@goondocks/myco 0.14.4 → 0.15.0

package/dist/{chunk-TNCBMGWB.js → chunk-X5IXK5KO.js}

@@ -1,8 +1,143 @@
 import { createRequire as __cr } from 'node:module'; const require = __cr(import.meta.url);
 
 // src/symbionts/installer.ts
+import fs3 from "fs";
+import path3 from "path";
+
+// src/symbionts/toml-helpers.ts
+var TOML_SECTION_RE = /^\[([^\]]+)\]/;
+function findTomlSectionEnd(raw, searchStart, serverName) {
+  const subsectionPrefix = `mcp_servers.${serverName}.`;
+  const rawLines = raw.slice(searchStart).split("\n");
+  let offset = searchStart;
+  for (const line of rawLines) {
+    offset += line.length + 1;
+    const m = line.match(TOML_SECTION_RE);
+    if (m && !m[1].startsWith(subsectionPrefix) && m[1] !== `mcp_servers.${serverName}`) {
+      return offset - line.length - 1;
+    }
+  }
+  return raw.length;
+}
+function buildTomlMcpSection(raw, serverName, server) {
+  const sectionHeader = `[mcp_servers.${serverName}]`;
+  const lines = [sectionHeader];
+  for (const [key, val] of Object.entries(server)) {
+    if (key === "env" && typeof val === "object" && val !== null) continue;
+    if (typeof val === "string") {
+      lines.push(`${key} = "${val}"`);
+    } else if (Array.isArray(val)) {
+      lines.push(`${key} = [${val.map((v) => `"${v}"`).join(", ")}]`);
+    } else if (typeof val === "boolean") {
+      lines.push(`${key} = ${val}`);
+    }
+  }
+  const env = server.env;
+  if (env && Object.keys(env).length > 0) {
+    lines.push("");
+    lines.push(`[mcp_servers.${serverName}.env]`);
+    for (const [key, val] of Object.entries(env)) {
+      lines.push(`${key} = "${val}"`);
+    }
+  }
+  const block = lines.join("\n");
+  let updated;
+  if (raw.includes(sectionHeader)) {
+    const startIdx = raw.indexOf(sectionHeader);
+    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, serverName);
+    const before = raw.slice(0, startIdx).trimEnd();
+    const after = raw.slice(endIdx);
+    const separator = before ? "\n\n" : "";
+    updated = (before + separator + block + after).trimEnd() + "\n";
+  } else {
+    const separator = raw.trim() ? "\n\n" : "";
+    updated = (raw.trimEnd() + separator + block).trimEnd() + "\n";
+  }
+  return updated;
+}
+
+// src/symbionts/settings-merge.ts
+function deepMergeSettings(target, source) {
+  const result = { ...target };
+  for (const [key, sourceVal] of Object.entries(source)) {
+    const targetVal = result[key];
+    if (Array.isArray(sourceVal) && Array.isArray(targetVal)) {
+      result[key] = [.../* @__PURE__ */ new Set([...targetVal, ...sourceVal])];
+    } else if (isPlainObject(sourceVal) && isPlainObject(targetVal)) {
+      result[key] = deepMergeSettings(
+        targetVal,
+        sourceVal
+      );
+    } else {
+      result[key] = sourceVal;
+    }
+  }
+  return result;
+}
+function isPlainObject(val) {
+  return typeof val === "object" && val !== null && !Array.isArray(val);
+}
+function deepRemoveSettings(target, template) {
+  let changed = false;
+  for (const [key, templateVal] of Object.entries(template)) {
+    const targetVal = target[key];
+    if (targetVal === void 0) continue;
+    if (Array.isArray(templateVal) && Array.isArray(targetVal)) {
+      const templateSet = new Set(templateVal.map(String));
+      const filtered = targetVal.filter((v) => !templateSet.has(String(v)));
+      if (filtered.length !== targetVal.length) {
+        if (filtered.length > 0) {
+          target[key] = filtered;
+        } else {
+          delete target[key];
+        }
+        changed = true;
+      }
+    } else if (isPlainObject(templateVal) && isPlainObject(targetVal)) {
+      if (deepRemoveSettings(targetVal, templateVal)) {
+        if (Object.keys(targetVal).length === 0) {
+          delete target[key];
+        }
+        changed = true;
+      }
