diff --git a/src/e2e/e2e-mcp.spec.ts b/src/e2e/e2e-mcp.spec.ts
index 8864ae00f..42123e250 100644
--- a/src/e2e/e2e-mcp.spec.ts
+++ b/src/e2e/e2e-mcp.spec.ts
@@ -5,7 +5,7 @@ import { setTimeout } from "node:timers/promises";
 import { describe, expect, it } from "vitest";
 
 import { RULESYNC_MCP_RELATIVE_FILE_PATH } from "../constants/rulesync-paths.js";
-import { readFileContent, writeFileContent } from "../utils/file.js";
+import { fileExists, readFileContent, writeFileContent } from "../utils/file.js";
 import {
   runGenerate,
   runImport,
@@ -221,7 +221,7 @@ describe("E2E: mcp (global mode)", () => {
   const { getProjectDir, getHomeDir } = useGlobalTestDirectories();
 
   it.each([
-    { target: "claudecode", outputPath: join(".claude", ".claude.json") },
+    { target: "claudecode", outputPath: ".claude.json" },
     { target: "cursor", outputPath: join(".cursor", "mcp.json") },
     { target: "geminicli", outputPath: join(".gemini", "settings.json") },
     { target: "opencode", outputPath: join(".config", "opencode", "opencode.jsonc") },
@@ -266,6 +266,78 @@ describe("E2E: mcp (global mode)", () => {
     expect(generatedContent).toContain("test-server");
   });
 
+  it("should preserve legacy ~/.claude/.claude.json when writing to recommended path (global)", async () => {
+    // Pins both behaviors end-to-end: (a) canonical ~/.claude.json receives
+    // fresh mcpServers AND preserves Claude Code's own user-config keys via
+    // RMW; (b) legacy ~/.claude/.claude.json is byte-identical after
+    // generate (matches the no-destructive-action invariant from PR #333).
+    const projectDir = getProjectDir();
+    const homeDir = getHomeDir();
+
+    // Pre-seed the canonical ~/.claude.json with Claude Code's own keys.
+    await writeFileContent(
+      join(homeDir, ".claude.json"),
+      JSON.stringify(
+        {
+          mcpServers: { "previously-managed": { command: "node" } },
+          projects: { "/home/user/proj-a": { allowedTools: ["*"] } },
+          feedbackSurveyState: { lastShownAt: 1234567890 },
+        },
+        null,
+        2,
+      ),
+    );
+
+    // Pre-seed a legacy orphan with specific content for byte-identical check.
+    const legacyPath = join(homeDir, ".claude", ".claude.json");
+    const legacyContent = JSON.stringify(
+      { mcpServers: { "stale-server": { command: "node", args: ["stale.js"] } } },
+      null,
+      2,
+    );
+    await writeFileContent(legacyPath, legacyContent);
+
+    // Source: a fresh server in .rulesync/mcp.json.
+    const mcpContent = JSON.stringify(
+      {
+        root: true,
+        mcpServers: {
+          "test-server": {
+            description: "Test MCP server",
+            type: "stdio",
+            command: "echo",
+            args: ["hello"],
+            env: {},
+          },
+        },
+      },
+      null,
+      2,
+    );
+    await writeFileContent(join(projectDir, RULESYNC_MCP_RELATIVE_FILE_PATH), mcpContent);
+
+    await runGenerate({
+      target: "claudecode",
+      features: "mcp",
+      global: true,
+      env: { HOME_DIR: homeDir },
+    });
+
+    // Canonical ~/.claude.json has fresh mcpServers from rulesync and
+    // retains Claude Code's own user-config keys via RMW spread.
+    const newContent = await readFileContent(join(homeDir, ".claude.json"));
+    expect(newContent).toContain("test-server");
+    expect(newContent).not.toContain("previously-managed");
+    expect(newContent).toContain("projects");
+    expect(newContent).toContain("/home/user/proj-a");
+    expect(newContent).toContain("feedbackSurveyState");
+    expect(newContent).toContain("1234567890");
+
+    // Legacy file is preserved byte-for-byte. rulesync never modifies it.
+    expect(await fileExists(legacyPath)).toBe(true);
+    expect(await readFileContent(legacyPath)).toBe(legacyContent);
+  });
+
   it("should ignore non-root mcp in global mode", async () => {
     const projectDir = getProjectDir();
     const homeDir = getHomeDir();
@@ -314,7 +386,7 @@ describe("E2E: mcp (global mode)", () => {
     });
 
