pkm-mcp-server 1.3.0 → 1.3.2

package/CHANGELOG.md

@@ -6,6 +6,16 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 ## [Unreleased]
 
+## [1.3.2] - 2026-03-21
+
+### Fixed
+- Fix `claude mcp add` argument ordering — the `-e` flag is variadic and was greedily consuming the server name. Moved `--` separator before the server name to terminate option parsing.
+
+## [1.3.1] - 2026-03-21
+
+### Fixed
+- `pkm-mcp-server init` now correctly registers the MCP server with Claude Code via `claude mcp add` instead of writing to the wrong config file (`~/.claude/settings.json`). Previously, the server appeared to register successfully but was never visible to Claude Code.
+
 ## [1.3.0] - 2026-03-19
 
 ### Added

package/README.md

@@ -82,69 +82,59 @@ Ambiguous matches return an error listing candidates. Exact paths always work un
 
 ## Quick Start
 
-### 1. Install
+### 1. Install and Set Up
 
 **From npm** (recommended):
 
 ```bash
 npm install -g pkm-mcp-server
+pkm-mcp-server init
 ```
 
+The setup wizard walks you through:
+1. Vault path (existing or new)
+2. Note templates (full set, minimal, or skip)
+3. PARA folder structure
+4. OpenAI API key for semantic search (optional)
+5. Automatic registration with Claude Code
+
+Restart Claude Code after setup. The server provides all tools except semantic search out of the box.
+
 **From source:**
 
 ```bash
 git clone https://github.com/AdrianV101/Obsidian-MCP.git
 cd Obsidian-MCP
 npm install
+node cli.js init
 ```
 
-### 2. Register with Claude Code
-
-Add to `~/.claude/settings.json`:
+### 2. Manual Registration (alternative)
 
-**If installed from npm:**
+If you prefer to skip the wizard, register directly with the Claude CLI:
 
-```json
-{
-  "mcpServers": {
-    "obsidian-pkm": {
-      "command": "npx",
-      "args": ["-y", "pkm-mcp-server"],
-      "env": {
-        "VAULT_PATH": "/absolute/path/to/your/obsidian/vault"
-      }
-    }
-  }
-}
+```bash
+claude mcp add -s user -e VAULT_PATH=/absolute/path/to/your/vault -- obsidian-pkm npx -y pkm-mcp-server
 ```
 
-**If installed from source:**
+For a source install:
 
-```json
-{
-  "mcpServers": {
-    "obsidian-pkm": {
-      "command": "node",
-      "args": ["/absolute/path/to/index.js"],
-      "env": {
-        "VAULT_PATH": "/absolute/path/to/your/obsidian/vault"
-      }
-    }
-  }
-}
+```bash
+claude mcp add -s user -e VAULT_PATH=/absolute/path/to/your/vault -- obsidian-pkm node /absolute/path/to/cli.js
 ```
 
-Restart Claude Code. The server provides all tools except semantic search out of the box.
+Verify with `claude mcp list` — you should see `obsidian-pkm: ... - Connected`.
 
 ### 3. Enable Semantic Search (optional)
 
-Add your OpenAI API key to the env block:
+If you didn't set this up during `init`, add your OpenAI API key by re-registering:
 