+    } else {
+      if (String(targetVal) === String(templateVal)) {
+        delete target[key];
+        changed = true;
+      }
+    }
+  }
+  return changed;
+}
+
+// src/symbionts/json-helpers.ts
 import fs from "fs";
 import path from "path";
+function readJsonFile(filePath) {
+  try {
+    return JSON.parse(fs.readFileSync(filePath, "utf-8"));
+  } catch {
+    return {};
+  }
+}
+function writeJsonFile(filePath, data) {
+  fs.mkdirSync(path.dirname(filePath), { recursive: true });
+  fs.writeFileSync(filePath, JSON.stringify(data, null, 2) + "\n", "utf-8");
+}
+function writeOrDeleteJsonFile(filePath, data) {
+  if (Object.keys(data).length === 0) {
+    try {
+      fs.unlinkSync(filePath);
+    } catch {
+    }
+  } else {
+    writeJsonFile(filePath, data);
+  }
+}
+
+// src/symbionts/install-helpers.ts
+import fs2 from "fs";
+import path2 from "path";
 var MYCO_HOOK_COMMAND_PREFIX = "myco-run";
 var MYCO_HOOK_GUARD_PREFIX = "node .agents/myco-hook.cjs";
 function isMycoHookCommand(command) {
@@ -13,6 +148,35 @@ function isMycoHookGroup(group) {
   if (typeof group.command === "string" && isMycoHookCommand(group.command)) return true;
   return false;
 }
+function ensureAgentsMd(projectRoot, packageRoot) {
+  const agentsMdPath = path2.join(projectRoot, "AGENTS.md");
+  if (fs2.existsSync(agentsMdPath)) return;
+  const candidates = [
+    path2.join(packageRoot, "src/symbionts/templates/agents-starter.md"),
+    path2.join(packageRoot, "dist/src/symbionts/templates/agents-starter.md")
+  ];
+  for (const p of candidates) {
+    try {
+      const content = fs2.readFileSync(p, "utf-8");
+      fs2.writeFileSync(agentsMdPath, content, "utf-8");
+      return;
+    } catch {
+    }
+  }
+}
+function ensureSymlink(linkPath, target) {
+  try {
+    if (fs2.readlinkSync(linkPath) === target) return;
+  } catch {
+  }
+  try {
+    fs2.rmSync(linkPath, { recursive: true, force: true });
+  } catch {
+  }
+  fs2.symlinkSync(target, linkPath);
+}
+
+// src/symbionts/installer.ts
 var GITIGNORE_COMMENT = "# Myco managed (machine-specific)";
 var GITIGNORE_SKILLS_COMMENT_LEGACY = "# Myco skill symlinks (machine-specific)";
 var WRANGLER_CACHE_DIR = ".wrangler/";
@@ -46,13 +210,13 @@ var SymbiontInstaller = class {
     if (!reg?.hooksTarget) return false;
     const guardTemplate = this.loadHookGuardTemplate();
     if (!guardTemplate) return false;
-    const targetPath = path.join(this.projectRoot, HOOK_GUARD_PROJECT_PATH);
+    const targetPath = path3.join(this.projectRoot, HOOK_GUARD_PROJECT_PATH);
     try {
-      if (fs.readFileSync(targetPath, "utf-8") === guardTemplate) return false;
+      if (fs3.readFileSync(targetPath, "utf-8") === guardTemplate) return false;
     } catch {
     }
-    fs.mkdirSync(path.dirname(targetPath), { recursive: true });
-    fs.writeFileSync(targetPath, guardTemplate, "utf-8");
+    fs3.mkdirSync(path3.dirname(targetPath), { recursive: true });
+    fs3.writeFileSync(targetPath, guardTemplate, "utf-8");
     return true;
   }
   /**
@@ -62,9 +226,9 @@ var SymbiontInstaller = class {
   uninstallHookGuard() {
     const reg = this.manifest.registration;
     if (!reg?.hooksTarget) return false;
-    const targetPath = path.join(this.projectRoot, HOOK_GUARD_PROJECT_PATH);
+    const targetPath = path3.join(this.projectRoot, HOOK_GUARD_PROJECT_PATH);
     try {
-      fs.unlinkSync(targetPath);
+      fs3.unlinkSync(targetPath);
       return true;
     } catch {
       return false;
@@ -73,12 +237,12 @@ var SymbiontInstaller = class {
   /** Load the hook-guard template from package root. */
   loadHookGuardTemplate() {
     const candidates = [
-      path.join(this.packageRoot, TEMPLATES_SUBDIR, HOOK_GUARD_TEMPLATE_FILENAME),
-      path.join(this.packageRoot, "dist", TEMPLATES_SUBDIR, HOOK_GUARD_TEMPLATE_FILENAME)
