@deimoscloud/coreai 0.1.15 → 0.1.17

package/dist/cli/index.js

@@ -1,13 +1,13 @@
 #!/usr/bin/env node
 
 // src/cli/index.ts
-import { join as join14, dirname as dirname7 } from "path";
+import { join as join14, dirname as dirname8 } from "path";
 import { fileURLToPath as fileURLToPath2 } from "url";
 import { Command } from "commander";
 
 // src/index.ts
-import { readFileSync as readFileSync6 } from "fs";
-import { dirname as dirname5, join as join8 } from "path";
+import { readFileSync as readFileSync7 } from "fs";
+import { dirname as dirname6, join as join8 } from "path";
 import { fileURLToPath } from "url";
 
 // src/config/loader.ts
@@ -153,6 +153,61 @@ var AgentError = class extends Error {
     this.name = "AgentError";
   }
 };
+function extractFrontmatter(content) {
+  const match = content.match(/^---\n([\s\S]*?)\n---\n?([\s\S]*)$/);
+  if (!match) {
+    throw new AgentError(
+      "No YAML frontmatter found. Agent MD files must start with YAML frontmatter (---)",
+      "PARSE_ERROR"
+    );
+  }
+  const frontmatterYaml = match[1];
+  const body = match[2] ?? "";
+  let frontmatter;
+  try {
+    frontmatter = parseYaml2(frontmatterYaml);
+  } catch (error) {
+    const message = error instanceof Error ? error.message : "Unknown parse error";
+    throw new AgentError(`Failed to parse YAML frontmatter: ${message}`, "PARSE_ERROR", error);
+  }
+  if (!frontmatter || typeof frontmatter !== "object") {
+    throw new AgentError("Invalid frontmatter: expected an object", "PARSE_ERROR");
+  }
+  return { frontmatter, body };
+}
+function loadAgentFromMdFile(filePath) {
+  if (!existsSync2(filePath)) {
+    throw new AgentError(`Agent file not found: ${filePath}`, "NOT_FOUND");
+  }
+  let content;
+  try {
+    content = readFileSync2(filePath, "utf-8");
+  } catch (error) {
+    const message = error instanceof Error ? error.message : "Unknown read error";
+    throw new AgentError(`Failed to read agent file ${filePath}: ${message}`, "READ_ERROR", error);
+  }
+  const { frontmatter } = extractFrontmatter(content);
+  const role = frontmatter.name || getRoleFromFilename(filePath);
+  if (!role) {
+    throw new AgentError(
+      `Agent MD file must have a 'name' field in frontmatter or a valid filename: ${filePath}`,
+      "VALIDATION_ERROR"
+    );
+  }
+  const description = frontmatter.description || "";
+  const tools = typeof frontmatter.tools === "string" ? frontmatter.tools.split(",").map((t) => t.trim()).filter(Boolean) : void 0;
+  const definition = {
+    role,
+    type: "ic-engineer",
+    // Default, actual identity is in the MD content
+    display_name: role.split("-").map((w) => w.charAt(0).toUpperCase() + w.slice(1)).join(" "),
+    description
+  };
+  if (tools) {
+    definition.tools = tools;
+  }
+  return definition;
+}
 function parseAgentYaml(content, filePath) {
   try {
     return parseYaml2(content);
@@ -184,7 +239,7 @@ function validateAgentDefinition(agent) {
   }
   return agent;
 }
-function loadAgentFromFile(filePath) {
+function loadAgentFromYamlFile(filePath) {
   if (!existsSync2(filePath)) {
     throw new AgentError(`Agent file not found: ${filePath}`, "NOT_FOUND");
   }
@@ -198,18 +253,36 @@ function loadAgentFromFile(filePath) {
   const parsed = parseAgentYaml(content, filePath);
   return validateAgentDefinition(parsed);
 }
-function listYamlFiles(dir) {
+function loadAgentFromFile(filePath) {
+  const ext = extname(filePath).toLowerCase();
+  if (ext === ".md") {
+    return loadAgentFromMdFile(filePath);
+  }
+  if (ext === ".yaml" || ext === ".yml") {
+    console.warn(
+      `Warning: YAML agent definitions are deprecated and will be removed in a future version.
+  Please migrate ${basename(filePath)} to Markdown format.`
+    );
+    return loadAgentFromYamlFile(filePath);
+  }
+  throw new AgentError(
+    `Unsupported agent file format: ${ext}. Use .md (recommended) or .yaml/.yml (deprecated)`,
+    "PARSE_ERROR"
+  );
+}
+function listAgentFiles(dir) {
   if (!existsSync2(dir)) {
     return [];
   }
   return readdirSync(dir).filter((file) => {
+    if (file.startsWith("_")) return false;
     const ext = extname(file).toLowerCase();
-    return ext === ".yaml" || ext === ".yml";
+    return ext === ".md" || ext === ".yaml" || ext === ".yml";
   }).map((file) => join2(dir, file));
 }
 function loadAgentsFromDirectory(dir, source) {
   const agents2 = /* @__PURE__ */ new Map();
-  const files = listYamlFiles(dir);
+  const files = listAgentFiles(dir);
   for (const filePath of files) {
     try {
       const definition = loadAgentFromFile(filePath);
@@ -225,6 +298,11 @@ function loadAgentsFromDirectory(dir, source) {
   }
   return agents2;
 }
+function getRoleFromFilename(filePath) {
+  const fileName = basename(filePath);
+  const ext = extname(fileName);
+  return fileName.slice(0, -ext.length);
+}
 
 // src/agents/resolver.ts
 var ResolutionError = class extends Error {
@@ -363,193 +441,73 @@ function resolveAgentDefinition(agent, config, options = {}) {
 }
 
 // src/agents/compiler.ts
-import { existsSync as existsSync3, mkdirSync, writeFileSync } from "fs";
-import { join as join3, dirname as dirname2 } from "path";
+import { existsSync as existsSync3, mkdirSync, readFileSync as readFileSync3, writeFileSync } from "fs";
+import { join as join3, dirname as dirname2, extname as extname2, isAbsolute } from "path";
+import { parse as parseYaml3, stringify as stringifyYaml } from "yaml";
 function buildAgentTools(agent, mcpServers) {
   const tools = agent.tools ? [...agent.tools] : [...DEFAULT_AGENT_TOOLS];
   if (mcpServers && mcpServers.length > 0) {
     for (const server of mcpServers) {
-      tools.push(`mcp__${server}`);
-    }
-  }
-  return tools.join(", ");
-}
-function generateKnowledgeLibrarySection(agent, lines) {
-  const kl = agent.knowledge_library;
-  if (!kl) return;
-  lines.push("## Knowledge Library Structure");
-  lines.push("");
-  if (kl.shared) {
-    lines.push("### Shared Context (Root - All Agents)");
-    lines.push("```");
-    lines.push("/KnowledgeLibrary/");
-    if (kl.shared.context) {
-      const filename = kl.shared.context.split("/").pop() ?? "context.txt";
-      lines.push(`\u251C\u2500\u2500 ${filename}`);
-    }
-    if (kl.shared.architecture) {
-      const filename = kl.shared.architecture.split("/").pop() ?? "architecture.txt";
-      lines.push(`\u251C\u2500\u2500 ${filename}`);
-    }
-    if (kl.shared.prd) {
-      const filename = kl.shared.prd.split("/").pop() ?? "prd.txt";
-      lines.push(`\u2514\u2500\u2500 ${filename}`);
-    }
-    lines.push("```");
-    if (kl.shared.remote && kl.shared.remote.length > 0) {
-      lines.push("");
-      lines.push("**Remote Documentation:**");
-      for (const remote of kl.shared.remote) {
-        lines.push(`- ${remote}`);
-      }
-    }
-    lines.push("");
-  }
-  if (kl.personal) {
-    lines.push(`### Personal Context (${agent.role})`);
-    lines.push("```");
-    lines.push(`/KnowledgeLibrary/${agent.role}/`);
-    if (kl.personal.context) {
-      lines.push("\u251C\u2500\u2500 context/");
-      lines.push("\u2502   \u2514\u2500\u2500 current.txt    # Your current state, priorities, decisions, issues");
-    }
-    if (kl.personal.history) {
