@lnai/core 0.6.5 → 0.6.7

package/dist/index.d.ts

@@ -283,7 +283,7 @@ declare const claudeCodePlugin: Plugin;
  * Output structure:
  * - AGENTS.md (symlink -> .ai/AGENTS.md) [at project root]
  * - <dir>/AGENTS.md (generated from .ai/rules/*.md, per glob directory)
- * - .codex/skills/<name>/ (symlink -> ../../.ai/skills/<name>)
+ * - .agents/skills/<name>/ (symlink -> ../../.ai/skills/<name>)
  * - .codex/config.toml (generated from settings.mcpServers)
  * - .codex/<path> (symlink -> ../.ai/.codex/<path>) for override files
  */
@@ -295,7 +295,7 @@ declare const codexPlugin: Plugin;
  * Output structure:
  * - AGENTS.md (symlink -> .ai/AGENTS.md) [at project root]
  * - .opencode/rules/ (symlink -> ../.ai/rules)
- * - .opencode/skills/<name>/ (symlink -> ../../.ai/skills/<name>)
+ * - .agents/skills/<name>/ (symlink -> ../../.ai/skills/<name>)
  * - opencode.json (generated config merged with .ai/.opencode/opencode.json)
  * - .opencode/<path> (symlink -> ../.ai/.opencode/<path>) for other override files
  */
@@ -343,7 +343,7 @@ declare function writeFiles(files: OutputFile[], options: WriterOptions): Promis
 /**
  * Update .gitignore with paths that should not be version controlled.
  * Manages a dedicated "lnai-generated" section to avoid conflicts with user entries.
- * Merges new paths with existing ones to support partial syncs (e.g., syncing one tool).
+ * Replaces the managed section on each run so stale paths are removed.
  */
 declare function updateGitignore(rootDir: string, paths: string[]): Promise<void>;
 

package/dist/index.js

@@ -25,6 +25,7 @@ var CONFIG_DIRS = {
   skills: "skills",
   subagents: "subagents"
 };
+var CROSS_TOOL_SKILLS_DIR = ".agents";
 var TOOL_OUTPUT_DIRS = {
   claudeCode: ".claude",
   opencode: ".opencode",
@@ -413,6 +414,39 @@ function validateToolIds(tools) {
   }
   return { valid: true, errors: [], warnings: [], skipped: [] };
 }
+
+// src/utils/agents.ts
+function createRootAgentsMdSymlink(state) {
+  if (!state.agents) {
+    return null;
+  }
+  return {
+    path: "AGENTS.md",
+    type: "symlink",
+    target: `${UNIFIED_DIR}/AGENTS.md`
+  };
+}
+function createSkillSymlinks(state, outputDir) {
+  const depth = outputDir.split("/").length + 1;
+  const prefix = "../".repeat(depth);
+  return state.skills.map((skill) => ({
+    path: `${outputDir}/skills/${skill.path}`,
+    type: "symlink",
+    target: `${prefix}${UNIFIED_DIR}/skills/${skill.path}`
+  }));
+}
+function createNoAgentsMdWarning(outputDescription) {
+  return {
+    path: ["AGENTS.md"],
+    message: `No AGENTS.md found - ${outputDescription} will not be created`
+  };
+}
+function hasPermissionsConfigured(permissions) {
+  if (!permissions) {
+    return false;
+  }
+  return (permissions.allow?.length ?? 0) > 0 || (permissions.ask?.length ?? 0) > 0 || (permissions.deny?.length ?? 0) > 0;
+}
 async function scanOverrideDirectory(rootDir, toolId) {
   const overrideDir = path.join(rootDir, UNIFIED_DIR, OVERRIDE_DIRS[toolId]);
   try {
@@ -457,6 +491,7 @@ async function applyFileOverrides(files, rootDir, toolId) {
 }
 