+      path3.join(this.packageRoot, TEMPLATES_SUBDIR, HOOK_GUARD_TEMPLATE_FILENAME),
+      path3.join(this.packageRoot, "dist", TEMPLATES_SUBDIR, HOOK_GUARD_TEMPLATE_FILENAME)
     ];
     for (const p of candidates) {
       try {
-        return fs.readFileSync(p, "utf-8");
+        return fs3.readFileSync(p, "utf-8");
       } catch {
       }
     }
@@ -87,13 +251,13 @@ var SymbiontInstaller = class {
   /** Load a JSON template file for this symbiont. Returns null if not found. */
   loadTemplate(name) {
     const candidates = [
-      path.join(this.packageRoot, TEMPLATES_SUBDIR, this.manifest.name, `${name}.json`),
+      path3.join(this.packageRoot, TEMPLATES_SUBDIR, this.manifest.name, `${name}.json`),
       // tsup preserves the src/ prefix under dist/, so the same subdir works in both layouts
-      path.join(this.packageRoot, "dist", TEMPLATES_SUBDIR, this.manifest.name, `${name}.json`)
+      path3.join(this.packageRoot, "dist", TEMPLATES_SUBDIR, this.manifest.name, `${name}.json`)
     ];
     for (const filePath of candidates) {
       try {
-        return JSON.parse(fs.readFileSync(filePath, "utf-8"));
+        return JSON.parse(fs3.readFileSync(filePath, "utf-8"));
       } catch {
       }
     }
@@ -130,7 +294,7 @@ var SymbiontInstaller = class {
    * Single read → apply all transforms in memory → single write.
    */
   installBatchedJson(reg) {
-    const targetPath = path.join(this.projectRoot, reg.hooksTarget ?? reg.mcpTarget ?? reg.settingsTarget);
+    const targetPath = path3.join(this.projectRoot, reg.hooksTarget ?? reg.mcpTarget ?? reg.settingsTarget);
     let data = readJsonFile(targetPath);
     let hooks = false, mcp = false, settings = false;
     const hooksTemplate = reg.hooksTarget ? this.loadTemplate("hooks") : null;
@@ -188,7 +352,7 @@ var SymbiontInstaller = class {
    * Batched uninstall for agents where hooks, MCP, and settings share one JSON file.
    */
   uninstallBatchedJson(reg) {
-    const targetPath = path.join(this.projectRoot, reg.hooksTarget ?? reg.mcpTarget ?? reg.settingsTarget);
+    const targetPath = path3.join(this.projectRoot, reg.hooksTarget ?? reg.mcpTarget ?? reg.settingsTarget);
     const data = readJsonFile(targetPath);
     if (Object.keys(data).length === 0) {
       return { hooks: false, mcp: false, skills: this.uninstallSkills(), settings: false, instructions: this.uninstallInstructions() };
@@ -238,35 +402,35 @@ var SymbiontInstaller = class {
     const reg = this.manifest.registration;
     if (!reg?.instructionsFile) return false;
     ensureAgentsMd(this.projectRoot, this.packageRoot);
-    const targetPath = path.join(this.projectRoot, reg.instructionsFile);
+    const targetPath = path3.join(this.projectRoot, reg.instructionsFile);
     let existing = null;
     try {
-      existing = fs.readFileSync(targetPath, "utf-8");
+      existing = fs3.readFileSync(targetPath, "utf-8");
     } catch {
     }
     if (existing !== null) {
       if (existing.includes(INSTRUCTIONS_REF_START) || existing.includes(INSTRUCTIONS_STUB_MARKER)) {
         return false;
       }
-      fs.writeFileSync(targetPath, INSTRUCTIONS_REF_BLOCK + existing, "utf-8");
+      fs3.writeFileSync(targetPath, INSTRUCTIONS_REF_BLOCK + existing, "utf-8");
       return true;
     }
     const templateCandidates = [
-      path.join(this.packageRoot, "src/symbionts/templates/instructions-stub.md"),
-      path.join(this.packageRoot, "dist/src/symbionts/templates/instructions-stub.md")
+      path3.join(this.packageRoot, "src/symbionts/templates/instructions-stub.md"),
+      path3.join(this.packageRoot, "dist/src/symbionts/templates/instructions-stub.md")
     ];
     let stub = null;
     for (const p of templateCandidates) {
       try {
-        stub = fs.readFileSync(p, "utf-8");
+        stub = fs3.readFileSync(p, "utf-8");