-      lines.push("\u251C\u2500\u2500 history/");
-      lines.push("\u2502   \u2514\u2500\u2500 [archived context files, timestamped]");
-    }
-    if (kl.personal.inbox) {
-      lines.push("\u251C\u2500\u2500 inbox/");
-      lines.push("\u2502   \u2514\u2500\u2500 YYYYMMDD_HHMM-[agent-name]-[topic].txt  # Messages from other agents");
-    }
-    if (kl.personal.outbox) {
-      lines.push("\u251C\u2500\u2500 outbox/");
-      lines.push("\u2502   \u2514\u2500\u2500 YYYYMMDD_HHMM-to-[agent-name]-[topic].txt  # Copies of sent messages");
-    }
-    if (kl.personal.tech) {
-      lines.push("\u251C\u2500\u2500 tech/");
-      lines.push("\u2502   \u2514\u2500\u2500 [Technical docs, implementation details, working drafts]");
-    }
-    if (kl.personal.control) {
-      lines.push("\u2514\u2500\u2500 control/");
-      if (kl.personal.control.objectives) {
-        lines.push("    \u251C\u2500\u2500 objectives.txt    # Current job objectives and goals");
-      }
-      if (kl.personal.control.decisions) {
-        lines.push("    \u251C\u2500\u2500 decisions.txt     # Log of key decisions with rationale");
-      }
-      if (kl.personal.control.dependencies) {
-        lines.push("    \u251C\u2500\u2500 dependencies.txt  # Dependencies on other jobs");
-      }
-      if (kl.personal.control.index) {
-        lines.push("    \u2514\u2500\u2500 index.txt         # Optional index of files/folders");
+      const mcpTool = `mcp__${server}`;
+      if (!tools.includes(mcpTool)) {
+        tools.push(mcpTool);
       }
     }
-    lines.push("```");
-    lines.push("");
-  }
-  lines.push("---");
-  lines.push("");
-}
-function generateCommunicationSection(agent, lines) {
-  const comm = agent.communication;
-  if (!comm) return;
-  lines.push("## Communication");
-  lines.push("");
-  if (comm.inbox) {
-    lines.push(`**Inbox:** \`${comm.inbox}\``);
-  }
-  if (comm.outbox) {
-    lines.push(`**Outbox:** \`${comm.outbox}\``);
-  }
-  lines.push("");
-  if (comm.message_format || comm.outbox_format || comm.processed_dir) {
-    lines.push("### Message Conventions");
-    lines.push("");
-    if (comm.message_format) {
-      lines.push(`- **Inbox message naming:** \`${comm.message_format}\``);
-    }
-    if (comm.outbox_format) {
-      lines.push(`- **Outbox message naming:** \`${comm.outbox_format}\``);
-    }
-    if (comm.processed_dir) {
-      lines.push(`- **Processed messages:** Move handled inbox messages to \`${comm.processed_dir}\``);
-    }
-    lines.push("");
   }
+  return tools.join(", ");
 }
-function generateStartupProtocolSection(agent, lines) {
-  const protocols = agent.protocols;
-  if (!protocols?.startup) return;
-  lines.push("## When Invoked");
-  lines.push("");
-  lines.push("> **MANDATORY STARTUP PROTOCOL** - Execute before proceeding with any task.");
-  lines.push("");
-  lines.push("### Session Context Check");
-  lines.push("");
-  lines.push("First, determine if you have already loaded context in this session:");
-  lines.push("");
-  if (protocols.startup.first_session && protocols.startup.first_session.length > 0) {
-    lines.push("**If this is your FIRST invocation in this session** (no prior context loaded):");
-    lines.push("");
-    for (const step of protocols.startup.first_session) {
-      lines.push(`- [ ] ${step}`);
-    }
-    lines.push("");
-    lines.push('Acknowledge: "Startup protocol complete. Full context loaded."');
-    lines.push("");
-  }
-  if (protocols.startup.subsequent && protocols.startup.subsequent.length > 0) {
-    lines.push("**If you have ALREADY loaded context in this session** (subsequent invocation):");
-    lines.push("");
-    for (const step of protocols.startup.subsequent) {
-      lines.push(`- [ ] ${step}`);
-    }
-    lines.push("");
-    lines.push('Acknowledge: "Context already loaded. Checked inbox for new messages."');
-    lines.push("");
-  }
-  lines.push("Then proceed with the task.");
-  lines.push("");
-  lines.push("---");
-  lines.push("");
+function processIncludes(template, templateDir, depth = 0, maxDepth = 3) {
+  if (depth > maxDepth) {
+    throw new Error(`Include depth exceeded maximum of ${maxDepth}`);
+  }
+  const includePattern = /<!--\s*include:\s*(\S+)\s*-->/g;
+  return template.replace(includePattern, (_match, includePath) => {
+    const resolvedPath = isAbsolute(includePath) ? includePath : join3(templateDir, includePath);
+    if (!existsSync3(resolvedPath)) {
+      throw new Error(`Include file not found: ${includePath} (resolved to ${resolvedPath})`);
+    }
+    const includedContent = readFileSync3(resolvedPath, "utf-8");
+    return processIncludes(includedContent, dirname2(resolvedPath), depth + 1, maxDepth);
+  });
 }
-function generateCompletionProtocolSection(agent, lines) {
-  const protocols = agent.protocols;
-  if (!protocols?.completion || protocols.completion.length === 0) return;
-  lines.push("## Before Finishing");
-  lines.push("");
-  lines.push("> **MANDATORY COMPLETION PROTOCOL** - Execute ALL steps before ending any task.");
-  lines.push("");
-  for (let i = 0; i < protocols.completion.length; i++) {
-    lines.push(`### ${i + 1}. ${protocols.completion[i]}`);
-    lines.push("");
+function processAgentTemplate(templatePath, agent, config, mcpServers) {
+  const template = readFileSync3(templatePath, "utf-8");
+  const templateDir = dirname2(templatePath);
+  const expandedTemplate = processIncludes(template, templateDir);
+  const earlyMatch = expandedTemplate.match(/^---\n([\s\S]*?)\n---\n?([\s\S]*)$/);
+  if (!earlyMatch) {
+    throw new Error(`Invalid markdown format in ${templatePath}: no frontmatter found`);
+  }
+  const earlyFrontmatter = parseYaml3(earlyMatch[1]);
+  const reservedKeys = /* @__PURE__ */ new Set(["name", "description", "tools"]);
+  const extendedAgent = { ...agent };
+  for (const [key, value] of Object.entries(earlyFrontmatter)) {
+    if (!reservedKeys.has(key) && !(key in extendedAgent)) {
+      extendedAgent[key] = value;
+    }
+  }
+  const context = { agent: extendedAgent };
+  if (config) {
+    context.config = config;
   }
-  lines.push('Acknowledge: "Completion protocol finished. Context updated."');
-  lines.push("");
-  lines.push("---");
-  lines.push("");
-}
-function generateLegacyContextSourcesSection(agent, lines) {
-  if (!agent.context_sources) return;
-  if (agent.knowledge_library) return;
-  lines.push("## Context Sources");
-  lines.push("");
-  if (agent.context_sources.shared && agent.context_sources.shared.length > 0) {
-    lines.push("### Shared");
-    lines.push("");
-    for (const source of agent.context_sources.shared) {
-      lines.push(`- ${source}`);
-    }
-    lines.push("");
+  const resolved = resolveString(expandedTemplate, context);
+  const frontmatterMatch = resolved.match(/^---\n([\s\S]*?)\n---\n?([\s\S]*)$/);
+  if (!frontmatterMatch) {
+    throw new Error(`Invalid markdown format after resolution in ${templatePath}`);
   }
-  if (agent.context_sources.personal && agent.context_sources.personal.length > 0) {
-    lines.push("### Personal");
-    lines.push("");
-    for (const source of agent.context_sources.personal) {
-      lines.push(`- ${source}`);
-    }
-    lines.push("");
+  const frontmatterYaml = frontmatterMatch[1];
