@pharaoh-so/mcp 0.3.9 → 0.3.10

package/dist/helpers.js

@@ -42,7 +42,7 @@ export function parseArgs(argv = process.argv.slice(2)) {
     return { server, logout };
 }
 export function printUsage() {
-    printLines("Usage: pharaoh-mcp [options]", "", "Options:", "  --server <url>    Pharaoh server URL (default: https://mcp.pharaoh.so)", "  --logout          Clear stored credentials and exit", "  --install-skills  Force reinstall Pharaoh skills (Claude Code + OpenClaw)", "  --help, -h        Show this help", "", "Get started:", `  ${NPX_COMMAND}`, "");
+    printLines("Usage: pharaoh-mcp [options]", "", "Options:", "  --server <url>    Pharaoh server URL (default: https://mcp.pharaoh.so)", "  --logout          Clear credentials and MCP config, then exit", "  --clean           Remove all Pharaoh MCP entries from Claude Code config", "  --install-skills  Force reinstall Pharaoh skills (Claude Code + OpenClaw)", "  --help, -h        Show this help", "", "Get started:", `  ${NPX_COMMAND}`, "");
 }
 /**
  * Validate that a server-supplied SSE URL shares the same origin as the configured server.

package/dist/index.js

@@ -41,10 +41,20 @@ async function main() {
         runInstallSkills();
         return;
     }
+    // Clean mode — remove all pharaoh traces from Claude Code config (MCP entries,
+    // disabled states, project-scoped configs). Useful for resetting broken installs.
+    if (args.includes("--clean")) {
+        const { cleanSlate } = await import("./setup.js");
+        cleanSlate();
+        printLines("Pharaoh: cleaned all MCP entries from Claude Code config");
+        process.exit(0);
+    }
     const { server, logout } = parseArgs(args);
     if (logout) {
+        const { cleanSlate } = await import("./setup.js");
+        cleanSlate();
         deleteCredentials();
-        printLines("Pharaoh: credentials cleared");
+        printLines("Pharaoh: credentials and MCP config cleared");
         process.exit(0);
     }
     const creds = readCredentials();

package/dist/setup.d.ts

@@ -1,5 +1,16 @@
 /**
- * Full automated setup: remove stale entries, register MCP server globally,
+ * Remove all traces of pharaoh from Claude Code's internal config (~/.claude.json).
+ *
+ * The `claude mcp remove` CLI only removes the server definition from one scope
+ * at a time and does NOT clear:
+ * - `disabledMcpServers` arrays (set when user disables via UI)
+ * - Project-scoped `mcpServers.pharaoh` entries in other workspaces
+ *
+ * This function handles what the CLI cannot — a true clean slate.
+ */
+export declare function cleanSlate(home?: string): void;
+/**
+ * Full automated setup: clean slate removal, register MCP server globally,
  * install skills. Requires valid credentials (caller handles auth first).
  *
  * @returns true if setup succeeded, false if Claude CLI not found.

package/dist/setup.js

@@ -6,6 +6,9 @@
  * One command does everything: `npx @pharaoh-so/mcp`
  */
 import { execFileSync } from "node:child_process";
+import { existsSync, readFileSync, writeFileSync } from "node:fs";
+import { homedir } from "node:os";
+import { join } from "node:path";
 import { NPX_COMMAND, printLines } from "./helpers.js";
 /** Check if `claude` CLI is available in PATH. */
 function hasClaude() {
@@ -41,7 +44,64 @@ function runClaude(args) {
     }
 }
 /**
- * Full automated setup: remove stale entries, register MCP server globally,
+ * Remove all traces of pharaoh from Claude Code's internal config (~/.claude.json).
+ *
+ * The `claude mcp remove` CLI only removes the server definition from one scope
+ * at a time and does NOT clear:
+ * - `disabledMcpServers` arrays (set when user disables via UI)
+ * - Project-scoped `mcpServers.pharaoh` entries in other workspaces
+ *
+ * This function handles what the CLI cannot — a true clean slate.
+ */
+export function cleanSlate(home = homedir()) {
+    const claudeJsonPath = join(home, ".claude.json");
+    if (!existsSync(claudeJsonPath))
+        return;
+    let raw;
+    let data;
+    try {
+        raw = readFileSync(claudeJsonPath, "utf-8");
+        data = JSON.parse(raw);
+    }
+    catch {
+        // Corrupt or unreadable — don't risk making it worse
+        return;
+    }
+    let changed = false;
+    // Remove global User MCP server definition
+    if (data.mcpServers?.pharaoh) {
+        delete data.mcpServers.pharaoh;
+        changed = true;
+    }
+    // Walk all project/workspace entries
+    if (data.projects) {
+        for (const proj of Object.values(data.projects)) {
+            // Remove project-scoped pharaoh server definitions
+            if (proj.mcpServers?.pharaoh) {
+                delete proj.mcpServers.pharaoh;
+                changed = true;
+            }
+            // Remove pharaoh from disabled lists (UI "disable" state).
+            // filter() handles duplicates — indexOf+splice would leave extras.
+            if (Array.isArray(proj.disabledMcpServers)) {
+                const before = proj.disabledMcpServers.length;
+                proj.disabledMcpServers = proj.disabledMcpServers.filter((s) => s !== "pharaoh");
+                if (proj.disabledMcpServers.length !== before)
+                    changed = true;
+            }
+        }
+    }
+    if (changed) {
+        try {
+            writeFileSync(claudeJsonPath, JSON.stringify(data, null, "  "));
+        }
+        catch {
+            // Read-only file or permissions issue — fall through to CLI removal
+        }
+    }
+}
+/**
+ * Full automated setup: clean slate removal, register MCP server globally,
  * install skills. Requires valid credentials (caller handles auth first).
  *
  * @returns true if setup succeeded, false if Claude CLI not found.
@@ -54,9 +114,13 @@ export function runSetup(options) {
     }
     if (!silent)
         printLines("Pharaoh: setting up...");
-    // Step 1: Remove any stale entry (ignore failures — may not exist)
-    runClaude(["mcp", "remove", "pharaoh"]);
-    // Step 2: Register as global stdio MCP server
+    // Step 1: Clean slate — remove pharaoh from all scopes, disabled lists,
+    // and project-scoped configs. Direct file edit handles what CLI cannot.
+    cleanSlate();
+    // Step 2: Belt-and-suspenders — also remove via CLI (both scopes)
+    runClaude(["mcp", "remove", "pharaoh", "-s", "user"]);
+    runClaude(["mcp", "remove", "pharaoh", "-s", "project"]);
+    // Step 3: Register as global stdio MCP server
     const added = runClaude([
         "mcp",
         "add",

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@pharaoh-so/mcp",
   "mcpName": "so.pharaoh/pharaoh",
-  "version": "0.3.9",
+  "version": "0.3.10",
   "description": "MCP proxy for Pharaoh — maps codebases into queryable knowledge graphs for AI agents. Enables Claude Code in headless environments (VPS, SSH, CI) via device flow auth.",
   "type": "module",
   "main": "dist/index.js",