         break;
       } catch {
       }
     }
     if (!stub) return false;
     stub = stub.replace("{agentDisplayName}", this.manifest.displayName);
-    fs.mkdirSync(path.dirname(targetPath), { recursive: true });
-    fs.writeFileSync(targetPath, stub, "utf-8");
+    fs3.mkdirSync(path3.dirname(targetPath), { recursive: true });
+    fs3.writeFileSync(targetPath, stub, "utf-8");
     return true;
   }
   /**
@@ -277,15 +441,15 @@ var SymbiontInstaller = class {
   uninstallInstructions() {
     const reg = this.manifest.registration;
     if (!reg?.instructionsFile) return false;
-    const targetPath = path.join(this.projectRoot, reg.instructionsFile);
+    const targetPath = path3.join(this.projectRoot, reg.instructionsFile);
     let content;
     try {
-      content = fs.readFileSync(targetPath, "utf-8");
+      content = fs3.readFileSync(targetPath, "utf-8");
     } catch {
       return false;
     }
     if (content.includes(INSTRUCTIONS_STUB_MARKER)) {
-      fs.unlinkSync(targetPath);
+      fs3.unlinkSync(targetPath);
       return true;
     }
     if (content.includes(INSTRUCTIONS_REF_START)) {
@@ -294,7 +458,7 @@ var SymbiontInstaller = class {
       if (endIdx > startIdx) {
         const afterEnd = endIdx + INSTRUCTIONS_REF_END.length;
         const cleaned = (content.slice(0, startIdx) + content.slice(afterEnd)).replace(/^\n+/, "");
-        fs.writeFileSync(targetPath, cleaned, "utf-8");
+        fs3.writeFileSync(targetPath, cleaned, "utf-8");
         return true;
       }
     }
@@ -303,7 +467,7 @@ var SymbiontInstaller = class {
   /** List skill directory names from the package root. Returns empty array if not found. */
   listSkillDirs() {
     try {
-      return fs.readdirSync(path.join(this.packageRoot, SKILLS_SUBDIR), { withFileTypes: true }).filter((d) => d.isDirectory()).map((d) => d.name);
+      return fs3.readdirSync(path3.join(this.packageRoot, SKILLS_SUBDIR), { withFileTypes: true }).filter((d) => d.isDirectory()).map((d) => d.name);
     } catch {
       return [];
     }
@@ -319,13 +483,12 @@ var SymbiontInstaller = class {
     const skillNames = this.listSkillDirs();
     const desired = [
       ...skillNames.map((name) => `${CANONICAL_SKILLS_DIR}/${name}`),
-      ...reg.skillsTarget !== CANONICAL_SKILLS_DIR ? skillNames.map((name) => `${reg.skillsTarget}/${name}`) : [],
       WRANGLER_CACHE_DIR
     ];
-    const gitignorePath = path.join(this.projectRoot, ".gitignore");
+    const gitignorePath = path3.join(this.projectRoot, ".gitignore");
     let content = "";
     try {
-      content = fs.readFileSync(gitignorePath, "utf-8");
+      content = fs3.readFileSync(gitignorePath, "utf-8");
     } catch {
     }
     const stripped = this.stripMycoGitignoreBlock(content, skillNames);
@@ -337,7 +500,7 @@ ${desired.join("\n")}
     const spacer = stripped.length > 0 && desiredBlock.length > 0 ? "\n" : "";
     const result = stripped + separator + spacer + desiredBlock;
     if (result === content) return;
-    fs.writeFileSync(gitignorePath, result, "utf-8");
+    fs3.writeFileSync(gitignorePath, result, "utf-8");
   }
   /**
    * Remove all Myco-owned gitignore entries: the comment header, per-skill
@@ -372,7 +535,7 @@ ${desired.join("\n")}
     if (!reg?.hooksTarget) return false;
     const template = this.loadTemplate("hooks");
     if (!template) return false;
-    const targetPath = path.join(this.projectRoot, reg.hooksTarget);
+    const targetPath = path3.join(this.projectRoot, reg.hooksTarget);
     const settings = readJsonFile(targetPath);
     const existingHooks = settings.hooks ?? {};
     const mergedHooks = {};
@@ -400,7 +563,7 @@ ${desired.join("\n")}
     if (!reg?.mcpTarget) return false;
     const template = this.loadTemplate("mcp");
     if (!template) return false;