-```json
-"env": {
-  "VAULT_PATH": "/absolute/path/to/your/obsidian/vault",
-  "OPENAI_API_KEY": "sk-..."
-}
+```bash
+claude mcp remove obsidian-pkm
+claude mcp add -s user \
+  -e VAULT_PATH=/absolute/path/to/your/vault \
+  -e OPENAI_API_KEY=sk-... \
+  -- obsidian-pkm npx -y pkm-mcp-server
 ```
 
 This enables `vault_semantic_search` and `vault_suggest_links`. Uses `text-embedding-3-large` with a SQLite + sqlite-vec index stored at `.obsidian/semantic-index.db`. The index rebuilds automatically — delete the DB file to force a full re-embed.
@@ -290,13 +280,16 @@ All paths passed to tools are relative to vault root. The server includes path s
 You need C++ build tools. See [Prerequisites](#prerequisites) for your platform. On Linux, `sudo apt install build-essential python3` usually fixes it.
 
 **Server starts but all tool calls fail with ENOENT**
-Your `VAULT_PATH` is wrong or missing. The server now validates this at startup and exits with a clear error. Set it explicitly in your `settings.json` env block.
+Your `VAULT_PATH` is wrong or missing. The server validates this at startup and exits with a clear error. Re-register with the correct path: `claude mcp remove obsidian-pkm && claude mcp add -s user -e VAULT_PATH=/correct/path -- obsidian-pkm npx -y pkm-mcp-server`
 
 **`vault_write` says "no templates available"**
-Copy the `templates/` files from this repo into your vault's `05-Templates/` directory. The server loads templates from there at startup.
+Run `pkm-mcp-server init` to install templates, or copy the `templates/` files from this repo into your vault's `05-Templates/` directory. The server loads templates from there at startup.
 
 **Semantic search not appearing in tool list**
-Set `OPENAI_API_KEY` in your `settings.json` env block. Without it, `vault_semantic_search` and `vault_suggest_links` are hidden entirely.
+Set `OPENAI_API_KEY` in your MCP server registration. See [Enable Semantic Search](#3-enable-semantic-search-optional). Without it, `vault_semantic_search` and `vault_suggest_links` are hidden entirely.
+
+**Server not showing up in Claude Code after install**
+Run `claude mcp list` to check. If `obsidian-pkm` is missing, register it with `claude mcp add` (see [Manual Registration](#2-manual-registration-alternative)). Note: editing `~/.claude/settings.json` directly does **not** register MCP servers — use the CLI.
 
 **Semantic index not updating after file changes**
 Check your Node version with `node -v`. The file watcher uses `fs.watch({ recursive: true })` which requires Node.js >= 18.13 on Linux.

package/init.js

@@ -2,6 +2,10 @@ import os from "os";
 import path from "path";
 import fs from "fs/promises";
 import { fileURLToPath } from "url";
+import { execFile as execFileCb } from "child_process";
+import { promisify } from "util";
+
+const execFileAsync = promisify(execFileCb);
 
 /**
  * Resolve user-provided path input: expand ~, $HOME, resolve relative, normalise.
@@ -119,41 +123,44 @@ export async function backupVault(vaultPath) {
 }
 
 /**
- * Read/merge/write settings.json atomically.
- * @param {string} settingsPath - Absolute path to settings.json
- * @param {object} serverConfig - The obsidian-pkm server config block
- * @returns {Promise<object>} The full merged config object
+ * Build argument array for `claude mcp add` command.
+ * @param {{ vaultPath: string, openaiKey: string|null, installType: { command: string, args: string[] } }} opts
+ * @returns {string[]}
  */
-export async function updateSettingsJson(settingsPath, serverConfig) {
-  // Create parent directory
-  await fs.mkdir(path.dirname(settingsPath), { recursive: true });
+export function buildMcpAddArgs({ vaultPath, openaiKey, installType }) {
+  const args = ["mcp", "add", "-s", "user"];
+  args.push("-e", `VAULT_PATH=${vaultPath}`);
+  if (openaiKey) {
+    args.push("-e", `OPENAI_API_KEY=${openaiKey}`);
+  }
+  args.push("--", "obsidian-pkm", installType.command, ...installType.args);
+  return args;
+}
 
-  // Read existing or start fresh