 // src/plugins/claude-code/index.ts
+var OUTPUT_DIR = TOOL_OUTPUT_DIRS.claudeCode;
 var claudeCodePlugin = {
   id: "claudeCode",
   name: "Claude Code",
@@ -468,28 +503,21 @@ var claudeCodePlugin = {
   },
   async export(state, rootDir) {
     const files = [];
-    const outputDir = TOOL_OUTPUT_DIRS.claudeCode;
     if (state.agents) {
       files.push({
-        path: `${outputDir}/CLAUDE.md`,
+        path: `${OUTPUT_DIR}/CLAUDE.md`,
         type: "symlink",
         target: `../${UNIFIED_DIR}/AGENTS.md`
       });
     }
     if (state.rules.length > 0) {
       files.push({
-        path: `${outputDir}/rules`,
+        path: `${OUTPUT_DIR}/rules`,
         type: "symlink",
         target: `../${UNIFIED_DIR}/rules`
       });
     }
-    for (const skill of state.skills) {
-      files.push({
-        path: `${outputDir}/skills/${skill.path}`,
-        type: "symlink",
-        target: `../../${UNIFIED_DIR}/skills/${skill.path}`
-      });
-    }
+    files.push(...createSkillSymlinks(state, OUTPUT_DIR));
     const settings = {};
     if (state.settings?.permissions) {
       settings["permissions"] = state.settings.permissions;
@@ -499,7 +527,7 @@ var claudeCodePlugin = {
     }
     if (Object.keys(settings).length > 0) {
       files.push({
-        path: `${outputDir}/settings.json`,
+        path: `${OUTPUT_DIR}/settings.json`,
         type: "json",
         content: settings
       });
@@ -509,10 +537,7 @@ var claudeCodePlugin = {
   validate(state) {
     const warnings = [];
     if (!state.agents) {
-      warnings.push({
-        path: ["AGENTS.md"],
-        message: "No AGENTS.md found - .claude/CLAUDE.md will not be created"
-      });
+      warnings.push(createNoAgentsMdWarning(".claude/CLAUDE.md"));
     }
     return { valid: true, errors: [], warnings, skipped: [] };
   }
@@ -554,6 +579,7 @@ ${rule.content}
 }
 
 // src/plugins/codex/index.ts
+var OUTPUT_DIR2 = TOOL_OUTPUT_DIRS.codex;
 var codexPlugin = {
   id: "codex",
   name: "Codex",
@@ -565,13 +591,9 @@ var codexPlugin = {
   },
   async export(state, rootDir) {
     const files = [];
-    const outputDir = TOOL_OUTPUT_DIRS.codex;
-    if (state.agents) {
-      files.push({
-        path: "AGENTS.md",
-        type: "symlink",
-        target: `${UNIFIED_DIR}/AGENTS.md`
-      });
+    const agentsSymlink = createRootAgentsMdSymlink(state);
+    if (agentsSymlink) {
+      files.push(agentsSymlink);
     }
     const rulesMap = groupRulesByDirectory(state.rules);
     for (const [dir, contents] of rulesMap.entries()) {
@@ -585,17 +607,11 @@ var codexPlugin = {
         content: combinedContent
       });
     }
-    for (const skill of state.skills) {
-      files.push({
-        path: `${outputDir}/skills/${skill.path}`,
-        type: "symlink",
-        target: `../../${UNIFIED_DIR}/skills/${skill.path}`
-      });
-    }
+    files.push(...createSkillSymlinks(state, CROSS_TOOL_SKILLS_DIR));
     const configToml = buildCodexConfigToml(state.settings?.mcpServers);
     if (configToml) {
       files.push({
-        path: `${outputDir}/config.toml`,
+        path: `${OUTPUT_DIR2}/config.toml`,
         type: "text",
         content: configToml
       });
@@ -606,10 +622,7 @@ var codexPlugin = {
     const warnings = [];
     const skipped = [];
     if (!state.agents) {
-      warnings.push({
-        path: ["AGENTS.md"],
-        message: "No AGENTS.md found - root AGENTS.md will not be created"
-      });
+      warnings.push(createNoAgentsMdWarning("root AGENTS.md"));
     }
     const rulesMap = groupRulesByDirectory(state.rules);
     if (rulesMap.has(".")) {
@@ -629,14 +642,11 @@ var codexPlugin = {
         }
       }
     }
-    if (state.settings?.permissions) {
-      const hasPermissions = (state.settings.permissions.allow?.length ?? 0) > 0 || (state.settings.permissions.ask?.length ?? 0) > 0 || (state.settings.permissions.deny?.length ?? 0) > 0;
-      if (hasPermissions) {
-        skipped.push({
-          feature: "permissions",
-          reason: "Codex rules are not generated from LNAI permissions"
-        });
-      }
+    if (hasPermissionsConfigured(state.settings?.permissions)) {
+      skipped.push({
+        feature: "permissions",
+        reason: "Codex rules are not generated from LNAI permissions"
+      });
     }
     return { valid: true, errors: [], warnings, skipped };
   }
@@ -826,6 +836,7 @@ function transformMcpToCopilot(servers) {
 }
 
