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAWxE;AAED,yEAAyE;AACzE,wBAAsB,SAAS,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAW9D;AAED,mEAAmE;AACnE,wBAAgB,WAAW,CAAC,YAAY,EAAE,MAAM,GAAG,MAAM,CAUxD;AAED,+DAA+D;AAC/D,wBAAgB,YAAY,IAAI,OAAO,CAQtC;AAED;;;;;;;GAOG;AACH,wBAAsB,SAAS,CAAC,OAAO,EAAE;IACvC,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyJhB;AAMD;;GAEG;AACH,eAAO,MAAM,WAAW,SAoBpB,CAAC"}
+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/commands/init.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAWpC,+EAA+E;AAC/E,eAAO,MAAM,iBAAiB,oBAAoB,CAAC;AAEnD;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB,OAAO,EAAE,OAAO,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,OAAO,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,KAAK,EAAE,OAAO,CAAC;CAChB;AAED;;GAEG;AACH,MAAM,WAAW,kBAAkB;IACjC,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,KAAK,EAAE,OAAO,CAAC;CAChB;AAED;;GAEG;AACH,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CA+BnC,CAAC;AAqDF;;GAEG;AACH,wBAAsB,UAAU,CAAC,OAAO,EAAE,iBAAiB,GAAG,OAAO,CAAC,UAAU,CAAC,CA2DhF;AAED;;GAEG;AACH,wBAAsB,WAAW,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,UAAU,CAAC,CA4BlF;AAMD,qDAAqD;AACrD,wBAAgB,aAAa,IAAI,OAAO,CAOvC;AAED,oCAAoC;AACpC,wBAAgB,YAAY,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAOtD;AAED,8BAA8B;AAC9B,wBAAgB,aAAa,IAAI,MAAM,CAEtC;AAED,4DAA4D;AAC5D,wBAAsB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAWxE;AAED,yEAAyE;AACzE,wBAAsB,SAAS,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAW9D;AAED,mEAAmE;AACnE,wBAAgB,WAAW,CAAC,YAAY,EAAE,MAAM,GAAG,MAAM,CAUxD;AAED,+DAA+D;AAC/D,wBAAgB,YAAY,IAAI,OAAO,CAQtC;AAED;;;;;;;GAOG;AACH,wBAAsB,SAAS,CAAC,OAAO,EAAE;IACvC,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB,GAAG,OAAO,CAAC,IAAI,CAAC,CAuKhB;AAMD;;GAEG;AACH,eAAO,MAAM,WAAW,SAoBpB,CAAC"}

package/dist/commands/init.js

@@ -11,6 +11,7 @@ import { Command } from "commander";
 import * as fs from "node:fs/promises";
 import * as path from "node:path";
 import { execFileSync } from "node:child_process";
+import { fileURLToPath } from "node:url";
 import { stringify as yamlStringify } from "yaml";
 import { expandPath, ensureDir, pathExists } from "@mycelish/core";
 import { ensureGitignore, generateEnvTemplate, getMissingEnvVars } from "../core/env-template.js";
@@ -132,6 +133,24 @@ export async function initGlobal(options) {
     await fs.writeFile(path.join(globalPath, ".env.local"), ENV_LOCAL_CONTENT, "utf-8");
     // Write global/mcps.yaml
     await fs.writeFile(path.join(globalPath, "global/mcps.yaml"), GLOBAL_MCPS_YAML_CONTENT, "utf-8");
+    // Copy bundled skills (e.g. debug-mycelium) if they don't already exist
+    const __dirname = path.dirname(fileURLToPath(import.meta.url));
+    const bundledSkillsDir = path.resolve(__dirname, "../../skills");
+    const globalSkillsDir = path.join(globalPath, "global", "skills");
+    try {
+        const entries = await fs.readdir(bundledSkillsDir);
+        const skills = entries.filter((f) => f.endsWith(".md"));
+        for (const skill of skills) {
+            const dest = path.join(globalSkillsDir, skill);
+            if (!(await pathExists(dest))) {
+                await fs.copyFile(path.join(bundledSkillsDir, skill), dest);
+                console.log(`  Bundled skill: ${skill}`);
+            }
+        }
+    }
+    catch {
+        // bundled skills dir doesn't exist in this build — skip
+    }
     return {
         success: true,
         path: globalPath,
@@ -398,6 +417,20 @@ export async function autoSetup(options) {
             // Push failed — non-critical
         }
     }
+    // Self-register Mycelium as an MCP in all detected tools
+    try {
+        const { selfRegister } = await import("../core/self-register.js");
+        const { getTracer } = await import("../core/global-tracer.js");
+        const log = getTracer().createTrace("init");
+        const regResults = await selfRegister(log);
+        const registered = Object.entries(regResults).filter(([, ok]) => ok).map(([t]) => t);
+        if (registered.length > 0) {
+            console.log(`\n  Mycelium MCP registered in: ${registered.join(", ")}`);
+        }
+    }
+    catch (err) {
+        console.warn("Self-registration failed:", err instanceof Error ? err.message : String(err));
+    }
     console.log("\nSetup complete. Next steps:");
     console.log("  mycelium sync          # Push config to all installed tools");
     console.log(`  mycelium serve         # Start dashboard at http://localhost:${DEFAULT_PORT}`);

