gnosys 5.11.1 → 5.11.3

package/README.md

@@ -36,6 +36,7 @@ gnosys setup          # configures provider, API key, and your IDE/agent
 ## Quick start
 
 ```bash
+gnosys setup ides                                        # wire MCP into your IDEs (once)
 cd your-project
 gnosys init                                              # register the project
 gnosys add "We chose PostgreSQL over MySQL for JSON support"
@@ -61,7 +62,7 @@ All tools are exposed over stdio and HTTP transports. Many tools accept an optio
 
 This package installs two binaries:
 
-- **`gnosys`** — the CLI. `gnosys serve` starts the MCP server (stdio by default, `--transport http` for the central-server topology). `gnosys init <ide>` wires this into your IDE/agent automatically.
+- **`gnosys`** — the CLI. `gnosys serve` starts the MCP server (stdio by default, `--transport http` for the central-server topology). `gnosys setup ides` wires `gnosys-mcp` into your IDE/agent configs.
 - **`gnosys-mcp`** — a direct alias for the MCP stdio server entry, for MCP clients that prefer to spawn the server binary directly (e.g. `npx -y gnosys-mcp`). Equivalent to `gnosys serve`.
 
 | Tool | Description |

package/dist/cli.js

@@ -973,7 +973,7 @@ setupCmd
 // `gnosys setup ides` — configure IDE / MCP integrations standalone
 setupCmd
     .command("ides")
-    .description("Configure IDE integrations (Claude Code/Desktop, Cursor, Codex, Gemini CLI, Antigravity)")
+    .description("Configure IDE MCP integrations (Claude Code/Desktop, Cursor, Codex, Grok Build, Gemini CLI, Antigravity)")
     .action(async () => {
     const readline = await import("readline/promises");
     const { runIdesSetup } = await import("./lib/setup/sections/ides.js");
@@ -1021,11 +1021,11 @@ setupCmd
 // we need to revive a top-level shortcut later.
 // ─── gnosys init ─────────────────────────────────────────────────────────
 program
-    .command("init [ide]")
-    .description("Initialize Gnosys in the current directory. Optionally specify IDE: cursor, claude, claude-desktop, codex, gemini-cli, or antigravity to force IDE setup.")
+    .command("init")
+    .description("Initialize Gnosys in the current directory (project store, identity, central DB). Wire IDE MCP servers with: gnosys setup ides")
     .option("-d, --directory <dir>", "Target directory (default: cwd)")
     .option("-n, --name <name>", "Project name (default: directory basename)")
-    .action(async (ide, opts) => {
+    .action(async (opts) => {
     const targetDir = opts.directory
         ? path.resolve(opts.directory)
         : process.cwd();
@@ -1127,62 +1127,8 @@ program
     else {
         console.log(`\nIDE hooks: ${hookResult.details}`);
     }
-    // If a specific IDE was requested, force-create its config
-    if (ide) {
-        const validIdes = ["cursor", "claude", "claude-desktop", "codex", "gemini-cli", "antigravity"];
-        const normalizedIde = ide.toLowerCase();
-        if (!validIdes.includes(normalizedIde)) {
-            console.log(`\nUnknown IDE: "${ide}". Valid options: ${validIdes.join(", ")}`);
-        }
-        else {
-            const { configureCursor, configureClaudeCode, configureCodex } = await import("./lib/projectIdentity.js");
-            // Cursor/Claude/Codex have IDE-specific session hooks. Gemini CLI and
-            // Antigravity don't yet, so we skip the hook step for them.