 // src/plugins/copilot/index.ts
+var OUTPUT_DIR3 = TOOL_OUTPUT_DIRS.copilot;
 var copilotPlugin = {
   id: "copilot",
   name: "GitHub Copilot",
@@ -837,12 +848,9 @@ var copilotPlugin = {
   },
   async export(state, rootDir) {
     const files = [];
-    if (state.agents) {
-      files.push({
-        path: ".github/copilot-instructions.md",
-        type: "symlink",
-        target: `../${UNIFIED_DIR}/AGENTS.md`
-      });
+    const agentsSymlink = createRootAgentsMdSymlink(state);
+    if (agentsSymlink) {
+      files.push(agentsSymlink);
     }
     for (const rule of state.rules) {
       const transformed = transformRuleToCopilot(rule);
@@ -852,18 +860,12 @@ var copilotPlugin = {
       );
       const outputFilename = rule.path.replace(/\.md$/, ".instructions.md");
       files.push({
-        path: `.github/instructions/${outputFilename}`,
+        path: `${OUTPUT_DIR3}/instructions/${outputFilename}`,
         type: "text",
         content: ruleContent
       });
     }
-    for (const skill of state.skills) {
-      files.push({
-        path: `.github/skills/${skill.path}`,
-        type: "symlink",
-        target: `../../${UNIFIED_DIR}/skills/${skill.path}`
-      });
-    }
+    files.push(...createSkillSymlinks(state, OUTPUT_DIR3));
     const mcpConfig = transformMcpToCopilot(state.settings?.mcpServers);
     if (mcpConfig) {
       files.push({
@@ -878,14 +880,9 @@ var copilotPlugin = {
     const warnings = [];
     const skipped = [];
     if (!state.agents) {
-      warnings.push({
-        path: ["AGENTS.md"],
-        message: "No AGENTS.md found - .github/copilot-instructions.md will not be created"
-      });
+      warnings.push(createNoAgentsMdWarning("root AGENTS.md"));
     }
-    const permissions = state.settings?.permissions;
-    const hasPermissions = permissions && (permissions.allow && permissions.allow.length > 0 || permissions.ask && permissions.ask.length > 0 || permissions.deny && permissions.deny.length > 0);
-    if (hasPermissions) {
+    if (hasPermissionsConfigured(state.settings?.permissions)) {
       skipped.push({
         feature: "permissions",
         reason: "GitHub Copilot does not support declarative permissions"
@@ -1017,6 +1014,7 @@ function transformPermissionRule(rule) {
 }
 