+  const body = frontmatterMatch[2] ?? "";
+  const frontmatter = parseYaml3(frontmatterYaml);
+  const tools = buildAgentTools(agent, mcpServers);
+  frontmatter.tools = tools;
+  if (typeof frontmatter.description === "string") {
+    frontmatter.description = frontmatter.description.replace(/\n/g, " ").trim();
   }
+  const updatedFrontmatter = stringifyYaml(frontmatter, { lineWidth: 0 }).trim();
+  return `---
+${updatedFrontmatter}
+---
+${body}`;
 }
 function generateAgentMarkdown(agent, mcpServers) {
   const lines = [];
@@ -572,8 +530,8 @@ function generateAgentMarkdown(agent, mcpServers) {
   if (agent.responsibilities && agent.responsibilities.length > 0) {
     lines.push("## Responsibilities");
     lines.push("");
-    for (const responsibility of agent.responsibilities) {
-      lines.push(`- ${responsibility}`);
+    for (const r of agent.responsibilities) {
+      lines.push(`- ${r}`);
     }
     lines.push("");
   }
@@ -591,12 +549,12 @@ function generateAgentMarkdown(agent, mcpServers) {
     if (agent.expertise.tech_stack) {
       lines.push("### Tech Stack");
       lines.push("");
-      const techStack = agent.expertise.tech_stack;
-      if (typeof techStack === "string") {
-        lines.push(techStack);
-      } else if (typeof techStack === "object") {
+      const ts = agent.expertise.tech_stack;
+      if (typeof ts === "string") {
+        lines.push(ts);
+      } else if (typeof ts === "object") {
         lines.push("```json");
-        lines.push(JSON.stringify(techStack, null, 2));
+        lines.push(JSON.stringify(ts, null, 2));
         lines.push("```");
       }
       lines.push("");
@@ -615,7 +573,7 @@ function generateAgentMarkdown(agent, mcpServers) {
     lines.push("");
     for (const [category, items] of Object.entries(agent.principles)) {
       if (items && Array.isArray(items) && items.length > 0) {
-        const title = formatTitle(category);
+        const title = category.replace(/[_-]/g, " ").replace(/\b\w/g, (c) => c.toUpperCase());
         lines.push(`### ${title}`);
         lines.push("");
         for (const item of items) {
@@ -646,21 +604,161 @@ function generateAgentMarkdown(agent, mcpServers) {
       lines.push("");
     }
   }
-  generateKnowledgeLibrarySection(agent, lines);
-  generateCommunicationSection(agent, lines);
-  generateStartupProtocolSection(agent, lines);
-  generateCompletionProtocolSection(agent, lines);
-  generateLegacyContextSourcesSection(agent, lines);
+  if (agent.knowledge_library) {
+    generateKnowledgeLibrarySection(agent, lines);
+  }
+  if (agent.communication) {
+    generateCommunicationSection(agent, lines);
+  }
+  if (agent.protocols?.startup) {
+    generateStartupProtocolSection(agent, lines);
+  }
+  if (agent.protocols?.completion) {
+    generateCompletionProtocolSection(agent, lines);
+  }
+  if (agent.context_sources && !agent.knowledge_library) {
+    lines.push("## Context Sources");
+    lines.push("");
+    if (agent.context_sources.shared?.length) {
+      lines.push("### Shared");
+      lines.push("");
+      for (const s of agent.context_sources.shared) lines.push(`- ${s}`);
+      lines.push("");
+    }
+    if (agent.context_sources.personal?.length) {
+      lines.push("### Personal");
+      lines.push("");
+      for (const p of agent.context_sources.personal) lines.push(`- ${p}`);
+      lines.push("");
+    }
+  }
   lines.push("---");
   lines.push("");
   lines.push("*Generated by CoreAI*");
   lines.push("");
   return lines.join("\n");
 }
-function formatTitle(str) {
-  return str.replace(/[_-]/g, " ").replace(/\b\w/g, (c) => c.toUpperCase());
+function generateKnowledgeLibrarySection(agent, lines) {
+  const kl = agent.knowledge_library;
+  if (!kl) return;
+  lines.push("## Knowledge Library Structure");
+  lines.push("");
+  if (kl.shared) {
+    lines.push("### Shared Context (Root - All Agents)");
+    lines.push("```");
+    lines.push("/KnowledgeLibrary/");
+    if (kl.shared.context) lines.push(`\u251C\u2500\u2500 ${kl.shared.context.split("/").pop()}`);
+    if (kl.shared.architecture) lines.push(`\u251C\u2500\u2500 ${kl.shared.architecture.split("/").pop()}`);
+    if (kl.shared.prd) lines.push(`\u2514\u2500\u2500 ${kl.shared.prd.split("/").pop()}`);
+    lines.push("```");
+    if (kl.shared.remote?.length) {
+      lines.push("");
+      lines.push("**Remote Documentation:**");
+      for (const r of kl.shared.remote) lines.push(`- ${r}`);
+    }
+    lines.push("");
+  }
+  if (kl.personal) {
+    lines.push(`### Personal Context (${agent.role})`);
+    lines.push("```");
+    lines.push(`/KnowledgeLibrary/${agent.role}/`);
+    if (kl.personal.context) {
+      lines.push("\u251C\u2500\u2500 context/");
+      lines.push("\u2502   \u2514\u2500\u2500 current.txt");
+    }
+    if (kl.personal.history) {
+      lines.push("\u251C\u2500\u2500 history/");
+    }
+    if (kl.personal.inbox) {
+      lines.push("\u251C\u2500\u2500 inbox/");
+    }
+    if (kl.personal.outbox) {
+      lines.push("\u251C\u2500\u2500 outbox/");
+    }
+    if (kl.personal.tech) {
+      lines.push("\u251C\u2500\u2500 tech/");
+    }
+    if (kl.personal.control) {
+      lines.push("\u2514\u2500\u2500 control/");
+      if (kl.personal.control.objectives) lines.push("    \u251C\u2500\u2500 objectives.txt");
+      if (kl.personal.control.decisions) lines.push("    \u251C\u2500\u2500 decisions.txt");
+      if (kl.personal.control.dependencies) lines.push("    \u251C\u2500\u2500 dependencies.txt");
+      if (kl.personal.control.index) lines.push("    \u2514\u2500\u2500 index.txt");
+    }
+    lines.push("```");
+    lines.push("");
+  }
+  lines.push("---");
+  lines.push("");
+}
+function generateCommunicationSection(agent, lines) {
+  const comm = agent.communication;
+  if (!comm) return;
+  lines.push("## Communication");
+  lines.push("");
+  if (comm.inbox) lines.push(`**Inbox:** \`${comm.inbox}\``);
+  if (comm.outbox) lines.push(`**Outbox:** \`${comm.outbox}\``);
+  lines.push("");
+  if (comm.message_format || comm.outbox_format || comm.processed_dir) {
+    lines.push("### Message Conventions");
+    lines.push("");
+    if (comm.message_format) lines.push(`- **Inbox message naming:** \`${comm.message_format}\``);
+    if (comm.outbox_format) lines.push(`- **Outbox message naming:** \`${comm.outbox_format}\``);
+    if (comm.processed_dir) lines.push(`- **Processed messages:** Move handled inbox messages to \`${comm.processed_dir}\``);
+    lines.push("");
+  }
+}
+function generateStartupProtocolSection(agent, lines) {
+  const p = agent.protocols;
+  if (!p?.startup) return;
+  lines.push("## When Invoked");
+  lines.push("");
+  lines.push("> **MANDATORY STARTUP PROTOCOL** - Execute before proceeding with any task.");
+  lines.push("");
+  lines.push("### Session Context Check");
+  lines.push("");
+  if (p.startup.first_session?.length) {
+    lines.push("**If this is your FIRST invocation in this session:**");
+    lines.push("");
+    for (const s of p.startup.first_session) lines.push(`- [ ] ${s}`);
+    lines.push("");
+    lines.push('Acknowledge: "Startup protocol complete. Full context loaded."');
+    lines.push("");
+  }
+  if (p.startup.subsequent?.length) {