     // Verify: root mcp content is present, non-root mcp content is absent
-    const generatedContent = await readFileContent(join(homeDir, ".claude", ".claude.json"));
+    const generatedContent = await readFileContent(join(homeDir, ".claude.json"));
     expect(generatedContent).toContain("root-server");
     expect(generatedContent).not.toContain("non-root-server");
   });
diff --git a/src/features/mcp/claudecode-mcp.test.ts b/src/features/mcp/claudecode-mcp.test.ts
index 9b6f285cd..ef4c0f5f0 100644
--- a/src/features/mcp/claudecode-mcp.test.ts
+++ b/src/features/mcp/claudecode-mcp.test.ts
@@ -6,9 +6,11 @@ import {
   RULESYNC_MCP_SCHEMA_URL,
   RULESYNC_RELATIVE_DIR_PATH,
 } from "../../constants/rulesync-paths.js";
+import { createMockLogger } from "../../test-utils/mock-logger.js";
 import { setupTestDirectory } from "../../test-utils/test-directories.js";
-import { ensureDir, writeFileContent } from "../../utils/file.js";
+import { ensureDir, fileExists, readFileContent, writeFileContent } from "../../utils/file.js";
 import { ClaudecodeMcp } from "./claudecode-mcp.js";
+import { McpProcessor } from "./mcp-processor.js";
 import { RulesyncMcp } from "./rulesync-mcp.js";
 
 describe("ClaudecodeMcp", () => {
@@ -34,9 +36,16 @@ describe("ClaudecodeMcp", () => {
     });
 
     it("should return correct paths for global mode", () => {
+      // Per Claude Code docs (https://docs.claude.com/en/docs/claude-code/mcp),
+      // user-scope MCP servers are stored in ~/.claude.json at HOME root —
+      // NOT inside ~/.claude/. The earlier (≤ v8.17.0) path of
+      // `.claude/.claude.json` is now treated as a legacy read-only
+      // fallback in `fromFile` (with a deprecation warning) and is
+      // never modified by rulesync. Mirrors the backward-compatibility
+      // pattern from PR #333 (`RulesyncMcp.fromFile`).
       const paths = ClaudecodeMcp.getSettablePaths({ global: true });
 
-      expect(paths.relativeDirPath).toBe(".claude");
+      expect(paths.relativeDirPath).toBe(".");
       expect(paths.relativeFilePath).toBe(".claude.json");
     });
   });
@@ -55,7 +64,7 @@ describe("ClaudecodeMcp", () => {
 
     it("should return false in global mode", () => {
       const claudecodeMcp = new ClaudecodeMcp({
-        relativeDirPath: ".claude",
+        relativeDirPath: ".",
         relativeFilePath: ".claude.json",
         fileContent: JSON.stringify({ mcpServers: {} }),
         global: true,
@@ -66,7 +75,7 @@ describe("ClaudecodeMcp", () => {
 
     it("should return false when created via forDeletion with global: true", () => {
       const claudecodeMcp = ClaudecodeMcp.forDeletion({
-        relativeDirPath: ".claude",
+        relativeDirPath: ".",
         relativeFilePath: ".claude.json",
         global: true,
       });
@@ -305,11 +314,7 @@ describe("ClaudecodeMcp", () => {
           },
         },
       };
-      await ensureDir(join(testDir, ".claude"));
-      await writeFileContent(
-        join(testDir, ".claude/.claude.json"),
-        JSON.stringify(jsonData, null, 2),
-      );
+      await writeFileContent(join(testDir, ".claude.json"), JSON.stringify(jsonData, null, 2));
 
       const claudecodeMcp = await ClaudecodeMcp.fromFile({
         outputRoot: testDir,
@@ -318,7 +323,7 @@ describe("ClaudecodeMcp", () => {
 
       expect(claudecodeMcp).toBeInstanceOf(ClaudecodeMcp);
       expect(claudecodeMcp.getJson()).toEqual(jsonData);
-      expect(claudecodeMcp.getFilePath()).toBe(join(testDir, ".claude/.claude.json"));
+      expect(claudecodeMcp.getFilePath()).toBe(join(testDir, ".claude.json"));
       expect(claudecodeMcp.isDeletable()).toBe(false);
     });
 