-    const targetPath = path.join(this.projectRoot, reg.mcpTarget);
+    const targetPath = path3.join(this.projectRoot, reg.mcpTarget);
     const mcpFormat = reg.mcpFormat ?? "json";
     if (mcpFormat === "toml") {
       return this.installMcpToml(targetPath, template);
@@ -422,14 +585,14 @@ ${desired.join("\n")}
   installMcpToml(targetPath, template) {
     let raw = "";
     try {
-      raw = fs.readFileSync(targetPath, "utf-8");
+      raw = fs3.readFileSync(targetPath, "utf-8");
     } catch {
     }
     for (const [name, def] of Object.entries(template)) {
       raw = buildTomlMcpSection(raw, name, def);
     }
-    fs.mkdirSync(path.dirname(targetPath), { recursive: true });
-    fs.writeFileSync(targetPath, raw, "utf-8");
+    fs3.mkdirSync(path3.dirname(targetPath), { recursive: true });
+    fs3.writeFileSync(targetPath, raw, "utf-8");
     return true;
   }
   /**
@@ -442,23 +605,24 @@ ${desired.join("\n")}
     if (!reg?.skillsTarget) return false;
     const skillNames = this.listSkillDirs();
     if (skillNames.length === 0) return false;
-    const skillsSrc = path.join(this.packageRoot, SKILLS_SUBDIR);
-    const canonicalDir = path.join(this.projectRoot, CANONICAL_SKILLS_DIR);
-    fs.mkdirSync(canonicalDir, { recursive: true });
+    const skillsSrc = path3.join(this.packageRoot, SKILLS_SUBDIR);
+    const canonicalDir = path3.join(this.projectRoot, CANONICAL_SKILLS_DIR);
+    fs3.mkdirSync(canonicalDir, { recursive: true });
     for (const name of skillNames) {
-      const canonicalLink = path.join(canonicalDir, name);
-      const target = path.join(skillsSrc, name);
+      const canonicalLink = path3.join(canonicalDir, name);
+      const target = path3.join(skillsSrc, name);
       ensureSymlink(canonicalLink, target);
     }
-    const agentSkillsDir = path.join(this.projectRoot, reg.skillsTarget);
-    const canonicalRel = path.relative(agentSkillsDir, canonicalDir);
+    const agentSkillsDir = path3.join(this.projectRoot, reg.skillsTarget);
+    const canonicalRel = path3.relative(agentSkillsDir, canonicalDir);
     if (reg.skillsTarget !== CANONICAL_SKILLS_DIR) {
-      fs.mkdirSync(agentSkillsDir, { recursive: true });
+      fs3.mkdirSync(agentSkillsDir, { recursive: true });
       for (const name of skillNames) {
-        const agentLink = path.join(agentSkillsDir, name);
-        const relTarget = path.join(canonicalRel, name);
+        const agentLink = path3.join(agentSkillsDir, name);
+        const relTarget = path3.join(canonicalRel, name);
         ensureSymlink(agentLink, relTarget);
       }
+      ensureLocalSkillsGitignore(agentSkillsDir);
     }
     return true;
   }
@@ -471,7 +635,7 @@ ${desired.join("\n")}
     if (!reg?.settingsTarget) return false;
     const template = this.loadTemplate("settings");
     if (!template) return false;
-    const targetPath = path.join(this.projectRoot, reg.settingsTarget);
+    const targetPath = path3.join(this.projectRoot, reg.settingsTarget);
     const existing = readJsonFile(targetPath);
     const merged = deepMergeSettings(existing, template);
     writeJsonFile(targetPath, merged);
@@ -488,7 +652,7 @@ ${desired.join("\n")}
     if (!reg?.settingsTarget) return false;
     const template = this.loadTemplate("settings");
     if (!template) return false;
-    const targetPath = path.join(this.projectRoot, reg.settingsTarget);
+    const targetPath = path3.join(this.projectRoot, reg.settingsTarget);
     const settings = readJsonFile(targetPath);
     if (Object.keys(settings).length === 0) return false;
     const changed = deepRemoveSettings(settings, template);
@@ -500,7 +664,7 @@ ${desired.join("\n")}
   uninstallHooks() {
     const reg = this.manifest.registration;
     if (!reg?.hooksTarget) return false;
-    const targetPath = path.join(this.projectRoot, reg.hooksTarget);