+    lines.push("**If you have ALREADY loaded context in this session:**");
+    lines.push("");
+    for (const s of p.startup.subsequent) lines.push(`- [ ] ${s}`);
+    lines.push("");
+    lines.push('Acknowledge: "Context already loaded. Checked inbox for new messages."');
+    lines.push("");
+  }
+  lines.push("Then proceed with the task.");
+  lines.push("");
+  lines.push("---");
+  lines.push("");
+}
+function generateCompletionProtocolSection(agent, lines) {
+  const p = agent.protocols;
+  if (!p?.completion?.length) return;
+  lines.push("## Before Finishing");
+  lines.push("");
+  lines.push("> **MANDATORY COMPLETION PROTOCOL** - Execute ALL steps before ending any task.");
+  lines.push("");
+  for (let i = 0; i < p.completion.length; i++) {
+    lines.push(`### ${i + 1}. ${p.completion[i]}`);
+    lines.push("");
+  }
+  lines.push('Acknowledge: "Completion protocol finished. Context updated."');
+  lines.push("");
+  lines.push("---");
+  lines.push("");
 }
-function compileAgent(agent, config, mcpServers) {
+function compileAgent(agent, filePath, config, mcpServers) {
+  const ext = extname2(filePath).toLowerCase();
+  if (ext === ".md") {
+    return processAgentTemplate(filePath, agent, config, mcpServers);
+  }
   const resolved = resolveAgentDefinition(agent, config);
   return generateAgentMarkdown(resolved, mcpServers);
 }
@@ -720,7 +818,12 @@ function compileAgents(config, options = {}) {
       continue;
     }
     try {
-      const markdown = compileAgent(metadata.definition, config, options.mcpServers);
+      const markdown = compileAgent(
+        metadata.definition,
+        metadata.filePath,
+        config,
+        options.mcpServers
+      );
       const outputPath = join3(outputDir, `${role}.md`);
       writeFileSync(outputPath, markdown, "utf-8");
       result.compiled.push({
@@ -764,7 +867,7 @@ import { Client } from "@modelcontextprotocol/sdk/client/index.js";
 import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js";
 
 // src/adapters/mcp/discovery.ts
-import { existsSync as existsSync4, readFileSync as readFileSync3 } from "fs";
+import { existsSync as existsSync4, readFileSync as readFileSync4 } from "fs";
 import { join as join4, dirname as dirname3 } from "path";
 import { homedir } from "os";
 var CONFIG_FILENAMES = ["mcp.json", ".mcp.json", "claude_desktop_config.json"];
@@ -813,7 +916,7 @@ function loadServersFromFile(filePath) {
   if (!existsSync4(filePath)) {
     throw new McpError(`Config file not found: ${filePath}`, "invalid_config");
   }
-  const content = readFileSync3(filePath, "utf-8");
+  const content = readFileSync4(filePath, "utf-8");
   let config;
   try {
     config = JSON.parse(content);
@@ -1800,470 +1903,124 @@ var CacheManager = class {
 };
 
 // src/skills/generator.ts
-import { existsSync as existsSync5, mkdirSync as mkdirSync2, writeFileSync as writeFileSync2, readFileSync as readFileSync4, readdirSync as readdirSync2, statSync } from "fs";
-import { join as join6, basename as basename2 } from "path";
-
-// src/skills/templates.ts
-var checkInboxSkill = {
-  name: "check-inbox",
-  description: "Check your inbox for pending tasks and messages",
-  category: "core",
-  content: `---
-description: Check your inbox for pending tasks and messages
----
-
-# Check Inbox
-
-Check the inbox at \`KnowledgeLibrary/{{AGENT_NAME}}/inbox/\` for new messages.
-
-## Instructions
-
-1. Read all unprocessed messages in the inbox directory
-2. For each message:
-   - Parse the frontmatter (type, from, date, priority)
-   - Understand the request or task
-   - Take appropriate action based on message type
-3. After processing, move message to \`inbox/processed/\`
-4. Update your context file at \`KnowledgeLibrary/{{AGENT_NAME}}/context/current.txt\`
-
-## Message Types
-
-- **task-assignment**: New work assigned to you
-- **completion-report**: Another agent completed work
-- **review-request**: Code review needed
-- **feedback**: Response to your previous work
-
-## Output Format
-
-Report what messages were processed and actions taken.
-`
-};
-var delegateSkill = {
-  name: "delegate",
-  description: "Delegate a task to another agent via inbox messaging",
-  argumentHint: "<task-description> to <agent-name>",
-  category: "core",
-  content: `---
-description: Delegate a task to another agent via inbox messaging
-argument-hint: <task-description> to <agent-name>
----
-
-# Delegate Task
-
-Delegate work to another agent using the inbox-based messaging system.
-
-## CRITICAL: Do NOT use the Task tool
-
-Agent-to-agent delegation MUST use file-based messaging, not the Task tool.
-The Task tool spawns subagents that lose MCP access.
-
-## Instructions
-
-1. Parse the delegation request to identify:
-   - The task to delegate
-   - The target agent
-
-2. Create a message file in the target agent's inbox:
-   - Path: \`KnowledgeLibrary/<target-agent>/inbox/\`
-   - Filename: \`YYYYMMDD_HHMM-{{AGENT_NAME}}-<subject>.md\`
-
-3. Use this message format:
-\`\`\`markdown
----
-type: task-assignment
-from: {{AGENT_NAME}}
-to: <target-agent>
-date: YYYY-MM-DD HH:MM
-priority: P2
----
-
-## Task Assignment
-
-### Description
-<Clear description of what needs to be done>
-
-### Context
-<Any relevant context or background>
-
-### Expected Deliverables
-1. <Deliverable 1>
-2. <Deliverable 2>
-
-### Success Criteria
-- <Criterion 1>
-- <Criterion 2>
-\`\`\`
-
-4. Tell the user to invoke the target agent:
-   "Please invoke @<target-agent> to process this task."
-
-## Output
-
-Confirm the delegation message was created and instruct user to invoke the agent.
-`
-};
-var gitCommitSkill = {
-  name: "git-commit",
-  description: "Create a quality-gated git commit",
-  argumentHint: "<commit-message>",
-  category: "core",
-  dependencies: [{ type: "git", required: false, description: "For commit operations" }],
-  content: `---
-description: Create a quality-gated git commit
-argument-hint: <commit-message>
-optional: [git]
----
-
-# Git Commit
-
-Create a git commit after passing all quality gates.
-
-## Quality Gates
-
-Run these checks before committing:
-
-1. **Lint**: \`{{LINT_CMD}}\`
-2. **Tests**: \`{{TEST_CMD}}\`
-3. **Build**: \`{{BUILD_CMD}}\`
-
-## Instructions
-
-1. Stage the relevant files with \`git add\`
-2. Run all quality gate commands
-3. If any gate fails:
-   - Fix the issues
-   - Re-run the failed gate
-   - Continue only when all pass
-4. Create the commit with the provided message
-5. Format: Include ticket reference if applicable
-
-## Commit Message Format
-
-\`\`\`
-<type>(<scope>): <description>
-
-[optional body]
-
-[optional footer]
-\`\`\`
-
-Types: feat, fix, docs, style, refactor, test, chore
-
-## Fallbacks
-
-If quality gate commands are not configured:
-- Ask the user what commands to run
-- Or skip gates with user confirmation
-`
-};
-var prCreateSkill = {
-  name: "pr-create",
-  description: "Create a pull request with proper format",
-  argumentHint: "[branch-name]",
-  category: "core",
-  dependencies: [{ type: "git", required: true, description: "For PR creation" }],
-  content: `---
-description: Create a pull request with proper format
-argument-hint: [branch-name]
-requires: [git]
----
-
-# Create Pull Request
-
-Create a well-formatted pull request for the current branch.