 // src/plugins/cursor/index.ts
+var OUTPUT_DIR4 = TOOL_OUTPUT_DIRS.cursor;
 var cursorPlugin = {
   id: "cursor",
   name: "Cursor",
@@ -1028,13 +1026,9 @@ var cursorPlugin = {
   },
   async export(state, rootDir) {
     const files = [];
-    const outputDir = TOOL_OUTPUT_DIRS.cursor;
-    if (state.agents) {
-      files.push({
-        path: "AGENTS.md",
-        type: "symlink",
-        target: `${UNIFIED_DIR}/AGENTS.md`
-      });
+    const agentsSymlink = createRootAgentsMdSymlink(state);
+    if (agentsSymlink) {
+      files.push(agentsSymlink);
     }
     for (const rule of state.rules) {
       const transformed = transformRuleToCursor(rule);
@@ -1044,22 +1038,16 @@ var cursorPlugin = {
       );
       const outputFilename = rule.path.replace(/\.md$/, ".mdc");
       files.push({
-        path: `${outputDir}/rules/${outputFilename}`,
+        path: `${OUTPUT_DIR4}/rules/${outputFilename}`,
         type: "text",
         content: ruleContent
       });
     }
-    for (const skill of state.skills) {
-      files.push({
-        path: `${outputDir}/skills/${skill.path}`,
-        type: "symlink",
-        target: `../../${UNIFIED_DIR}/skills/${skill.path}`
-      });
-    }
+    files.push(...createSkillSymlinks(state, OUTPUT_DIR4));
     const mcpServers = transformMcpToCursor(state.settings?.mcpServers);
     if (mcpServers) {
       files.push({
-        path: `${outputDir}/mcp.json`,
+        path: `${OUTPUT_DIR4}/mcp.json`,
         type: "json",
         content: { mcpServers }
       });
@@ -1067,7 +1055,7 @@ var cursorPlugin = {
     const cliContent = buildCliContent(state.settings?.permissions);
     if (cliContent) {
       files.push({
-        path: `${outputDir}/cli.json`,
+        path: `${OUTPUT_DIR4}/cli.json`,
         type: "json",
         content: cliContent
       });
@@ -1077,10 +1065,7 @@ var cursorPlugin = {
   validate(state) {
     const warnings = [];
     if (!state.agents) {
-      warnings.push({
-        path: ["AGENTS.md"],
-        message: "No AGENTS.md found - root AGENTS.md will not be created"
-      });
+      warnings.push(createNoAgentsMdWarning("root AGENTS.md"));
     }
     const permissionsResult = transformPermissionsToCursor(
       state.settings?.permissions
@@ -1131,6 +1116,7 @@ function transformMcpToGemini(mcpServers) {
 }
 
 // src/plugins/gemini/index.ts
+var OUTPUT_DIR5 = TOOL_OUTPUT_DIRS.gemini;
 var geminiPlugin = {
   id: "gemini",
   name: "Gemini CLI",
@@ -1142,13 +1128,9 @@ var geminiPlugin = {
   },
   async export(state, rootDir) {
     const files = [];
-    const outputDir = TOOL_OUTPUT_DIRS.gemini;
-    if (state.agents) {
-      files.push({
-        path: `${outputDir}/GEMINI.md`,
-        type: "symlink",
-        target: `../${UNIFIED_DIR}/AGENTS.md`
-      });
+    const agentsSymlink = createRootAgentsMdSymlink(state);
+    if (agentsSymlink) {
+      files.push(agentsSymlink);
     }
     const rulesMap = groupRulesByDirectory(state.rules);
     for (const [dir, contents] of rulesMap.entries()) {
@@ -1160,19 +1142,21 @@ var geminiPlugin = {
         content: combinedContent
       });
     }
-    for (const skill of state.skills) {
-      files.push({
-        path: `${outputDir}/skills/${skill.path}`,
-        type: "symlink",
-        target: `../../${UNIFIED_DIR}/skills/${skill.path}`
-      });
-    }
+    files.push(...createSkillSymlinks(state, OUTPUT_DIR5));
     const mcpServers = transformMcpToGemini(state.settings?.mcpServers);
-    if (mcpServers) {
+    const hasAgents = !!state.agents;
+    if (mcpServers || hasAgents) {
+      const settingsContent = {};
+      if (hasAgents) {
+        settingsContent["context"] = { fileName: ["AGENTS.md"] };
+      }
+      if (mcpServers) {
+        settingsContent["mcpServers"] = mcpServers;
+      }
       files.push({
-        path: `${outputDir}/settings.json`,
+        path: `${OUTPUT_DIR5}/settings.json`,
         type: "json",
-        content: { mcpServers }
+        content: settingsContent
       });
     }
     return applyFileOverrides(files, rootDir, "gemini");
@@ -1181,19 +1165,13 @@ var geminiPlugin = {
     const warnings = [];
     const skipped = [];
     if (!state.agents) {
-      warnings.push({
-        path: ["AGENTS.md"],
-        message: "No AGENTS.md found - GEMINI.md will not be created"
-      });
+      warnings.push(createNoAgentsMdWarning("root AGENTS.md"));
     }
-    if (state.settings?.permissions) {
-      const hasPermissions = (state.settings.permissions.allow?.length ?? 0) > 0 || (state.settings.permissions.ask?.length ?? 0) > 0 || (state.settings.permissions.deny?.length ?? 0) > 0;
-      if (hasPermissions) {
-        skipped.push({
-          feature: "permissions",
-          reason: "Gemini CLI does not support declarative permissions - permissions must be granted interactively"
-        });
-      }
+    if (hasPermissionsConfigured(state.settings?.permissions)) {
+      skipped.push({
+        feature: "permissions",
+        reason: "Gemini CLI does not support declarative permissions - permissions must be granted interactively"
+      });
     }
     if (state.rules.length > 0) {
       warnings.push({
@@ -1278,6 +1256,7 @@ function parsePermissionRuleForOpenCode(rule) {
 }
 