package/dist/commands/init.js.map

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

@@ -0,0 +1,9 @@
+/**
+ * mcp command — starts the Mycelium MCP server (stdio transport).
+ *
+ * Usage:
+ *   mycelium mcp              # Start MCP server on stdio
+ */
+import { Command } from "commander";
+export declare const mcpCommand: Command;
+//# sourceMappingURL=mcp.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"mcp.d.ts","sourceRoot":"","sources":["../../src/commands/mcp.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,eAAO,MAAM,UAAU,SAWnB,CAAC"}

package/dist/commands/mcp.js

@@ -0,0 +1,17 @@
+/**
+ * mcp command — starts the Mycelium MCP server (stdio transport).
+ *
+ * Usage:
+ *   mycelium mcp              # Start MCP server on stdio
+ */
+import { Command } from "commander";
+export const mcpCommand = new Command("mcp")
+    .description("Start Mycelium MCP server (stdio transport)")
+    .action(async () => {
+    const { StdioServerTransport } = await import("@modelcontextprotocol/sdk/server/stdio.js");
+    const { createMyceliumMcpServer } = await import("../mcp/server.js");
+    const server = createMyceliumMcpServer();
+    const transport = new StdioServerTransport();
+    await server.connect(transport);
+});
+//# sourceMappingURL=mcp.js.map

package/dist/commands/mcp.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"mcp.js","sourceRoot":"","sources":["../../src/commands/mcp.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,MAAM,CAAC,MAAM,UAAU,GAAG,IAAI,OAAO,CAAC,KAAK,CAAC;KACzC,WAAW,CAAC,6CAA6C,CAAC;KAC1D,MAAM,CAAC,KAAK,IAAI,EAAE;IACjB,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,MAAM,CAC3C,2CAA2C,CAC5C,CAAC;IACF,MAAM,EAAE,uBAAuB,EAAE,GAAG,MAAM,MAAM,CAAC,kBAAkB,CAAC,CAAC;IAErE,MAAM,MAAM,GAAG,uBAAuB,EAAE,CAAC;IACzC,MAAM,SAAS,GAAG,IAAI,oBAAoB,EAAE,CAAC;IAC7C,MAAM,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;AAClC,CAAC,CAAC,CAAC"}

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

@@ -1 +1 @@
-{"version":3,"file":"migrate.d.ts","sourceRoot":"","sources":["../../src/commands/migrate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAiBpC,eAAO,MAAM,cAAc,SA0LvB,CAAC"}
+{"version":3,"file":"migrate.d.ts","sourceRoot":"","sources":["../../src/commands/migrate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAsBpC,eAAO,MAAM,cAAc,SA0OvB,CAAC"}

