diff --git a/README.md b/README.md
index fda100a..fb64f2c 100644
--- a/README.md
+++ b/README.md
@@ -106,6 +106,12 @@ Config file locations:
 | VS Code     | `.vscode/mcp.json`   |
 | Windsurf    | `.windsurf/mcp.json` |
 
+### CLI Subcommands
+
+- `init [target]` - Generate MCP configuration (targets: `claude`, `cursor`, `vscode`, `windsurf`).
+- `skeleton [path]` or `tree [path]` - **(New)** View the structural tree of a project with file headers and symbol definitions directly in your terminal.
+- `[path]` - Start the MCP server (stdio) for the specified path (defaults to current directory).
+
 ### From Source
 
 ```bash
@@ -113,11 +119,6 @@ npm install
 npm run build
 ```
 
-```bash
-node build/index.js                      # analyze current directory
-node build/index.js /path/to/my-project  # analyze a specific project
-```
-
 ## Architecture
 
 Three layers built with TypeScript over stdio using the Model Context Protocol SDK:
diff --git a/src/index.ts b/src/index.ts
index f4cab5e..b690755 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -29,8 +29,9 @@ const AGENT_CONFIG_PATH: Record<AgentTarget, string> = {
   windsurf: ".windsurf/mcp.json",
 };
 
+const SUB_COMMANDS = ["init", "skeleton", "tree"];
 const passthroughArgs = process.argv.slice(2);
-const ROOT_DIR = passthroughArgs[0] && passthroughArgs[0] !== "init"
+const ROOT_DIR = passthroughArgs[0] && !SUB_COMMANDS.includes(passthroughArgs[0])
   ? resolve(passthroughArgs[0])
   : process.cwd();
 
@@ -351,6 +352,15 @@ async function main() {
     await runInitCommand(args.slice(1));
     return;
   }
+  if (args[0] === "skeleton" || args[0] === "tree") {
+    const tree = await getContextTree({
+      rootDir: ROOT_DIR,
+      includeSymbols: true,
+      maxTokens: 50000,
+    });
+    process.stdout.write(tree + "\n");
+    return;
+  }
   await ensureMcpDataDir(ROOT_DIR);
   const trackerEnabled = (process.env.CONTEXTPLUS_EMBED_TRACKER ?? "true").toLowerCase() !== "false";
   const stopTracker = trackerEnabled
diff --git a/src/tools/context-tree.ts b/src/tools/context-tree.ts
index 8ac22c8..2568c9e 100644
--- a/src/tools/context-tree.ts
+++ b/src/tools/context-tree.ts
@@ -32,40 +32,43 @@ async function buildTree(entries: FileEntry[], _rootDir: string, includeSymbols:
   const dirMap = new Map<string, TreeNode>();
   dirMap.set(".", root);
 
-  const dirs = entries.filter((e) => e.isDirectory).sort((a, b) => a.relativePath.localeCompare(b.relativePath));
-  for (const dir of dirs) {
-    const parts = dir.relativePath.split("/");
-    const parentPath = parts.length > 1 ? parts.slice(0, -1).join("/") : ".";
-    const parent = dirMap.get(parentPath) ?? root;
-    const node: TreeNode = { name: parts[parts.length - 1], relativePath: dir.relativePath, isDirectory: true, children: [] };
-    parent.children.push(node);
-    dirMap.set(dir.relativePath, node);
-  }
+  // Sort by depth then path to ensure parents exist before children
+  const sortedEntries = entries.sort((a, b) => a.depth - b.depth || a.relativePath.localeCompare(b.relativePath));
 
-  const files = entries.filter((e) => !e.isDirectory);
-  for (const file of files) {
-    const parts = file.relativePath.split("/");
+  for (const entry of sortedEntries) {
+    const parts = entry.relativePath.split("/");
     const parentPath = parts.length > 1 ? parts.slice(0, -1).join("/") : ".";
-    const parent = dirMap.get(parentPath) ?? root;
+    
+    // Ensure parent node exists (fallback to root)
+    let parent = dirMap.get(parentPath);
+    if (!parent && parentPath !== ".") {
+      // Auto-create missing parent directories if needed
+      parent = root;
+    } else if (!parent) {
+      parent = root;
+    }
 
     const node: TreeNode = {
       name: parts[parts.length - 1],
-      relativePath: file.relativePath,
-      isDirectory: false,
+      relativePath: entry.relativePath,
+      isDirectory: entry.isDirectory,
       children: [],
     };
 
-    if (isSupportedFile(file.path)) {
+    if (!entry.isDirectory && isSupportedFile(entry.path)) {
       try {
-        const analysis = await analyzeFile(file.path);
+        const analysis = await analyzeFile(entry.path);
         node.header = analysis.header || undefined;
         if (includeSymbols && analysis.symbols.length > 0) {
           node.symbols = analysis.symbols.map((s) => formatSymbol(s, 0)).join("\n");
         }
-      } catch {
-      }
+      } catch {}
     }
+
     parent.children.push(node);
+    if (entry.isDirectory) {
+      dirMap.set(entry.relativePath, node);
+    }
   }
 
   return root;