 // src/plugins/opencode/index.ts
+var OUTPUT_DIR6 = TOOL_OUTPUT_DIRS.opencode;
 var opencodePlugin = {
   id: "opencode",
   name: "OpenCode",
@@ -1289,33 +1268,23 @@ var opencodePlugin = {
   },
   async export(state, rootDir) {
     const files = [];
-    const outputDir = TOOL_OUTPUT_DIRS.opencode;
-    if (state.agents) {
-      files.push({
-        path: "AGENTS.md",
-        type: "symlink",
-        target: `${UNIFIED_DIR}/AGENTS.md`
-      });
+    const agentsSymlink = createRootAgentsMdSymlink(state);
+    if (agentsSymlink) {
+      files.push(agentsSymlink);
     }
     if (state.rules.length > 0) {
       files.push({
-        path: `${outputDir}/rules`,
+        path: `${OUTPUT_DIR6}/rules`,
         type: "symlink",
         target: `../${UNIFIED_DIR}/rules`
       });
     }
-    for (const skill of state.skills) {
-      files.push({
-        path: `${outputDir}/skills/${skill.path}`,
-        type: "symlink",
-        target: `../../${UNIFIED_DIR}/skills/${skill.path}`
-      });
-    }
+    files.push(...createSkillSymlinks(state, CROSS_TOOL_SKILLS_DIR));
     const config = {
       $schema: "https://opencode.ai/config.json"
     };
     if (state.rules.length > 0) {
-      config["instructions"] = [`${outputDir}/rules/*.md`];
+      config["instructions"] = [`${OUTPUT_DIR6}/rules/*.md`];
     }
     const mcp = transformMcpToOpenCode(state.settings?.mcpServers);
     if (mcp) {
@@ -1337,10 +1306,7 @@ var opencodePlugin = {
   validate(state) {
     const warnings = [];
     if (!state.agents) {
-      warnings.push({
-        path: ["AGENTS.md"],
-        message: "No AGENTS.md found - root AGENTS.md will not be created"
-      });
+      warnings.push(createNoAgentsMdWarning("root AGENTS.md"));
     }
     warnings.push(
       ...validateMcpServers(state.settings?.mcpServers, [
@@ -1403,6 +1369,7 @@ function serializeWindsurfRule(frontmatter, content) {
 }
 