-
-## Instructions
-
-1. Ensure all changes are committed
-2. Push the branch to remote
-3. Create PR with proper format:
-
-\`\`\`markdown
-## Summary
-<Brief description of changes>
-
-## Changes
-- <Change 1>
-- <Change 2>
-
-## Test Plan
-- [ ] <Test case 1>
-- [ ] <Test case 2>
-
-## Related Issues
-Closes {{JIRA_PROJECT}}-XXX
-\`\`\`
-
-4. Request reviewers if specified
-
-## Using GitHub CLI
-
-\`\`\`bash
-gh pr create --title "<title>" --body "<body>"
-\`\`\`
-
-## Output
-
-Provide the PR URL and summary of what was created.
-`
-};
-var reviewSkill = {
-  name: "review",
-  description: "Request or perform a code review",
-  argumentHint: "<pr-number-or-url>",
-  category: "core",
-  dependencies: [{ type: "git", required: true, description: "For PR review" }],
-  content: `---
-description: Request or perform a code review
-argument-hint: <pr-number-or-url>
-requires: [git]
----
-
-# Code Review
-
-Review a pull request or delegate review to a specialist.
-
-## Instructions
-
-### If you are reviewing:
-
-1. Fetch the PR details and diff
-2. Review for:
-   - Code quality and style
-   - Logic errors or bugs
-   - Security concerns
-   - Test coverage
-   - Documentation
-3. Provide feedback with specific line references
-4. Approve, request changes, or comment
-
-### If delegating to a reviewer:
-
-1. Identify the appropriate reviewer based on the changes
-2. Create a review request message in their inbox
-3. Include PR link and context
-
-## Review Checklist
-
-- [ ] Code follows project conventions
-- [ ] No obvious bugs or edge cases
-- [ ] Tests cover the changes
-- [ ] Documentation updated if needed
-- [ ] No security vulnerabilities
-
-## Output
-
-Provide review summary with actionable feedback.
-`
-};
-var sprintStatusSkill = {
-  name: "sprint-status",
-  description: "Get current sprint status and progress",
-  category: "optional",
-  dependencies: [{ type: "issue_tracker", required: true, description: "For sprint data" }],
-  content: `---
-description: Get current sprint status and progress
-requires: [issue_tracker]
----
-
-# Sprint Status
-
-Get the current sprint status and team progress.
-
-## Instructions
-
-1. Query the active sprint for project {{JIRA_PROJECT}}
-2. Gather metrics:
-   - Total story points committed
-   - Points completed
-   - Points in progress
-   - Points remaining
-3. List tickets by status
-4. Identify blockers or at-risk items
-
-## Output Format
-
-\`\`\`
-Sprint: <sprint-name>
-Progress: XX/YY points (ZZ%)
-
-## Completed
-- [{{JIRA_PROJECT}}-123] Task name (3 pts)
-
-## In Progress
-- [{{JIRA_PROJECT}}-124] Task name (5 pts) - @assignee
-
-## To Do
-- [{{JIRA_PROJECT}}-125] Task name (2 pts)
-
-## Blocked
-- [{{JIRA_PROJECT}}-126] Task name - Reason
-\`\`\`
-
-## Fallbacks
-
-If issue tracker is unavailable:
-- Report that sprint data cannot be fetched
-- Suggest checking the issue tracker directly at {{JIRA_URL}}
-`
-};
-var jiraCreateSkill = {
-  name: "jira-create",
-  description: "Create a new Jira ticket",
-  argumentHint: "<ticket-type> <summary>",
-  category: "optional",
-  dependencies: [{ type: "issue_tracker", required: true, description: "For ticket creation" }],
-  content: `---
-description: Create a new Jira ticket
-argument-hint: <ticket-type> <summary>
-requires: [issue_tracker]
----
-
-# Create Jira Ticket
-
-Create a new ticket in project {{JIRA_PROJECT}}.
-
-## Instructions
-
-1. Parse the ticket type and summary from arguments
-2. Gather additional details:
-   - Description
-   - Priority
-   - Labels
-   - Components (if applicable)
-3. Create the ticket via the issue tracker integration
-4. Return the ticket key and URL
-
-## Ticket Types
-
-- **Story**: User-facing feature
-- **Bug**: Defect to fix
-- **Task**: Technical work
-- **Spike**: Research/investigation
-
-## Output
-
-\`\`\`
-Created: {{JIRA_PROJECT}}-XXX
-URL: {{JIRA_URL}}/browse/{{JIRA_PROJECT}}-XXX
-Summary: <summary>
-Type: <type>
-\`\`\`
-
-## Fallbacks
-
-If issue tracker is unavailable:
-- Provide the user with manual creation instructions
-- Include all details they should enter
-`
-};
-var jiraTransitionSkill = {
-  name: "jira-transition",
-  description: "Transition a Jira ticket to a new status",
-  argumentHint: "<ticket-key> to <status>",
-  category: "optional",
-  dependencies: [{ type: "issue_tracker", required: true, description: "For ticket transitions" }],
-  content: `---
-description: Transition a Jira ticket to a new status
-argument-hint: <ticket-key> to <status>
-requires: [issue_tracker]
----
-
-# Transition Jira Ticket
-
-Update the status of a ticket in {{JIRA_PROJECT}}.
-
-## Status Mapping
-
-| Workflow Status | Jira Status |
-|-----------------|-------------|
-| BACKLOG | Backlog |
-| IN_PROGRESS | In Progress |
-| PR_CREATED | In Review |
-| IN_REVIEW | In Review |
-| APPROVED | Ready to Merge |
-| MERGED | Done |
-| DONE | Done |
-
-## Instructions
-
-1. Parse ticket key and target status
-2. Validate the transition is allowed
-3. Add a comment explaining the transition
-4. Execute the transition
-
-## Transition Comment Format
-
-\`\`\`
-Status updated to <status>.
-<optional context about why>
-\`\`\`
-
-## Fallbacks
-
-If issue tracker is unavailable:
-- Instruct user to manually transition at {{JIRA_URL}}
-- Provide the target status name
-`
-};
-var docsUpdateSkill = {
-  name: "docs-update",
-  description: "Update project documentation",
-  argumentHint: "<doc-path-or-topic>",
-  category: "optional",
-  dependencies: [{ type: "documentation", required: false, description: "For remote docs" }],
-  content: `---
-description: Update project documentation
-argument-hint: <doc-path-or-topic>
-optional: [documentation]
----
-
-# Update Documentation
-
-Update project documentation for a specific topic or file.