+    const targetPath = path3.join(this.projectRoot, reg.hooksTarget);
     const settings = readJsonFile(targetPath);
     const existingHooks = settings.hooks ?? {};
     if (Object.keys(existingHooks).length === 0) return false;
@@ -525,7 +689,7 @@ ${desired.join("\n")}
   uninstallMcp() {
     const reg = this.manifest.registration;
     if (!reg?.mcpTarget) return false;
-    const targetPath = path.join(this.projectRoot, reg.mcpTarget);
+    const targetPath = path3.join(this.projectRoot, reg.mcpTarget);
     const mcpFormat = reg.mcpFormat ?? "json";
     if (mcpFormat === "toml") {
       return this.uninstallMcpToml(targetPath);
@@ -548,7 +712,7 @@ ${desired.join("\n")}
   uninstallMcpToml(targetPath) {
     let raw = "";
     try {
-      raw = fs.readFileSync(targetPath, "utf-8");
+      raw = fs3.readFileSync(targetPath, "utf-8");
     } catch {
       return false;
     }
@@ -561,11 +725,11 @@ ${desired.join("\n")}
     const updated = (before + (before && after ? "\n\n" : "") + after).trimEnd();
     if (!updated.trim()) {
       try {
-        fs.unlinkSync(targetPath);
+        fs3.unlinkSync(targetPath);
       } catch {
       }
     } else {
-      fs.writeFileSync(targetPath, updated + "\n", "utf-8");
+      fs3.writeFileSync(targetPath, updated + "\n", "utf-8");
     }
     return true;
   }
@@ -578,214 +742,69 @@ ${desired.join("\n")}
     let removed = false;
     if (reg.skillsTarget !== CANONICAL_SKILLS_DIR) {
       for (const name of skillNames) {
-        const link = path.join(this.projectRoot, reg.skillsTarget, name);
+        const link = path3.join(this.projectRoot, reg.skillsTarget, name);
         try {
-          fs.unlinkSync(link);
+          fs3.unlinkSync(link);
           removed = true;
         } catch {
         }
       }
       try {
-        fs.rmdirSync(path.join(this.projectRoot, reg.skillsTarget));
+        fs3.rmdirSync(path3.join(this.projectRoot, reg.skillsTarget));
       } catch {
       }
     }
-    const canonicalDir = path.join(this.projectRoot, CANONICAL_SKILLS_DIR);
+    const canonicalDir = path3.join(this.projectRoot, CANONICAL_SKILLS_DIR);
     for (const name of skillNames) {
-      const link = path.join(canonicalDir, name);
+      const link = path3.join(canonicalDir, name);
       try {
-        fs.unlinkSync(link);
+        fs3.unlinkSync(link);
         removed = true;
       } catch {
       }
     }
     try {
-      fs.rmdirSync(canonicalDir);
+      fs3.rmdirSync(canonicalDir);
     } catch {
     }
     try {
-      fs.rmdirSync(path.join(this.projectRoot, ".agents"));
+      fs3.rmdirSync(path3.join(this.projectRoot, ".agents"));
     } catch {
     }
     return removed;
   }
   /** Remove Myco entries from project .gitignore. */
   cleanGitignore() {
-    const gitignorePath = path.join(this.projectRoot, ".gitignore");
+    const gitignorePath = path3.join(this.projectRoot, ".gitignore");
     let content = "";
     try {
-      content = fs.readFileSync(gitignorePath, "utf-8");
+      content = fs3.readFileSync(gitignorePath, "utf-8");
     } catch {
       return;
     }
     const cleaned = this.stripMycoGitignoreBlock(content, this.listSkillDirs()).trim();
     if (cleaned) {
-      fs.writeFileSync(gitignorePath, cleaned + "\n", "utf-8");
+      fs3.writeFileSync(gitignorePath, cleaned + "\n", "utf-8");
     } else {
       try {
-        fs.unlinkSync(gitignorePath);
+        fs3.unlinkSync(gitignorePath);
       } catch {
       }
     }
   }
 };
-var TOML_SECTION_RE = /^\[([^\]]+)\]/;
-function findTomlSectionEnd(raw, searchStart, serverName) {
-  const subsectionPrefix = `mcp_servers.${serverName}.`;
-  const rawLines = raw.slice(searchStart).split("\n");
-  let offset = searchStart;
-  for (const line of rawLines) {
-    offset += line.length + 1;
-    const m = line.match(TOML_SECTION_RE);