-  let config = {};
+/**
+ * Check if the `claude` CLI is available on PATH.
+ * @returns {Promise<boolean>}
+ */
+export async function checkClaudeCli() {
   try {
-    const raw = await fs.readFile(settingsPath, "utf8");
-    try {
-      config = JSON.parse(raw);
-    } catch {
-      const err = new Error(`${settingsPath} is not valid JSON. Please fix it manually or delete it to start fresh.`);
-      err.code = "INVALID_JSON";
-      throw err;
-    }
-  } catch (e) {
-    if (e.code !== "ENOENT") throw e;
-    // File doesn't exist — start with {}
+    await execFileAsync("claude", ["--version"]);
+    return true;
+  } catch {
+    return false;
   }
+}
 
-  // Merge
-  config.mcpServers = config.mcpServers || {};
-  config.mcpServers["obsidian-pkm"] = serverConfig;
-
-  // Atomic write
-  const tmpPath = settingsPath + ".tmp";
-  await fs.writeFile(tmpPath, JSON.stringify(config, null, 2) + "\n");
-  await fs.rename(tmpPath, settingsPath);
-
-  return config;
+/**
+ * Check if obsidian-pkm is already registered in Claude Code.
+ * @returns {Promise<boolean>}
+ */
+export async function checkExistingRegistration() {
+  try {
+    await execFileAsync("claude", ["mcp", "get", "obsidian-pkm"]);
+    return true;
+  } catch {
+    return false;
+  }
 }
 
 /**
@@ -207,7 +214,6 @@ export async function runInit() {
   const { confirm: confirmPrompt, input, select, password } = await import("@inquirer/prompts");
 
   const bundledTemplatesDir = path.join(path.dirname(fileURLToPath(import.meta.url)), "templates");
-  const settingsPath = path.join(os.homedir(), ".claude", "settings.json");
   const steps = [];
 
   try {
@@ -299,8 +305,8 @@ Nothing is written until you confirm each step. Press Ctrl+C at any time to canc
       console.log(`
   Get an API key at: https://platform.openai.com/api-keys
 
-  This key is stored only in your local Claude Code settings file
-  (~/.claude/settings.json) and is never sent to us or anyone else.
+  This key is stored only in your Claude Code configuration
+  (~/.claude.json) and is never sent to us or anyone else.
   It's used solely for generating text embeddings via OpenAI's API.
 `);
       openaiKey = await password({ message: "OpenAI API key (Enter to skip):", mask: "*" });
@@ -309,79 +315,66 @@ Nothing is written until you confirm each step. Press Ctrl+C at any time to canc
       console.log("  You can add this later by setting OPENAI_API_KEY in your Claude Code settings.\n");
     }
     // ── Step 6: Registration ──
-    const installType = detectInstallType();
-    const serverConfig = {
-      command: installType.command,
-      args: [...installType.args],
-      env: { VAULT_PATH: vaultPath },
-    };
-    if (openaiKey) {
-      serverConfig.env.OPENAI_API_KEY = openaiKey;
-    }
+    const hasClaude = await checkClaudeCli();
+    if (!hasClaude) {
+      const installType = detectInstallType();
+      const manualCmd = `claude mcp add -s user -e VAULT_PATH=${vaultPath} -- obsidian-pkm ${installType.command} ${installType.args.join(" ")}`;
+      console.log(`
+  Claude Code CLI not found on PATH. To register manually, run:
 
-    // Check for existing registration
-    let hasExisting = false;
-    try {
-      const raw = await fs.readFile(settingsPath, "utf8");
-      const existing = JSON.parse(raw);
-      if (existing.mcpServers?.["obsidian-pkm"]) {
-        hasExisting = true;
-      }
-    } catch (e) {
-      if (e.code !== "ENOENT" && !(e instanceof SyntaxError)) {
-        console.warn(`  Warning: could not read ${settingsPath}: ${e.message}`);
+    ${manualCmd}
+`);
+      steps.push("MCP server: skipped (Claude CLI not found)");
+    } else {
+      const installType = detectInstallType();
+      const hasExisting = await checkExistingRegistration();
+
+      let skipRegistration = false;
+      if (hasExisting) {
+        const overwrite = await confirmPrompt({ message: "Claude Code is already configured for pkm-mcp-server. Overwrite?", default: false });
+        if (!overwrite) {