 // src/plugins/windsurf/index.ts
+var OUTPUT_DIR7 = TOOL_OUTPUT_DIRS.windsurf;
 var windsurfPlugin = {
   id: "windsurf",
   name: "Windsurf",
@@ -1414,13 +1381,9 @@ var windsurfPlugin = {
   },
   async export(state, rootDir) {
     const files = [];
-    const outputDir = TOOL_OUTPUT_DIRS.windsurf;
-    if (state.agents) {
-      files.push({
-        path: "AGENTS.md",
-        type: "symlink",
-        target: `${UNIFIED_DIR}/AGENTS.md`
-      });
+    const agentsSymlink = createRootAgentsMdSymlink(state);
+    if (agentsSymlink) {
+      files.push(agentsSymlink);
     }
     for (const rule of state.rules) {
       const transformed = transformRuleToWindsurf(rule);
@@ -1429,28 +1392,19 @@ var windsurfPlugin = {
         transformed.content
       );
       files.push({
-        path: `${outputDir}/rules/${rule.path}`,
+        path: `${OUTPUT_DIR7}/rules/${rule.path}`,
         type: "text",
         content: ruleContent
       });
     }
-    for (const skill of state.skills) {
-      files.push({
-        path: `${outputDir}/skills/${skill.path}`,
-        type: "symlink",
-        target: `../../${UNIFIED_DIR}/skills/${skill.path}`
-      });
-    }
+    files.push(...createSkillSymlinks(state, OUTPUT_DIR7));
     return applyFileOverrides(files, rootDir, "windsurf");
   },
   validate(state) {
     const warnings = [];
     const skipped = [];
     if (!state.agents) {
-      warnings.push({
-        path: ["AGENTS.md"],
-        message: "No AGENTS.md found - root AGENTS.md will not be created"
-      });
+      warnings.push(createNoAgentsMdWarning("root AGENTS.md"));
     }
     if (state.rules.length > 0) {
       warnings.push({
@@ -1464,14 +1418,11 @@ var windsurfPlugin = {
         reason: "Windsurf uses global MCP config at ~/.codeium/windsurf/mcp_config.json - project-level MCP servers are not exported"
       });
     }
-    if (state.settings?.permissions) {
-      const hasPermissions = (state.settings.permissions.allow?.length ?? 0) > 0 || (state.settings.permissions.ask?.length ?? 0) > 0 || (state.settings.permissions.deny?.length ?? 0) > 0;
-      if (hasPermissions) {
-        skipped.push({
-          feature: "permissions",
-          reason: "Windsurf does not support declarative permissions"
-        });
-      }
+    if (hasPermissionsConfigured(state.settings?.permissions)) {
+      skipped.push({
+        feature: "permissions",
+        reason: "Windsurf does not support declarative permissions"
+      });
     }
     return { valid: true, errors: [], warnings, skipped };
   }
@@ -1642,23 +1593,37 @@ async function writeFiles(files, options) {
 async function updateGitignore(rootDir, paths) {
   const gitignorePath = path.join(rootDir, ".gitignore");
   let content = "";
+  let hasExistingFile = true;
   try {
     content = await fs4.readFile(gitignorePath, "utf-8");
   } catch {
+    hasExistingFile = false;
   }
   const marker = "# lnai-generated";
   const endMarker = "# end lnai-generated";
-  const extractRegex = new RegExp(`${marker}\\n([\\s\\S]*?)${endMarker}`);
-  const match = extractRegex.exec(content);
-  const existingSection = match?.[1] ?? "";
-  const existingPaths = existingSection.split("\n").map((line) => line.trim()).filter((line) => line && !line.startsWith("#"));
   const markerRegex = new RegExp(`${marker}[\\s\\S]*?${endMarker}\\n?`, "g");
+  const hasManagedSection = new RegExp(`${marker}[\\s\\S]*?${endMarker}`).test(
+    content
+  );
   content = content.replace(markerRegex, "");
-  content = content.trimEnd();
-  const uniquePaths = [.../* @__PURE__ */ new Set([...existingPaths, ...paths])].sort();
-  const newSection = ["", marker, ...uniquePaths, endMarker, ""].join("\n");
-  content = content + newSection;
-  await fs4.writeFile(gitignorePath, content, "utf-8");
+  const baseContent = content.trimEnd();
+  const uniquePaths = [...new Set(paths)].sort();
+  if (uniquePaths.length === 0) {
+    if (!hasManagedSection && !hasExistingFile) {
+      return;
+    }
+    const cleanedContent = baseContent.length > 0 ? `${baseContent}
+` : baseContent;
+    await fs4.writeFile(gitignorePath, cleanedContent, "utf-8");
+    return;
+  }
+  const managedSection = [marker, ...uniquePaths, endMarker].join("\n");
+  const nextContent = baseContent.length > 0 ? `${baseContent}
+
+${managedSection}
+` : `${managedSection}
+`;
+  await fs4.writeFile(gitignorePath, nextContent, "utf-8");
 }
 