package/dist/commands/migrate.js

@@ -13,6 +13,11 @@
 import { Command } from "commander";
 import { scanAllTools, scanTool, generateMigrationPlan, executeMigration, clearMigration, writeHooksYaml, } from "../core/migrator/index.js";
 import { createSnapshot, restoreSnapshot, listSnapshots, deleteSnapshot, } from "../core/snapshot.js";
+import { migrateManifestV1ToV2 } from "../core/manifest-migrator.js";
+import * as fs from "node:fs/promises";
+import * as path from "node:path";
+import { homedir } from "node:os";
+import { getTracer } from "../core/global-tracer.js";
 export const migrateCommand = new Command("migrate")
     .description("Scan installed tools and migrate configs into Mycelium")
     .option("--apply", "Execute migration (default is dry-run)")
@@ -26,6 +31,7 @@ export const migrateCommand = new Command("migrate")
     .option("--snapshots", "List all saved snapshots")
     .option("--snapshot-delete <name>", "Delete a saved snapshot")
     .action(async (opts) => {
+    const log = getTracer().createTrace("migrate");
     const apply = opts.apply ?? false;
     const strategy = (opts.strategy ?? "latest");
     // Handle snapshot operations
@@ -89,6 +95,7 @@ export const migrateCommand = new Command("migrate")
         return;
     }
     // Scan
+    log.info({ scope: "migration", op: "scan", msg: "Scanning installed tools" });
     console.log("Scanning installed tools...\n");
     const scans = opts.tool
         ? [await scanTool(opts.tool)]
@@ -159,7 +166,49 @@ export const migrateCommand = new Command("migrate")
         console.log("\nRun with --apply to execute migration.");
         return;
     }
+    // Migrate v1 manifests (enabled → state) if needed
+    const myceliumDir = path.join(homedir(), ".mycelium");
+    const manifestPaths = ["skills.json", "mcps.json", "global.json"];
+    for (const manifestFile of manifestPaths) {
+        const manifestPath = path.join(myceliumDir, manifestFile);
+        try {
+            const raw = await fs.readFile(manifestPath, "utf-8");
+            const parsed = JSON.parse(raw);
+            // Detect v1 format: any item has "enabled" field
+            const sections = ["skills", "mcps", "hooks", "memory"];
+            const hasEnabledField = sections.some((s) => {
+                const items = parsed[s];
+                if (!items || typeof items !== "object")
+                    return false;
+                return Object.values(items).some((v) => typeof v === "object" && v !== null && "enabled" in v);
+            });
+            if (hasEnabledField) {
+                // Check for plugin-skills.json
+                const pluginSkillsPath = path.join(myceliumDir, "plugin-skills.json");
+                let pluginSkills;
+                try {
+                    const psRaw = await fs.readFile(pluginSkillsPath, "utf-8");
+                    pluginSkills = JSON.parse(psRaw);
+                }
+                catch {
+                    // No plugin-skills.json, that's fine
+                }
+                const migrated = migrateManifestV1ToV2(parsed, pluginSkills);
+                await fs.writeFile(manifestPath, JSON.stringify(migrated, null, 2) + "\n");
+                console.log(`  Migrated ${manifestFile} from v1 (enabled) to v2 (state)`);
+                // Delete plugin-skills.json after importing its data
+                if (pluginSkills) {
+                    await fs.rm(pluginSkillsPath, { force: true });
+                    console.log("  Removed plugin-skills.json (data imported into manifests)");
+                }
+            }
+        }
+        catch {
+            // File doesn't exist, skip
+        }
+    }
     // Execute
+    log.info({ scope: "migration", op: "execute", msg: `Applying migration: ${plan.skills.length} skills, ${plan.mcps.length} MCPs` });
     console.log("\nApplying migration...");
     const result = await executeMigration(plan);
     // Write hooks from scanned data
@@ -168,10 +217,12 @@ export const migrateCommand = new Command("migrate")
         await writeHooksYaml(allHooks);
         console.log(`Wrote ${allHooks.length} hooks to hooks.yaml`);
     }
+    log.info({ scope: "migration", op: "complete", msg: `Imported ${result.skillsImported} skills, ${result.mcpsImported} MCPs, ${result.memoryImported} memory` });
     console.log(`\nDone! Imported ${result.skillsImported} skills, ${result.mcpsImported} MCPs, ${result.memoryImported} memory files.`);
     if (result.errors.length > 0) {
         console.error("Errors:");
         for (const e of result.errors) {
+            log.error({ scope: "migration", op: "execute", msg: e, error: e });
             console.error(`  - ${e}`);
         }
     }