@@ -350,7 +355,7 @@ describe("ClaudecodeMcp", () => {
 
       expect(claudecodeMcp).toBeInstanceOf(ClaudecodeMcp);
       expect(claudecodeMcp.getJson()).toEqual({ mcpServers: {} });
-      expect(claudecodeMcp.getFilePath()).toBe(join(testDir, ".claude/.claude.json"));
+      expect(claudecodeMcp.getFilePath()).toBe(join(testDir, ".claude.json"));
       expect(claudecodeMcp.isDeletable()).toBe(false);
     });
 
@@ -368,9 +373,8 @@ describe("ClaudecodeMcp", () => {
         },
         version: "1.0.0",
       };
-      await ensureDir(join(testDir, ".claude"));
       await writeFileContent(
-        join(testDir, ".claude/.claude.json"),
+        join(testDir, ".claude.json"),
         JSON.stringify(existingGlobalConfig, null, 2),
       );
 
@@ -392,6 +396,183 @@ describe("ClaudecodeMcp", () => {
       });
       expect((json as any).version).toBe("1.0.0");
     });
+
+    it("should prefer recommended path when both recommended and legacy exist (global)", async () => {
+      // Mirrors the RulesyncMcp.fromFile precedent (PR #333).
+      const recommendedContent = {
+        mcpServers: { "recommended-server": { command: "node" } },
+      };
+      const legacyContent = {
+        mcpServers: { "legacy-server": { command: "node" } },
+      };
+      await writeFileContent(join(testDir, ".claude.json"), JSON.stringify(recommendedContent));
+      await ensureDir(join(testDir, ".claude"));
+      await writeFileContent(
+        join(testDir, ".claude", ".claude.json"),
+        JSON.stringify(legacyContent),
+      );
+
+      const logger = createMockLogger();
+      const claudecodeMcp = await ClaudecodeMcp.fromFile({
+        outputRoot: testDir,
+        global: true,
+        logger,
+      });
+
+      expect(claudecodeMcp.getJson()).toEqual(recommendedContent);
+      expect(claudecodeMcp.getFilePath()).toBe(join(testDir, ".claude.json"));
+      // No deprecation warning when recommended is used.
+      expect(logger.warn).not.toHaveBeenCalled();
+    });
+
+    it("should fall back to legacy path with deprecation warning when only legacy exists (global)", async () => {
+      // Also asserts byte-identity: fromFile is read-only on legacy by
+      // contract. Mirrors PR #333.
+      const legacyContent = {
+        mcpServers: { "legacy-server": { command: "node", args: ["legacy.js"] } },
+      };
+      const legacyPath = join(testDir, ".claude", ".claude.json");
+      const legacyOnDisk = JSON.stringify(legacyContent);
+      await ensureDir(join(testDir, ".claude"));
+      await writeFileContent(legacyPath, legacyOnDisk);
+
+      const logger = createMockLogger();
+      const claudecodeMcp = await ClaudecodeMcp.fromFile({
+        outputRoot: testDir,
+        global: true,
+        logger,
+      });
+
+      // Data loaded from the legacy path.
+      expect(claudecodeMcp.getJson()).toEqual(legacyContent);
+      // Instance reflects the legacy path so callers see where data came from.
+      expect(claudecodeMcp.getFilePath()).toBe(join(testDir, ".claude", ".claude.json"));
+
+      // Deprecation warning fired with both paths in the message.
+      expect(logger.warn).toHaveBeenCalledTimes(1);
+      const warnMessage = logger.warn.mock.calls[0]?.[0] as string;
+      expect(warnMessage).toContain(join(testDir, ".claude", ".claude.json"));
+      expect(warnMessage).toContain(join(testDir, ".claude.json"));
+      expect(warnMessage).toContain("deprecated");
+
+      // Read-only invariant: legacy file is byte-identical after read.
+      // Confirms fromFile never writes to the legacy path.
+      expect(await readFileContent(legacyPath)).toBe(legacyOnDisk);
+    });
+
+    it("should pass legacy fallback warnings through the processor path", async () => {
+      // Regression guard: `fromFile` warnings must surface through the
+      // real processor/CLI path, not just direct class calls.
+      const legacyContent = {
+        mcpServers: { "legacy-server": { command: "node", args: ["legacy.js"] } },
+      };
+      const legacyPath = join(testDir, ".claude", ".claude.json");
+      await ensureDir(join(testDir, ".claude"));