-
-## Instructions
-
-1. Identify the documentation to update:
-   - Local: \`{{DOCS_PATH}}/\`
-   - Remote: {{CONFLUENCE_SPACE}} (if configured)
-
-2. Make the necessary updates:
-   - Keep formatting consistent
-   - Update examples if code changed
-   - Add/update version information
-
-3. For remote documentation:
-   - Use the documentation integration
-   - Or provide content for manual update
-
-## Documentation Types
-
-- **README**: Project overview and setup
-- **API Docs**: Endpoint documentation
-- **Architecture**: Design decisions
-- **Runbooks**: Operational procedures
-
-## Fallbacks
-
-If documentation integration is unavailable:
-- Create/update local markdown files
-- Provide instructions for manual remote update
-`
-};
-var builtInSkills = [
-  checkInboxSkill,
-  delegateSkill,
-  gitCommitSkill,
-  prCreateSkill,
-  reviewSkill,
-  sprintStatusSkill,
-  jiraCreateSkill,
-  jiraTransitionSkill,
-  docsUpdateSkill
-];
-
-// src/skills/generator.ts
+import { existsSync as existsSync5, mkdirSync as mkdirSync2, writeFileSync as writeFileSync2, readFileSync as readFileSync5, readdirSync as readdirSync2, statSync } from "fs";
+import { join as join6, dirname as dirname5 } from "path";
+function getCoreSkillsDir() {
+  let currentDir = dirname5(import.meta.url.replace("file://", ""));
+  for (let i = 0; i < 5; i++) {
+    if (existsSync5(join6(currentDir, "package.json"))) {
+      return join6(currentDir, "skills");
+    }
+    currentDir = dirname5(currentDir);
+  }
+  return join6(dirname5(dirname5(dirname5(import.meta.url.replace("file://", "")))), "skills");
+}
+function discoverSkills(skillsDir) {
+  const templates = [];
+  if (!existsSync5(skillsDir)) {
+    return templates;
+  }
+  const categories = readdirSync2(skillsDir);
+  for (const category of categories) {
+    const categoryPath = join6(skillsDir, category);
+    const stat = statSync(categoryPath);
+    if (!stat.isDirectory()) continue;
+    if (category.startsWith(".") || category.startsWith("_")) continue;
+    const skillDirs = readdirSync2(categoryPath);
+    for (const skillName of skillDirs) {
+      const skillDir = join6(categoryPath, skillName);
+      const skillStat = statSync(skillDir);
+      if (!skillStat.isDirectory()) continue;
+      const skillFile = join6(skillDir, "SKILL.md");
+      if (!existsSync5(skillFile)) continue;
+      try {
+        const content = readFileSync5(skillFile, "utf-8");
+        const template = parseSkillFile(skillName, category, content);
+        templates.push(template);
+      } catch {
+      }
+    }
+  }
+  return templates;
+}
+function parseSkillFile(name, category, content) {
+  const template = {
+    name,
+    description: name,
+    category,
+    content
+  };
+  const frontmatterMatch = content.match(/^---\r?\n([\s\S]*?)\r?\n---\r?\n/);
+  if (!frontmatterMatch) {
+    return template;
+  }
+  const frontmatter = frontmatterMatch[1];
+  const lines = frontmatter.split(/\r?\n/);
+  const dependencies = [];
+  for (const line of lines) {
+    const colonIndex = line.indexOf(":");
+    if (colonIndex === -1) continue;
+    const key = line.slice(0, colonIndex).trim();
+    let value = line.slice(colonIndex + 1).trim();
+    if (value.startsWith('"') && value.endsWith('"') || value.startsWith("'") && value.endsWith("'")) {
+      value = value.slice(1, -1);
+    }
+    switch (key) {
+      case "name":
+        template.name = value;
+        break;
+      case "description":
+        template.description = value;
+        break;
+      case "argument-hint":
+        template.argumentHint = value;
+        break;
+      case "requires":
+        if (value.startsWith("[") && value.endsWith("]")) {
+          const items = value.slice(1, -1).split(",").map((s) => s.trim().replace(/['"]/g, ""));
+          for (const item of items) {
+            if (item) {
+              dependencies.push({
+                type: mapIntegrationName(item),
+                required: true
+              });
+            }
+          }
+        }
+        break;
+      case "optional":
+        if (value.startsWith("[") && value.endsWith("]")) {
+          const items = value.slice(1, -1).split(",").map((s) => s.trim().replace(/['"]/g, ""));
+          for (const item of items) {
+            if (item) {
+              dependencies.push({
+                type: mapIntegrationName(item),
+                required: false
+              });
+            }
+          }
+        }
+        break;
+    }
+  }
+  if (dependencies.length > 0) {
+    template.dependencies = dependencies;
+  }
+  return template;
+}
+function mapIntegrationName(name) {
+  const lower = name.toLowerCase();
+  if (["jira", "linear", "issue_tracker", "issues", "github-issues"].includes(lower)) {
+    return "issue_tracker";
+  }
+  if (["git", "github", "gitlab", "bitbucket"].includes(lower)) {
+    return "git";
+  }
+  if (["docs", "documentation", "confluence", "notion", "wiki"].includes(lower)) {
+    return "documentation";
+  }
+  return "state";
+}
 function extractVariables2(config) {
   const vars = {};
   if (!config) {
@@ -2373,112 +2130,12 @@ function checkDependencies(skill, config) {
     missing
   };
 }
-function loadCustomTemplates(templatesDir) {
-  const templates = [];
-  if (!existsSync5(templatesDir)) {
-    return templates;
-  }
-  const files = readdirSync2(templatesDir);
-  for (const file of files) {
-    if (!file.endsWith(".md")) continue;
-    const filePath = join6(templatesDir, file);
-    const stat = statSync(filePath);
-    if (!stat.isFile()) continue;
-    try {
-      const content = readFileSync4(filePath, "utf-8");
-      const template = parseSkillTemplate(file, content);
-      templates.push(template);
-    } catch {
-    }
-  }
-  return templates;
-}
-function parseSkillTemplate(filename, content) {
-  const name = basename2(filename, ".md");
-  const frontmatterMatch = content.match(/^---\r?\n([\s\S]*?)\r?\n---\r?\n([\s\S]*)$/);
-  let description = name;
-  let argumentHint;
-  const dependencies = [];
-  if (frontmatterMatch) {
-    const frontmatter = frontmatterMatch[1] ?? "";
-    const lines = frontmatter.split(/\r?\n/);
-    for (const line of lines) {
-      const colonIndex = line.indexOf(":");
-      if (colonIndex === -1) continue;
-      const key = line.slice(0, colonIndex).trim();
-      let value = line.slice(colonIndex + 1).trim();
-      if (value.startsWith('"') && value.endsWith('"') || value.startsWith("'") && value.endsWith("'")) {
-        value = value.slice(1, -1);
-      }
-      switch (key) {
-        case "description":
-          description = value;
-          break;
-        case "argument-hint":
-          argumentHint = value;
-          break;
-        case "requires":
-          if (value.startsWith("[") && value.endsWith("]")) {
-            const items = value.slice(1, -1).split(",").map((s) => s.trim().replace(/['"]/g, ""));
-            for (const item of items) {
-              if (item) {
-                dependencies.push({
-                  type: mapIntegrationName(item),
-                  required: true
-                });
-              }
-            }
-          }
-          break;
-        case "optional":
-          if (value.startsWith("[") && value.endsWith("]")) {
-            const items = value.slice(1, -1).split(",").map((s) => s.trim().replace(/['"]/g, ""));
-            for (const item of items) {
-              if (item) {
-                dependencies.push({
-                  type: mapIntegrationName(item),
-                  required: false
-                });
-              }
-            }
-          }
-          break;
-      }
-    }
-  }
-  const template = {
-    name,
-    description,
-    category: "custom",
-    content
-  };
-  if (argumentHint) {
-    template.argumentHint = argumentHint;
-  }
-  if (dependencies.length > 0) {
-    template.dependencies = dependencies;
-  }