+          console.log("  Registration skipped.\n");
+          skipRegistration = true;
+        } else {
+          // Remove existing before re-adding
+          try {
+            await execFileAsync("claude", ["mcp", "remove", "obsidian-pkm"]);
+          } catch (e) {
+            console.warn(`  Warning: could not remove existing registration: ${e.message}`);
+          }
+        }
       }
-    }
-
-    let skipRegistration = false;
-    if (hasExisting) {
-      const overwrite = await confirmPrompt({ message: "Claude Code is already configured for pkm-mcp-server. Overwrite?", default: false });
-      if (!overwrite) { console.log("  Registration skipped.\n"); skipRegistration = true; }
-    }
 
-    if (!skipRegistration) {
-      // Show preview
-      const previewObj = {
-        mcpServers: {
-          "obsidian-pkm": serverConfig,
-        },
-      };
-      console.log(`\nWill write to ${settingsPath}:\n`);
-      console.log(JSON.stringify(previewObj, null, 2));
-      console.log("\nThis only adds the \"obsidian-pkm\" key under \"mcpServers\". No other settings will be changed.");
-
-      const doRegister = await confirmPrompt({
-        message: "Register MCP server with Claude Code?",
-        default: true,
-      });
-
-      if (doRegister) {
-        let registered = false;
-        try {
-          await updateSettingsJson(settingsPath, serverConfig);
-          registered = true;
-        } catch (regErr) {
-          if (regErr.code === "INVALID_JSON") {
-            console.error(`\n  ${regErr.message}`);
+      if (!skipRegistration) {
+        const addArgs = buildMcpAddArgs({ vaultPath, openaiKey, installType });
+        const displayCmd = `claude ${addArgs.join(" ")}`;
+        console.log(`\nWill run:\n\n  ${displayCmd}\n`);
+
+        const doRegister = await confirmPrompt({
+          message: "Register MCP server with Claude Code?",
+          default: true,
+        });
+
+        if (doRegister) {
+          try {
+            await execFileAsync("claude", addArgs);
+            console.log("  MCP server registered with Claude Code");
+            steps.push("MCP server: registered");
+          } catch (regErr) {
+            console.error(`\n  Registration failed: ${regErr.message}`);
+            if (regErr.stderr) console.error(`  ${regErr.stderr.trim()}`);
             const skipReg = await confirmPrompt({ message: "Skip registration and finish setup?", default: true });
             if (!skipReg) throw regErr;
             console.log("  Registration skipped.\n");
-          } else {
-            throw regErr;
+            steps.push("MCP server: skipped (registration failed)");
           }
-        }
-        if (registered) {
-          console.log("  MCP server registered");
-          steps.push("MCP server: registered");
         } else {
-          steps.push("MCP server: skipped (malformed settings.json)");
+          console.log("  Registration: skipped (you can run `pkm-mcp-server init` again later)");
+          steps.push("MCP server: skipped");
         }
       } else {
-        console.log("  Registration: skipped (you can run `pkm-mcp-server init` again later)");
         steps.push("MCP server: skipped");
       }
-    } else {
-      steps.push("MCP server: skipped");
     }
 
     // ── Step 7: Summary ──
@@ -398,7 +391,7 @@ Nothing is written until you confirm each step. Press Ctrl+C at any time to canc
     // Determine registration summary from steps
     const regStep = steps.find(s => s.startsWith("MCP server:"));
     const registrationSummary = regStep && regStep.includes("registered")
-      ? `Registered in ${settingsPath}`
+      ? "Registered with Claude Code"
       : "Skipped";
 
     console.log(`

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "pkm-mcp-server",
-  "version": "1.3.0",
+  "version": "1.3.2",
   "description": "MCP server for Obsidian vault integration with Claude Code — 19 tools for notes, search, and graph traversal",
   "main": "cli.js",
   "exports": {