-    if (m && !m[1].startsWith(subsectionPrefix) && m[1] !== `mcp_servers.${serverName}`) {
-      return offset - line.length - 1;
-    }
-  }
-  return raw.length;
-}
-function buildTomlMcpSection(raw, serverName, server) {
-  const sectionHeader = `[mcp_servers.${serverName}]`;
-  const lines = [sectionHeader];
-  for (const [key, val] of Object.entries(server)) {
-    if (key === "env" && typeof val === "object" && val !== null) continue;
-    if (typeof val === "string") {
-      lines.push(`${key} = "${val}"`);
-    } else if (Array.isArray(val)) {
-      lines.push(`${key} = [${val.map((v) => `"${v}"`).join(", ")}]`);
-    } else if (typeof val === "boolean") {
-      lines.push(`${key} = ${val}`);
-    }
-  }
-  const env = server.env;
-  if (env && Object.keys(env).length > 0) {
-    lines.push("");
-    lines.push(`[mcp_servers.${serverName}.env]`);
-    for (const [key, val] of Object.entries(env)) {
-      lines.push(`${key} = "${val}"`);
-    }
-  }
-  const block = lines.join("\n");
-  let updated;
-  if (raw.includes(sectionHeader)) {
-    const startIdx = raw.indexOf(sectionHeader);
-    const endIdx = findTomlSectionEnd(raw, startIdx + sectionHeader.length, serverName);
-    const before = raw.slice(0, startIdx).trimEnd();
-    const after = raw.slice(endIdx);
-    const separator = before ? "\n\n" : "";
-    updated = (before + separator + block + after).trimEnd() + "\n";
-  } else {
-    const separator = raw.trim() ? "\n\n" : "";
-    updated = (raw.trimEnd() + separator + block).trimEnd() + "\n";
-  }
-  return updated;
-}
-function deepMergeSettings(target, source) {
-  const result = { ...target };
-  for (const [key, sourceVal] of Object.entries(source)) {
-    const targetVal = result[key];
-    if (Array.isArray(sourceVal) && Array.isArray(targetVal)) {
-      result[key] = [.../* @__PURE__ */ new Set([...targetVal, ...sourceVal])];
-    } else if (isPlainObject(sourceVal) && isPlainObject(targetVal)) {
-      result[key] = deepMergeSettings(
-        targetVal,
-        sourceVal
-      );
-    } else {
-      result[key] = sourceVal;
-    }
-  }
-  return result;
-}
-function isPlainObject(val) {
-  return typeof val === "object" && val !== null && !Array.isArray(val);
-}
-function deepRemoveSettings(target, template) {
-  let changed = false;
-  for (const [key, templateVal] of Object.entries(template)) {
-    const targetVal = target[key];
-    if (targetVal === void 0) continue;
-    if (Array.isArray(templateVal) && Array.isArray(targetVal)) {
-      const templateSet = new Set(templateVal.map(String));
-      const filtered = targetVal.filter((v) => !templateSet.has(String(v)));
-      if (filtered.length !== targetVal.length) {
-        if (filtered.length > 0) {
-          target[key] = filtered;
-        } else {
-          delete target[key];
-        }
-        changed = true;
-      }
-    } else if (isPlainObject(templateVal) && isPlainObject(targetVal)) {
-      if (deepRemoveSettings(targetVal, templateVal)) {
-        if (Object.keys(targetVal).length === 0) {
-          delete target[key];
-        }
-        changed = true;
-      }
-    } else {
-      if (String(targetVal) === String(templateVal)) {
-        delete target[key];
-        changed = true;
-      }
-    }
-  }
-  return changed;
-}
-function readJsonFile(filePath) {
-  try {
-    return JSON.parse(fs.readFileSync(filePath, "utf-8"));
-  } catch {
-    return {};
-  }
-}
-function writeJsonFile(filePath, data) {
-  fs.mkdirSync(path.dirname(filePath), { recursive: true });
-  fs.writeFileSync(filePath, JSON.stringify(data, null, 2) + "\n", "utf-8");
-}
-function writeOrDeleteJsonFile(filePath, data) {
-  if (Object.keys(data).length === 0) {
-    try {
-      fs.unlinkSync(filePath);
-    } catch {
-    }
-  } else {
-    writeJsonFile(filePath, data);