+      await writeFileContent(legacyPath, JSON.stringify(legacyContent));
+
+      const logger = createMockLogger();
+      const processor = new McpProcessor({
+        outputRoot: testDir,
+        toolTarget: "claudecode",
+        global: true,
+        logger,
+      });
+
+      const toolFiles = await processor.loadToolFiles();
+
+      expect(toolFiles).toHaveLength(1);
+      expect(toolFiles[0]?.getFilePath()).toBe(legacyPath);
+      expect(logger.warn).toHaveBeenCalledTimes(1);
+      const warnMessage = logger.warn.mock.calls[0]?.[0] as string;
+      expect(warnMessage).toContain(legacyPath);
+      expect(warnMessage).toContain(join(testDir, ".claude.json"));
+      expect(warnMessage).toContain("deprecated");
+    });
+
+    it("should NOT fall back to legacy path in local mode", async () => {
+      // Legacy fallback is a global-mode-only concession. Local mode
+      // reads `.mcp.json`, never `~/.claude/.claude.json`.
+      await ensureDir(join(testDir, ".claude"));
+      await writeFileContent(
+        join(testDir, ".claude", ".claude.json"),
+        JSON.stringify({ mcpServers: { "legacy-server": { command: "node" } } }),
+      );
+
+      const logger = createMockLogger();
+      const claudecodeMcp = await ClaudecodeMcp.fromFile({
+        outputRoot: testDir,
+        global: false,
+        logger,
+      });
+
+      expect(claudecodeMcp.getJson()).toEqual({ mcpServers: {} });
+      expect(logger.warn).not.toHaveBeenCalled();
+    });
+
+    it("should initialize empty mcpServers when neither file exists (global)", async () => {
+      // Fresh install: neither recommended nor legacy exists. fromFile
+      // returns an empty-mcpServers instance at the recommended path
+      // with no deprecation warning.
+      const logger = createMockLogger();
+      const claudecodeMcp = await ClaudecodeMcp.fromFile({
+        outputRoot: testDir,
+        global: true,
+        logger,
+      });
+
+      expect(claudecodeMcp.getJson()).toEqual({ mcpServers: {} });
+      expect(claudecodeMcp.getFilePath()).toBe(join(testDir, ".claude.json"));
+      expect(logger.warn).not.toHaveBeenCalled();
+    });
+
+    it("should work without a logger when reading the legacy path (global)", async () => {
+      // Pins the optional-logger contract.
+      const legacyContent = { mcpServers: { x: { command: "node" } } };
+      await ensureDir(join(testDir, ".claude"));
+      await writeFileContent(
+        join(testDir, ".claude", ".claude.json"),
+        JSON.stringify(legacyContent),
+      );
+
+      const claudecodeMcp = await ClaudecodeMcp.fromFile({
+        outputRoot: testDir,
+        global: true,
+      });
+
+      expect(claudecodeMcp.getJson()).toEqual(legacyContent);
+    });
+
+    it("should throw when only the legacy file exists and contains malformed JSON (global)", async () => {
+      // Pins the contract: corrupt legacy JSON throws on parse rather
+      // than silently falling through to an empty mcpServers.
+      await ensureDir(join(testDir, ".claude"));
+      await writeFileContent(join(testDir, ".claude", ".claude.json"), "{ broken json");
+
+      await expect(
+        ClaudecodeMcp.fromFile({
+          outputRoot: testDir,
+          global: true,
+        }),
+      ).rejects.toThrow();
+    });
+
+    it("should throw when recommended file is malformed even if legacy is valid (global)", async () => {
+      // Pins the contract: legacy fallback only triggers when the
+      // recommended file is *absent*, not when present-but-corrupt.
+      await writeFileContent(join(testDir, ".claude.json"), "{ broken json");
+      await ensureDir(join(testDir, ".claude"));
+      await writeFileContent(
+        join(testDir, ".claude", ".claude.json"),
+        JSON.stringify({ mcpServers: { x: { command: "node" } } }),
+      );
+
+      await expect(
+        ClaudecodeMcp.fromFile({
+          outputRoot: testDir,
+          global: true,
+        }),
+      ).rejects.toThrow();
+    });
   });
 
   describe("fromRulesyncMcp", () => {
@@ -535,7 +716,7 @@ describe("ClaudecodeMcp", () => {
 