-            let result;
-            switch (normalizedIde) {
-                case "cursor":
-                    result = await configureCursor(targetDir);
-                    break;
-                case "claude":
-                    result = await configureClaudeCode(targetDir);
-                    break;
-                case "codex":
-                    result = await configureCodex(targetDir);
-                    break;
-            }
-            if (result?.configured) {
-                console.log(`\nIDE setup (${result.ide}):`);
-                console.log(`  ${result.details}`);
-                console.log(`  File: ${result.filePath}`);
-            }
-            // Set up MCP config for the IDE
-            const { setupIDE } = await import("./lib/setup.js");
-            const mcp = await setupIDE(normalizedIde, targetDir);
-            if (mcp.success) {
-                console.log(`  MCP: ${mcp.message}`);
-            }
-            // Update agentRulesTarget in gnosys.json (only for IDEs with rules files)
-            const targetMap = {
-                cursor: ".cursor/rules/gnosys.mdc",
-                claude: "CLAUDE.md",
-                codex: "CODEX.md",
-            };
-            if (targetMap[normalizedIde]) {
-                const identityPath = path.join(storePath, "gnosys.json");
-                try {
-                    const identityContent = await fs.readFile(identityPath, "utf-8");
-                    const identity = JSON.parse(identityContent);
-                    identity.agentRulesTarget = targetMap[normalizedIde];
-                    await fs.writeFile(identityPath, JSON.stringify(identity, null, 2) + "\n", "utf-8");
-                    console.log(`  Config: agentRulesTarget → ${identity.agentRulesTarget}`);
-                }
-                catch {
-                    // Non-critical
-                }
-            }
-        }
-    }
-    console.log(`\nStart adding memories with: gnosys add "your knowledge here"`);
+    console.log(`\nWire IDE MCP servers: gnosys setup ides`);
+    console.log(`Start adding memories with: gnosys add "your knowledge here"`);
 });
 // ─── gnosys migrate ─────────────────────────────────────────────────────
 program
@@ -4422,7 +4368,7 @@ exportCmd
 // ─── gnosys serve ────────────────────────────────────────────────────────
 program
     .command("serve")
-    .description("Start the MCP server (stdio mode). Used by IDE integrations — Claude Code/Desktop, Cursor, Codex, etc. spawn this command in the background to talk to gnosys via the Model Context Protocol. You don't normally invoke this yourself; `gnosys init <ide>` wires it into the IDE config.")
+    .description("Start the MCP server (stdio mode). Used by IDE integrations — Claude Code/Desktop, Cursor, Codex, etc. spawn this command in the background to talk to gnosys via the Model Context Protocol. You don't normally invoke this yourself; `gnosys setup ides` wires gnosys-mcp into your IDE configs.")
     .option("--with-maintenance", "Run maintenance every 6 hours in background")
     .option("--transport <mode>", "Transport: 'stdio' (default) or 'http' (central-server topology)", "stdio")
     .option("--host <addr>", "HTTP bind address — http transport (default 127.0.0.1; use a tailnet addr to share)", "127.0.0.1")

package/dist/index.js

@@ -10,7 +10,7 @@
 // MCP stdio JSON protocol. parse() is a pure function with no side effects.
 import dotenv from "dotenv";
 import path from "path";
-import { readFileSync } from "fs";
+import { readFileSync, realpathSync } from "fs";
 import { fileURLToPath } from "url";
 const home = process.env.HOME || process.env.USERPROFILE || "/tmp";
 try {
@@ -3092,8 +3092,22 @@ export async function startMcpServer() {
         // Notification handler setup failed — non-critical
     }
 }
-const invokedAsScript = !!process.argv[1] && fileURLToPath(import.meta.url) === path.resolve(process.argv[1]);
-if (invokedAsScript) {
+/** True when this file is the process entry (direct path or npm `gnosys-mcp` bin symlink). */
+function isMcpEntryPoint() {
+    if (!process.argv[1])
+        return false;
+    const entry = path.resolve(process.argv[1]);
+    const self = fileURLToPath(import.meta.url);
+    if (entry === self)
+        return true;
+    try {
+        return realpathSync(entry) === realpathSync(self);
+    }
+    catch {
+        return false;
+    }
+}
+if (isMcpEntryPoint()) {
     startMcpServer().catch((err) => {
         console.error("Fatal error:", err);
         process.exit(1);

package/dist/lib/setup/sections/ides.js

@@ -38,7 +38,7 @@ const IDE_TARGET_DISPLAY = {
     codex: ".codex/mcp.json",
     "gemini-cli": "~/.gemini/settings.json",
     antigravity: "~/.gemini/antigravity/mcp_config.json",
-    "grok-build": "~/.grok/config.toml",
+    "grok-build": "~/.grok/config.toml ([mcp_servers.gnosys])",
 };
 function ideTarget(ide) {
     return IDE_TARGET_DISPLAY[ide] ?? `.${ide}/mcp.json`;

package/dist/lib/setup.d.ts

@@ -56,14 +56,11 @@ export declare function writeApiKey(provider: string, key: string): Promise<void
  */
 export declare function detectIDEs(projectDir: string): Promise<string[]>;
 /**
- * Replace (or append) a `[mcp.<name>]` block inside the TOML text for
- * Grok Build's config file. Preserves every line outside that block —
- * deci-046 read-then-merge rule. We can't pull in a TOML dependency
- * without adding to package.json, so we ship a minimal hand-rolled
- * updater scoped exactly to the `[mcp.gnosys]` use case.