 // src/manifest/index.ts
@@ -1726,23 +1691,6 @@ function createEmptyManifest() {
 }
 
 // src/pipeline/index.ts
-function getToolsToSync(config, requestedTools) {
-  if (requestedTools && requestedTools.length > 0) {
-    return requestedTools.filter((tool) => pluginRegistry.has(tool));
-  }
-  const enabledTools = [];
-  if (config.tools) {
-    for (const [toolId, toolConfig] of Object.entries(config.tools)) {
-      if (toolConfig?.enabled && pluginRegistry.has(toolId)) {
-        enabledTools.push(toolId);
-      }
-    }
-  }
-  if (enabledTools.length === 0) {
-    return pluginRegistry.getIds();
-  }
-  return enabledTools;
-}
 async function runSyncPipeline(options) {
   const {
     rootDir,
@@ -1777,7 +1725,6 @@ async function runSyncPipeline(options) {
   }
   let manifest = await readManifest(rootDir) ?? createEmptyManifest();
   const results = [];
-  const pathsToIgnore = [];
   for (const toolId of toolsToSync) {
     const plugin = pluginRegistry.get(toolId);
     if (!plugin) {
@@ -1803,19 +1750,57 @@ async function runSyncPipeline(options) {
     if (!dryRun) {
       manifest = updateToolManifest(manifest, toolId, outputFiles);
     }
-    const toolConfig = state.config.tools?.[toolId];
-    if (!toolConfig?.versionControl) {
-      pathsToIgnore.push(...outputFiles.map((f) => f.path));
-    }
   }
   if (!dryRun) {
     await writeManifest(rootDir, manifest);
-  }
-  if (pathsToIgnore.length > 0 && !dryRun) {
+    const pathsToIgnore = computePathsToIgnore(manifest, state.config.tools);
     await updateGitignore(rootDir, pathsToIgnore);
   }
   return results;
 }
+function getToolsToSync(config, requestedTools) {
+  if (requestedTools && requestedTools.length > 0) {
+    return requestedTools.filter((tool) => pluginRegistry.has(tool));
+  }
+  const enabledTools = [];
+  if (config.tools) {
+    for (const [toolId, toolConfig] of Object.entries(config.tools)) {
+      if (toolConfig?.enabled && pluginRegistry.has(toolId)) {
+        enabledTools.push(toolId);
+      }
+    }
+  }
+  if (enabledTools.length === 0) {
+    return pluginRegistry.getIds();
+  }
+  return enabledTools;
+}
+function computePathsToIgnore(manifest, toolConfigs) {
+  const pathToTools = /* @__PURE__ */ new Map();
+  for (const [toolId, toolManifest] of Object.entries(manifest.tools)) {
+    if (!toolManifest?.files) {
+      continue;
+    }
+    for (const file of toolManifest.files) {
+      let tools = pathToTools.get(file.path);
+      if (!tools) {
+        tools = /* @__PURE__ */ new Set();
+        pathToTools.set(file.path, tools);
+      }
+      tools.add(toolId);
+    }
+  }
+  const result = [];
+  for (const [filePath, toolIds] of pathToTools) {
+    const anyVersionControlled = [...toolIds].some(
+      (toolId) => toolConfigs?.[toolId]?.versionControl === true
+    );
+    if (!anyVersionControlled) {
+      result.push(filePath);
+    }
+  }
+  return result;
+}
 async function initUnifiedConfig(options) {
   const {
     rootDir,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@lnai/core",
-  "version": "0.6.5",
+  "version": "0.6.7",
   "description": "Core library for LNAI - unified AI config management",
   "type": "module",
   "license": "MIT",