       expect(claudecodeMcp).toBeInstanceOf(ClaudecodeMcp);
       expect(claudecodeMcp.getJson()).toEqual(jsonData);
-      expect(claudecodeMcp.getRelativeDirPath()).toBe(".claude");
+      expect(claudecodeMcp.getRelativeDirPath()).toBe(".");
       expect(claudecodeMcp.getRelativeFilePath()).toBe(".claude.json");
       expect(claudecodeMcp.isDeletable()).toBe(false);
     });
@@ -580,9 +761,8 @@ describe("ClaudecodeMcp", () => {
         },
         version: "1.0.0",
       };
-      await ensureDir(join(testDir, ".claude"));
       await writeFileContent(
-        join(testDir, ".claude/.claude.json"),
+        join(testDir, ".claude.json"),
         JSON.stringify(existingGlobalConfig, null, 2),
       );
 
@@ -629,9 +809,8 @@ describe("ClaudecodeMcp", () => {
         },
         customProperty: "value",
       };
-      await ensureDir(join(testDir, ".claude"));
       await writeFileContent(
-        join(testDir, ".claude/.claude.json"),
+        join(testDir, ".claude.json"),
         JSON.stringify(existingGlobalConfig, null, 2),
       );
 
@@ -673,6 +852,143 @@ describe("ClaudecodeMcp", () => {
       });
       expect((json as any).customProperty).toBe("value");
     });
+
+    it("should initialize ~/.claude.json on fresh install (no legacy, no existing config)", async () => {
+      const rulesyncMcp = new RulesyncMcp({
+        relativeDirPath: RULESYNC_RELATIVE_DIR_PATH,
+        relativeFilePath: ".mcp.json",
+        fileContent: JSON.stringify({
+          mcpServers: {
+            "fresh-server": { command: "node", args: ["fresh.js"] },
+          },
+        }),
+      });
+
+      const claudecodeMcp = await ClaudecodeMcp.fromRulesyncMcp({
+        outputRoot: testDir,
+        rulesyncMcp,
+        global: true,
+      });
+
+      // Canonical file is the new path, populated with rulesync source.
+      expect(claudecodeMcp.getFilePath()).toBe(join(testDir, ".claude.json"));
+      expect(claudecodeMcp.getJson()).toEqual({
+        mcpServers: {
+          "fresh-server": { command: "node", args: ["fresh.js"] },
+        },
+      });
+      // Legacy path stays absent.
+      expect(await fileExists(join(testDir, ".claude", ".claude.json"))).toBe(false);
+    });
+
+    it("should NOT modify the legacy file when writing to recommended path (global)", async () => {
+      // Pins the no-destructive-action invariant (precedent PR #333).
+      await ensureDir(join(testDir, ".claude"));
+      const legacyContent = JSON.stringify(
+        {
+          mcpServers: { "stale-server": { command: "node", args: ["stale.js"] } },
+          userAddedAtLegacyPath: { important: true },
+        },
+        null,
+        2,
+      );
+      const legacyPath = join(testDir, ".claude", ".claude.json");
+      await writeFileContent(legacyPath, legacyContent);
+
+      const rulesyncMcp = new RulesyncMcp({
+        relativeDirPath: RULESYNC_RELATIVE_DIR_PATH,
+        relativeFilePath: ".mcp.json",
+        fileContent: JSON.stringify({
+          mcpServers: { "new-server": { command: "node", args: ["new.js"] } },
+        }),
+      });
+
+      const claudecodeMcp = await ClaudecodeMcp.fromRulesyncMcp({
+        outputRoot: testDir,
+        rulesyncMcp,
+        global: true,
+      });
+
+      // Recommended path has fresh mcpServers from rulesync source.
+      expect(claudecodeMcp.getFilePath()).toBe(join(testDir, ".claude.json"));
+      expect(claudecodeMcp.getJson()).toEqual({
+        mcpServers: { "new-server": { command: "node", args: ["new.js"] } },
+      });
+      // Legacy file unchanged — byte-for-byte.
+      const after = await readFileContent(legacyPath);
+      expect(after).toBe(legacyContent);
+    });
+
+    it("should not touch ~/.claude/.claude.json in local mode (content preserved verbatim)", async () => {
+      // Legacy file unchanged byte-for-byte in local mode.
+      await ensureDir(join(testDir, ".claude"));
+      const legacyContent = JSON.stringify({
+        mcpServers: { other: { command: "node" } },
+      });
+      const legacyPath = join(testDir, ".claude", ".claude.json");
+      await writeFileContent(legacyPath, legacyContent);
+
+      const rulesyncMcp = new RulesyncMcp({
+        relativeDirPath: RULESYNC_RELATIVE_DIR_PATH,
+        relativeFilePath: ".mcp.json",
+        fileContent: JSON.stringify({
+          mcpServers: { local: { command: "node" } },
+        }),
+      });
+
+      await ClaudecodeMcp.fromRulesyncMcp({
+        outputRoot: testDir,
+        rulesyncMcp,
+        global: false,
+      });
+
+      // Legacy file content unchanged by local-mode generate.
+      const after = await readFileContent(legacyPath);
+      expect(after).toBe(legacyContent);
+    });
+
+    it("should preserve unrelated keys on ~/.claude.json (global mode)", async () => {
+      // RMW must preserve Claude Code's own keys (`projects`, `hooks`,
+      // `feedbackSurveyState`, etc.) while replacing only `mcpServers`.
+      const existingClaudeJson = {
+        mcpServers: {
+          "old-managed": { command: "node", args: ["old.js"] },
+        },
+        projects: { "/home/user/proj-a": { allowedTools: ["*"] } },
+        hooks: { PreToolUse: [] },
+        feedbackSurveyState: { lastShownAt: 1234567890 },
+      };
+      await writeFileContent(
+        join(testDir, ".claude.json"),
+        JSON.stringify(existingClaudeJson, null, 2),
+      );
+
+      const rulesyncMcp = new RulesyncMcp({
+        relativeDirPath: RULESYNC_RELATIVE_DIR_PATH,
+        relativeFilePath: ".mcp.json",
+        fileContent: JSON.stringify({
+          mcpServers: { "fresh-server": { command: "python" } },
+        }),
+      });
+
+      const claudecodeMcp = await ClaudecodeMcp.fromRulesyncMcp({
+        outputRoot: testDir,
+        rulesyncMcp,
+        global: true,
+      });
+
+      const json = claudecodeMcp.getJson();
+      // mcpServers replaced with rulesync source.
+      expect(json.mcpServers).toEqual({
+        "fresh-server": { command: "python" },
+      });
+      // Non-mcp keys preserved verbatim.
+      expect((json as any).projects).toEqual({
+        "/home/user/proj-a": { allowedTools: ["*"] },
+      });
+      expect((json as any).hooks).toEqual({ PreToolUse: [] });
+      expect((json as any).feedbackSurveyState).toEqual({ lastShownAt: 1234567890 });
+    });
   });
 