-  }
-}
-function ensureAgentsMd(projectRoot, packageRoot) {
-  const agentsMdPath = path.join(projectRoot, "AGENTS.md");
-  if (fs.existsSync(agentsMdPath)) return;
+function syncSkillSymlinks(projectRoot, skillName, opts) {
+  const selfDir = path3.dirname(new URL(import.meta.url).pathname);
   const candidates = [
-    path.join(packageRoot, "src/symbionts/templates/agents-starter.md"),
-    path.join(packageRoot, "dist/src/symbionts/templates/agents-starter.md")
+    path3.join(selfDir, "manifests"),
+    path3.join(selfDir, "src", "symbionts", "manifests")
   ];
-  for (const p of candidates) {
-    try {
-      const content = fs.readFileSync(p, "utf-8");
-      fs.writeFileSync(agentsMdPath, content, "utf-8");
-      return;
-    } catch {
-    }
-  }
-}
-function ensureSymlink(linkPath, target) {
-  try {
-    if (fs.readlinkSync(linkPath) === target) return;
-  } catch {
-  }
-  try {
-    fs.rmSync(linkPath, { recursive: true, force: true });
-  } catch {
-  }
-  fs.symlinkSync(target, linkPath);
-}
-function syncSkillSymlinks(projectRoot, skillName, opts) {
-  const manifestDir = path.join(path.dirname(new URL(import.meta.url).pathname), "manifests");
-  if (!fs.existsSync(manifestDir)) return;
+  const manifestDir = candidates.find((d) => fs3.existsSync(d));
+  if (!manifestDir) return;
   const targets = /* @__PURE__ */ new Set();
-  for (const file of fs.readdirSync(manifestDir).filter((f) => f.endsWith(".yaml"))) {
+  for (const file of fs3.readdirSync(manifestDir).filter((f) => f.endsWith(".yaml"))) {
     try {
-      const content = fs.readFileSync(path.join(manifestDir, file), "utf-8");
+      const content = fs3.readFileSync(path3.join(manifestDir, file), "utf-8");
       const match = content.match(/skillsTarget:\s*(.+)/);
       if (match) targets.add(match[1].trim());
     } catch {
@@ -793,29 +812,46 @@ function syncSkillSymlinks(projectRoot, skillName, opts) {
   }
   for (const target of targets) {
     if (target === CANONICAL_SKILLS_DIR) continue;
-    const agentSkillsDir = path.join(projectRoot, target);
-    const linkPath = path.join(agentSkillsDir, skillName);
+    const agentSkillsDir = path3.join(projectRoot, target);
+    const linkPath = path3.join(agentSkillsDir, skillName);
     if (opts?.remove) {
       try {
-        fs.unlinkSync(linkPath);
+        fs3.unlinkSync(linkPath);
       } catch {
       }
       try {
-        fs.rmdirSync(agentSkillsDir);
+        fs3.rmdirSync(agentSkillsDir);
       } catch {
       }
     } else {
-      fs.mkdirSync(agentSkillsDir, { recursive: true });
-      const canonicalDir = path.join(projectRoot, CANONICAL_SKILLS_DIR);
-      const relTarget = path.join(path.relative(agentSkillsDir, canonicalDir), skillName);
+      fs3.mkdirSync(agentSkillsDir, { recursive: true });
+      const canonicalDir = path3.join(projectRoot, CANONICAL_SKILLS_DIR);
+      const relTarget = path3.join(path3.relative(agentSkillsDir, canonicalDir), skillName);
       ensureSymlink(linkPath, relTarget);
+      ensureLocalSkillsGitignore(agentSkillsDir);
     }
   }
 }
+var LOCAL_SKILLS_GITIGNORE = `# Myco-managed symlinks \u2014 generated skills are symlinked here automatically.
+# The canonical location for all skills is .agents/skills/.
+#
+# To add your own skill to this directory, un-ignore it:
+#   !my-skill
+*
+!.gitignore
+`;
+function ensureLocalSkillsGitignore(agentSkillsDir) {
+  const gitignorePath = path3.join(agentSkillsDir, ".gitignore");
+  try {
+    if (fs3.readFileSync(gitignorePath, "utf-8") === LOCAL_SKILLS_GITIGNORE) return;
+  } catch {
+  }
+  fs3.writeFileSync(gitignorePath, LOCAL_SKILLS_GITIGNORE, "utf-8");
+}
 
 export {
   MYCO_MCP_SERVER_NAME,
   SymbiontInstaller,
   syncSkillSymlinks
 };
-//# sourceMappingURL=chunk-TNCBMGWB.js.map
+//# sourceMappingURL=chunk-X5IXK5KO.js.map