+ * Replace (or append) a `[mcp_servers.<name>]` block inside Grok Build's
+ * `~/.grok/config.toml`. Preserves every line outside that block (deci-046).
  *
- * Spec assumption: TOML headers we touch are simple `[a.b]` lines with
- * no inline tables or nested arrays. Any other content is left alone.
+ * Grok Build reads `mcp_servers.*` only — legacy `[mcp.*]` blocks are ignored
+ * by `grok mcp list` / the agent runtime (see ~/.grok/README.md).
  *
  * Exported for tests.
  */

package/dist/lib/setup.js

@@ -567,33 +567,48 @@ export async function detectIDEs(projectDir) {
     }
     return detected;
 }
+/** Remove a single `[section]` block from Grok TOML (hand-rolled; see upsertGrokMcpBlock). */
+function removeGrokTomlSection(existing, sectionHeader) {
+    const lines = existing.split("\n");
+    const headerIdx = lines.findIndex((line) => line.trim() === sectionHeader);
+    if (headerIdx === -1)
+        return existing;
+    let endIdx = lines.length;
+    for (let i = headerIdx + 1; i < lines.length; i++) {
+        if (/^\s*\[/.test(lines[i])) {
+            endIdx = i;
+            break;
+        }
+    }
+    const before = lines.slice(0, headerIdx).join("\n");
+    const after = lines.slice(endIdx).join("\n");
+    const merged = [before, after].filter((s) => s.length > 0).join("\n");
+    return merged.length > 0 ? `${merged}\n` : "";
+}
 /**
- * Replace (or append) a `[mcp.<name>]` block inside the TOML text for
- * Grok Build's config file. Preserves every line outside that block —
- * deci-046 read-then-merge rule. We can't pull in a TOML dependency
- * without adding to package.json, so we ship a minimal hand-rolled
- * updater scoped exactly to the `[mcp.gnosys]` use case.
+ * Replace (or append) a `[mcp_servers.<name>]` block inside Grok Build's
+ * `~/.grok/config.toml`. Preserves every line outside that block (deci-046).
  *
- * Spec assumption: TOML headers we touch are simple `[a.b]` lines with
- * no inline tables or nested arrays. Any other content is left alone.
+ * Grok Build reads `mcp_servers.*` only — legacy `[mcp.*]` blocks are ignored
+ * by `grok mcp list` / the agent runtime (see ~/.grok/README.md).
  *
  * Exported for tests.
  */
 export function upsertGrokMcpBlock(existing, name, entry) {
-    const sectionHeader = `[mcp.${name}]`;
-    const lines = existing.split("\n");
+    // Drop mistaken v5.9.4 `[mcp.<name>]` sections so we don't leave dead config.
+    let content = removeGrokTomlSection(existing, `[mcp.${name}]`);
+    const sectionHeader = `[mcp_servers.${name}]`;
+    const lines = content.split("\n");
     const headerIdx = lines.findIndex((line) => line.trim() === sectionHeader);
     const blockBody = renderGrokMcpBlock(entry);
     if (headerIdx === -1) {
-        // Append a fresh block, separated by a blank line if the file has content.