   describe("toRulesyncMcp", () => {
@@ -964,9 +1280,8 @@ describe("ClaudecodeMcp", () => {
           },
         },
       };
-      await ensureDir(join(testDir, ".claude"));
       await writeFileContent(
-        join(testDir, ".claude/.claude.json"),
+        join(testDir, ".claude.json"),
         JSON.stringify(originalJsonData, null, 2),
       );
 
@@ -988,7 +1303,7 @@ describe("ClaudecodeMcp", () => {
 
       // Verify data integrity
       expect(newClaudecodeMcp.getJson()).toEqual(originalJsonData);
-      expect(newClaudecodeMcp.getFilePath()).toBe(join(testDir, ".claude/.claude.json"));
+      expect(newClaudecodeMcp.getFilePath()).toBe(join(testDir, ".claude.json"));
     });
   });
 
@@ -1004,8 +1319,7 @@ describe("ClaudecodeMcp", () => {
     });
 
     it("should handle malformed JSON in global config gracefully", async () => {
-      await ensureDir(join(testDir, ".claude"));
-      await writeFileContent(join(testDir, ".claude/.claude.json"), "{ invalid: json }");
+      await writeFileContent(join(testDir, ".claude.json"), "{ invalid: json }");
 
       await expect(
         ClaudecodeMcp.fromFile({
diff --git a/src/features/mcp/claudecode-mcp.ts b/src/features/mcp/claudecode-mcp.ts
index c9cc8209b..a166ff4ee 100644
--- a/src/features/mcp/claudecode-mcp.ts
+++ b/src/features/mcp/claudecode-mcp.ts
@@ -1,7 +1,7 @@
 import { join } from "node:path";
 
 import { ValidationResult } from "../../types/ai-file.js";
-import { readFileContentOrNull, readOrInitializeFileContent } from "../../utils/file.js";
+import { fileExists, readFileContent, readOrInitializeFileContent } from "../../utils/file.js";
 import { RulesyncMcp } from "./rulesync-mcp.js";
 import {
   ToolMcp,
@@ -25,18 +25,28 @@ export class ClaudecodeMcp extends ToolMcp {
   }
 