-  return template;
-}
-function mapIntegrationName(name) {
-  const lower = name.toLowerCase();
-  if (["jira", "linear", "issue_tracker", "issues", "github-issues"].includes(lower)) {
-    return "issue_tracker";
-  }
-  if (["git", "github", "gitlab", "bitbucket"].includes(lower)) {
-    return "git";
-  }
-  if (["docs", "documentation", "confluence", "notion", "wiki"].includes(lower)) {
-    return "documentation";
-  }
-  return "state";
-}
 function generateSkills(config, options = {}) {
   const projectRoot = options.projectRoot ?? process.cwd();
-  const outputDir = options.outputDir ?? join6(projectRoot, ".claude", "commands");
+  const coreSkillsDir = options.coreSkillsDir ?? getCoreSkillsDir();
+  const outputDir = options.outputDir ?? join6(projectRoot, ".claude", "skills");
   const includeCoreSkills = options.includeCoreSkills ?? true;
-  const includeOptionalSkills = options.includeOptionalSkills ?? true;
-  const overwrite = options.overwrite ?? false;
+  const overwrite = options.overwrite ?? true;
   const result = {
     generated: [],
     errors: [],
@@ -2491,21 +2148,17 @@ function generateSkills(config, options = {}) {
   result.variables = variables;
   let templates = [];
   if (includeCoreSkills) {
-    templates.push(...builtInSkills.filter((s) => s.category === "core"));
-  }
-  if (includeOptionalSkills) {
-    templates.push(...builtInSkills.filter((s) => s.category === "optional"));
+    const discovered = discoverSkills(coreSkillsDir);
+    templates.push(...discovered);
   }
   if (options.customTemplatesDir && existsSync5(options.customTemplatesDir)) {
-    templates.push(...loadCustomTemplates(options.customTemplatesDir));
+    const custom = discoverSkills(options.customTemplatesDir);
+    templates.push(...custom);
   }
   if (options.skills && options.skills.length > 0) {
     const skillsToInclude = options.skills;
     templates = templates.filter((t) => skillsToInclude.includes(t.name));
   }
-  if (!existsSync5(outputDir)) {
-    mkdirSync2(outputDir, { recursive: true });
-  }
   for (const template of templates) {
     try {
       const generated = generateSkill(template, variables, config, outputDir, overwrite);
@@ -2520,7 +2173,8 @@ function generateSkills(config, options = {}) {
   return result;
 }
 function generateSkill(template, variables, config, outputDir, overwrite) {
-  const outputPath = join6(outputDir, `${template.name}.md`);
+  const skillDir = join6(outputDir, template.name);
+  const outputPath = join6(skillDir, "SKILL.md");
   if (existsSync5(outputPath) && !overwrite) {
     return {
       name: template.name,
@@ -2543,6 +2197,9 @@ function generateSkill(template, variables, config, outputDir, overwrite) {
   }
   const content = substituteVariables(template.content, variables);
   const isUpdate = existsSync5(outputPath);
+  if (!existsSync5(skillDir)) {
+    mkdirSync2(skillDir, { recursive: true });
+  }
   writeFileSync2(outputPath, content, "utf-8");
   return {
     name: template.name,
@@ -2586,7 +2243,7 @@ function formatGenerateResult(result) {
   }
   const total = created.length + updated.length;
   if (total > 0) {
-    lines.push(`Generated ${total} skill(s) to .claude/commands/`);
+    lines.push(`Generated ${total} skill(s) to .claude/skills/`);
   } else if (result.generated.length === 0 && result.errors.length === 0) {
     lines.push("No skills to generate.");
   }
@@ -2598,12 +2255,12 @@ import {
   existsSync as existsSync6,
   mkdirSync as mkdirSync3,
   writeFileSync as writeFileSync3,
-  readFileSync as readFileSync5,
+  readFileSync as readFileSync6,
   readdirSync as readdirSync3,
   renameSync,
   statSync as statSync2
 } from "fs";
-import { join as join7, basename as basename3 } from "path";
+import { join as join7, basename as basename2 } from "path";
 var DEFAULT_KNOWLEDGE_LIBRARY_PATH = "KnowledgeLibrary";
 var STANDARD_FILES = {
   context: "context.txt",
@@ -2853,7 +2510,7 @@ function getAgentKnowledgeState(agentName, options = {}) {
   let context;
   const currentContextPath = join7(dirs.context, "current.txt");
   if (existsSync6(currentContextPath)) {
-    const content = readFileSync5(currentContextPath, "utf-8");
+    const content = readFileSync6(currentContextPath, "utf-8");
     context = parseContextFile(content);
   }
   const state = {
@@ -2947,7 +2604,7 @@ function readInboxMessages(agentName, options = {}) {
     );
     for (const file of files) {
       const filePath = join7(dirs.inbox, file);
-      const rawContent = readFileSync5(filePath, "utf-8");
+      const rawContent = readFileSync6(filePath, "utf-8");
       const { metadata, body } = parseMessageFrontmatter(rawContent);
       if (options.type && metadata.type !== options.type) continue;
       if (options.from && metadata.from !== options.from) continue;
@@ -2967,7 +2624,7 @@ function readInboxMessages(agentName, options = {}) {
     );
     for (const file of files) {
       const filePath = join7(dirs.inboxProcessed, file);
-      const rawContent = readFileSync5(filePath, "utf-8");
+      const rawContent = readFileSync6(filePath, "utf-8");
       const { metadata, body } = parseMessageFrontmatter(rawContent);
       if (options.type && metadata.type !== options.type) continue;
       if (options.from && metadata.from !== options.from) continue;
@@ -3016,18 +2673,18 @@ function getKnowledgeLibraryState(options = {}) {
 
 // src/index.ts
 function findPackageJson() {
-  let dir = dirname5(fileURLToPath(import.meta.url));
-  while (dir !== dirname5(dir)) {
+  let dir = dirname6(fileURLToPath(import.meta.url));
+  while (dir !== dirname6(dir)) {
     const pkgPath = join8(dir, "package.json");
     try {
-      const content = readFileSync6(pkgPath, "utf-8");
+      const content = readFileSync7(pkgPath, "utf-8");
       const pkg = JSON.parse(content);
       if (pkg.name === "@deimoscloud/coreai") {
         return content;
       }
     } catch {
     }
-    dir = dirname5(dir);
+    dir = dirname6(dir);
   }
   return '{"version": "unknown"}';
 }
@@ -3304,8 +2961,8 @@ function formatSyncResult(result) {
 }
 
 // src/cli/commands/init.ts
-import { existsSync as existsSync7, writeFileSync as writeFileSync4, mkdirSync as mkdirSync4, readFileSync as readFileSync7 } from "fs";
-import { join as join11, basename as basename4 } from "path";
+import { existsSync as existsSync7, writeFileSync as writeFileSync4, mkdirSync as mkdirSync4, readFileSync as readFileSync8 } from "fs";
+import { join as join11, basename as basename3 } from "path";
 import { execSync } from "child_process";
 function detectGitInfo() {
   try {
@@ -3335,14 +2992,14 @@ function detectProjectName(projectRoot) {
   const packageJsonPath = join11(projectRoot, "package.json");
   if (existsSync7(packageJsonPath)) {
     try {
-      const content = JSON.parse(readFileSync7(packageJsonPath, "utf-8"));
+      const content = JSON.parse(readFileSync8(packageJsonPath, "utf-8"));
       if (content.name) {
         return content.name;
       }
     } catch {
     }
   }
-  return basename4(projectRoot);
+  return basename3(projectRoot);
 }
 function generateConfigYaml(options) {
   let yaml = `# CoreAI Configuration
@@ -3539,6 +3196,14 @@ function build(options = {}) {
         warnings
       };
     }
+    let skillsResult;
+    if (!options.skipSkills) {
+      skillsResult = generateSkills(config, {
+        projectRoot,
+        skills: options.skills,
+        overwrite: true
+      });
+    }
     let knowledgeLibraryInitialized;
     if (options.initKnowledgeLibrary) {
       knowledgeLibraryInitialized = [];
@@ -3555,6 +3220,7 @@ function build(options = {}) {
     return {
       success: true,
       result,
+      skillsResult,
       config,
       warnings: warnings.length > 0 ? warnings : void 0,
       knowledgeLibraryInitialized,
@@ -3624,6 +3290,24 @@ function formatBuildResult(result) {
     }
     lines.push("");
   }
+  if (result.skillsResult) {