-        const prefix = existing.length === 0 || existing.endsWith("\n\n")
-            ? existing
-            : existing.endsWith("\n") ? `${existing}\n` : `${existing}\n\n`;
+        const prefix = content.length === 0 || content.endsWith("\n\n")
+            ? content
+            : content.endsWith("\n")
+                ? `${content}\n`
+                : `${content}\n\n`;
         return `${prefix}${sectionHeader}\n${blockBody}`;
     }
-    // Replace the existing block — everything from sectionHeader up to the
-    // next `[` header (or EOF). Count blank lines immediately after the block
-    // so we can preserve the original spacing before the next section.
     let endIdx = lines.length;
     for (let i = headerIdx + 1; i < lines.length; i++) {
         if (/^\s*\[/.test(lines[i])) {
@@ -611,7 +626,6 @@ export function upsertGrokMcpBlock(existing, name, entry) {
     const beforeBlock = lines.slice(0, headerIdx).join("\n");
     const head = beforeBlock.length > 0 ? `${beforeBlock}\n` : "";
     if (!hasFollowingSection) {
-        // No following section — drop trailing blank lines and end with a single \n.
         return `${head}${sectionHeader}\n${blockBody}`;
     }
     const gap = "\n".repeat(Math.max(1, trailingBlankBeforeNext));
@@ -814,10 +828,9 @@ export async function setupIDE(ide, projectDir) {
                 return { success: true, message: "Antigravity MCP config updated (~/.gemini/antigravity/mcp_config.json)" };
             }
             case "grok-build": {
-                // v5.9.4 Bug 12 — Grok Build reads its MCP servers from a
-                // `[mcp.<name>]` block in ~/.grok/config.toml. We never clobber
-                // unrelated TOML content (per deci-046 read-then-merge rule); the
-                // helper preserves every line outside the `[mcp.gnosys]` block.
+                // v5.9.4 Bug 12 — Grok Build reads MCP from `[mcp_servers.<name>]`
+                // in ~/.grok/config.toml (not `[mcp.<name>]`). We never clobber
+                // unrelated TOML content (per deci-046 read-then-merge rule).
                 const grokDir = path.join(os.homedir(), ".grok");
                 const configPath = path.join(grokDir, "config.toml");
                 await fs.mkdir(grokDir, { recursive: true });

package/dist/postinstall.js

@@ -77,8 +77,9 @@ async function main() {
         out();
         out("  Get started:");
         out("    1. gnosys setup                configure LLM providers and preferences");
-        out("    2. gnosys init                 initialize gnosys in a project directory");
-        out("    3. gnosys status               check project status");
+        out("    2. gnosys setup ides           wire MCP into your IDEs (once per machine)");
+        out("    3. gnosys init                 initialize gnosys in a project directory");
+        out("    4. gnosys status               check project status");
         out();
         // If interactive, offer to run setup automatically
         if (isInteractive) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gnosys",
-  "version": "5.11.1",
+  "version": "5.11.3",
   "description": "Gnosys — Persistent Memory for AI Agents. Sandbox-first runtime, central SQLite brain, federated search, Dream Mode, Web Knowledge Base, Obsidian export.",
   "type": "module",
   "main": "dist/index.js",
@@ -34,7 +34,7 @@
     "docs:mcp-tools": "node scripts/gen-mcp-tools.mjs --write",
     "docs:cli": "node scripts/gen-cli-docs.mjs --write",
     "postinstall": "node dist/postinstall.js || true",
-    "prepublishOnly": "npm run build:publish"
+    "prepublishOnly": "npm run build:publish && node -e \"const fs=require('fs');for (const f of ['dist/cli.js','dist/index.js']) fs.chmodSync(f,0o755)\""
   },
   "dependencies": {
     "@anthropic-ai/sdk": "^0.78.0",