+    const created = result.skillsResult.generated.filter((g) => g.action === "created");
+    const updated = result.skillsResult.generated.filter((g) => g.action === "updated");
+    const total = created.length + updated.length;
+    if (total > 0) {
+      lines.push(`Generated ${total} skill(s):`);
+      for (const skill of [...created, ...updated]) {
+        lines.push(`  \u2713 ${skill.name} \u2192 ${skill.outputPath}`);
+      }
+      lines.push("");
+    }
+    if (result.skillsResult.errors.length > 0) {
+      for (const error of result.skillsResult.errors) {
+        lines.push(`  \u2717 skill ${error.name}: ${error.error}`);
+      }
+      lines.push("");
+    }
+  }
   if (result.mcpServers && result.mcpServers.length > 0) {
     lines.push(`MCP tools included: ${result.mcpServers.map((s) => `mcp__${s}`).join(", ")}`);
     lines.push("");
@@ -3868,8 +3552,7 @@ function skillsGenerate(options = {}) {
   const generateOptions = {
     projectRoot,
     includeCoreSkills: options.includeCoreSkills ?? true,
-    includeOptionalSkills: options.includeOptionalSkills ?? true,
-    overwrite: options.overwrite ?? false
+    overwrite: options.overwrite ?? true
   };
   if (options.outputDir) {
     generateOptions.outputDir = options.outputDir;
@@ -3935,11 +3618,11 @@ function formatSkillsGenerateResult(result) {
 function skillsList(options = {}) {
   try {
     const skills = [];
+    const coreSkillsDir = getCoreSkillsDir();
+    const discovered = discoverSkills(coreSkillsDir);
     const includeCoreSkills = options.includeCoreSkills ?? true;
-    const includeOptionalSkills = options.includeOptionalSkills ?? true;
-    for (const skill of builtInSkills) {
+    for (const skill of discovered) {
       if (skill.category === "core" && !includeCoreSkills) continue;
-      if (skill.category === "optional" && !includeOptionalSkills) continue;
       skills.push({
         name: skill.name,
         description: skill.description,
@@ -3949,7 +3632,7 @@ function skillsList(options = {}) {
       });
     }
     if (options.customTemplatesDir) {
-      const customSkills = loadCustomTemplates(options.customTemplatesDir);
+      const customSkills = discoverSkills(options.customTemplatesDir);
       for (const skill of customSkills) {
         skills.push({
           name: skill.name,
@@ -3981,7 +3664,6 @@ function formatSkillsListResult(result) {
   const lines = [];
   lines.push("Available skills:\n");
   const coreSkills = result.skills.filter((s) => s.category === "core");
-  const optionalSkills = result.skills.filter((s) => s.category === "optional");
   const customSkills = result.skills.filter((s) => s.category === "custom");
   if (coreSkills.length > 0) {
     lines.push("Core skills:");
@@ -3994,18 +3676,6 @@ function formatSkillsListResult(result) {
     }
     lines.push("");
   }
-  if (optionalSkills.length > 0) {
-    lines.push("Optional skills:");
-    for (const skill of optionalSkills) {
-      const deps = skill.dependencies?.length ? ` (requires: ${skill.dependencies.join(", ")})` : "";
-      lines.push(`  ${skill.name}${deps}`);
-      lines.push(`    ${skill.description}`);
-      if (skill.argumentHint) {
-        lines.push(`    Argument: ${skill.argumentHint}`);
-      }
-    }
-    lines.push("");
-  }
   if (customSkills.length > 0) {
     lines.push("Custom skills:");
     for (const skill of customSkills) {
@@ -4181,22 +3851,22 @@ function formatStatusResult(result) {
 }
 
 // src/cli/commands/agents.ts
-import { readFileSync as readFileSync8, writeFileSync as writeFileSync5 } from "fs";
-import { join as join13, dirname as dirname6 } from "path";
-import { parse as parseYaml3, stringify as stringifyYaml } from "yaml";
+import { readFileSync as readFileSync9, writeFileSync as writeFileSync5 } from "fs";
+import { join as join13, dirname as dirname7 } from "path";
+import { parse as parseYaml4, stringify as stringifyYaml2 } from "yaml";
 function readConfigFile(configPath) {
-  const content = readFileSync8(configPath, "utf-8");
-  const parsed = parseYaml3(content);
+  const content = readFileSync9(configPath, "utf-8");
+  const parsed = parseYaml4(content);
   return { content, parsed };
 }
 function updateConfigAgents(configPath, agents2) {
-  const content = readFileSync8(configPath, "utf-8");
-  const parsed = parseYaml3(content);
+  const content = readFileSync9(configPath, "utf-8");
+  const parsed = parseYaml4(content);
   if (!parsed.team) {
     parsed.team = {};
   }
   parsed.team.agents = agents2;
-  const newContent = stringifyYaml(parsed, {
+  const newContent = stringifyYaml2(parsed, {
     indent: 2,
     lineWidth: 0,
     singleQuote: false
@@ -4216,7 +3886,7 @@ function getAvailableAgents(coreAgentsDir, customAgentsDir) {
 }
 function agentsAdd(agents2, options = {}) {
   const projectRoot = options.projectRoot ?? process.cwd();
-  const coreAgentsDir = options.coreAgentsDir ?? join13(dirname6(dirname6(dirname6(__dirname))), "agents");
+  const coreAgentsDir = options.coreAgentsDir ?? join13(dirname7(dirname7(dirname7(__dirname))), "agents");
   const customAgentsDir = join13(projectRoot, "coreai", "agents");
   const configPath = findConfigFile(projectRoot);
   if (!configPath) {
@@ -4398,7 +4068,7 @@ function formatAgentsRemoveResult(result) {
 
 // src/cli/index.ts
 var __filename = fileURLToPath2(import.meta.url);
-var __dirname2 = dirname7(__filename);
+var __dirname2 = dirname8(__filename);
 function getCoreAgentsPath() {
   return join14(__dirname2, "..", "..", "agents");
 }
@@ -4708,7 +4378,7 @@ program.command("status").description("Show agent states and pending messages").
   }
 });
 var skillsCmd = program.command("skills").description("Manage Claude skills");
-skillsCmd.command("generate").description("Generate Claude skills from templates").option("-o, --output <dir>", "output directory (default: .claude/commands)").option("--skills <skills>", "comma-separated list of skills to generate").option("--no-core", "exclude core skills").option("--no-optional", "exclude optional skills").option("--overwrite", "overwrite existing skill files").option("--json", "output as JSON").action(
+skillsCmd.command("generate").description("Generate Claude skills from source files").option("-o, --output <dir>", "output directory (default: .claude/skills)").option("--skills <skills>", "comma-separated list of skills to generate").option("--no-core", "exclude core skills").option("--no-overwrite", "do not overwrite existing skill files").option("--json", "output as JSON").action(
   (options) => {
     console.log("Generating skills...\n");
     const result = skillsGenerate({
@@ -4716,8 +4386,7 @@ skillsCmd.command("generate").description("Generate Claude skills from templates
       outputDir: options.output,
       skills: options.skills?.split(",").map((s) => s.trim()),
       includeCoreSkills: options.core !== false,
-      includeOptionalSkills: options.optional !== false,
-      overwrite: options.overwrite
+      overwrite: options.overwrite !== false
     });
     if (options.json) {
       console.log(JSON.stringify(result, null, 2));
@@ -4729,11 +4398,10 @@ skillsCmd.command("generate").description("Generate Claude skills from templates
     }
   }
 );
-skillsCmd.command("list").description("List available skills").option("--no-core", "exclude core skills").option("--no-optional", "exclude optional skills").option("--json", "output as JSON").action((options) => {
+skillsCmd.command("list").description("List available skills").option("--no-core", "exclude core skills").option("--json", "output as JSON").action((options) => {
   const result = skillsList({
     projectRoot: process.cwd(),
-    includeCoreSkills: options.core !== false,
-    includeOptionalSkills: options.optional !== false
+    includeCoreSkills: options.core !== false
   });
   if (options.json) {
     console.log(JSON.stringify(result, null, 2));