   /**
-   * In global mode, ~/.claude/.claude.json should not be deleted
-   * as it may contain other user settings.
+   * In global mode, ~/.claude.json should not be deleted as it is the
+   * user's primary Claude Code config and contains many other settings
+   * managed by Claude Code itself (feature flags, project trust list,
+   * hooks, user settings, model selection, etc.).
    * In local mode, .mcp.json can be safely deleted.
    */
   override isDeletable(): boolean {
     return !this.global;
   }
 
+  /**
+   * Legacy global path used by rulesync ≤ v8.17.0. The documented store
+   * is `~/.claude.json`; `fromFile` falls back here with a deprecation
+   * warning (mirrors PR #333). Never modified or removed by rulesync.
+   */
+  private static readonly LEGACY_GLOBAL_DIR = ".claude";
+  private static readonly LEGACY_GLOBAL_FILE = ".claude.json";
+
   static getSettablePaths({ global }: { global?: boolean } = {}): ToolMcpSettablePaths {
     if (global) {
       return {
-        relativeDirPath: ".claude",
+        relativeDirPath: ".",
         relativeFilePath: ".claude.json",
       };
     }
@@ -50,20 +60,61 @@ export class ClaudecodeMcp extends ToolMcp {
     outputRoot = process.cwd(),
     validate = true,
     global = false,
+    logger,
   }: ToolMcpFromFileParams): Promise<ClaudecodeMcp> {
     const paths = this.getSettablePaths({ global });
-    const fileContent =
-      (await readFileContentOrNull(
-        join(outputRoot, paths.relativeDirPath, paths.relativeFilePath),
-      )) ?? '{"mcpServers":{}}';
-    const json = JSON.parse(fileContent);
-    const newJson = { ...json, mcpServers: json.mcpServers ?? {} };
+    const recommendedPath = join(outputRoot, paths.relativeDirPath, paths.relativeFilePath);
+
+    // Try the recommended path first.
+    if (await fileExists(recommendedPath)) {
+      const fileContent = await readFileContent(recommendedPath);
+      const json = JSON.parse(fileContent);
+      const newJson = { ...json, mcpServers: json.mcpServers ?? {} };
+      return new ClaudecodeMcp({
+        outputRoot,
+        relativeDirPath: paths.relativeDirPath,
+        relativeFilePath: paths.relativeFilePath,
+        fileContent: JSON.stringify(newJson, null, 2),
+        validate,
+        global,
+      });
+    }
 
+    // Backward compatibility: fall back to the legacy path with a
+    // deprecation warning. Mirrors `RulesyncMcp.fromFile` (PR #333).
+    if (global) {
+      const legacyPath = join(
+        outputRoot,
+        ClaudecodeMcp.LEGACY_GLOBAL_DIR,
+        ClaudecodeMcp.LEGACY_GLOBAL_FILE,
+      );
+      if (await fileExists(legacyPath)) {
+        logger?.warn(
+          `Warning: using deprecated path "${legacyPath}". Please migrate to "${recommendedPath}"`,
+        );
+        const fileContent = await readFileContent(legacyPath);
+        const json = JSON.parse(fileContent);
+        const newJson = { ...json, mcpServers: json.mcpServers ?? {} };
+        // Reflect the legacy path so callers see where data came from;
+        // `fromRulesyncMcp` always writes to the recommended path.
+        return new ClaudecodeMcp({
+          outputRoot,
+          relativeDirPath: ClaudecodeMcp.LEGACY_GLOBAL_DIR,
+          relativeFilePath: ClaudecodeMcp.LEGACY_GLOBAL_FILE,
+          fileContent: JSON.stringify(newJson, null, 2),
+          validate,
+          global,
+        });
+      }
+    }
+
+    // Neither recommended nor legacy exists: initialize empty mcpServers
+    // at the recommended path (existing fromFile contract).
     return new ClaudecodeMcp({
       outputRoot,
       relativeDirPath: paths.relativeDirPath,
       relativeFilePath: paths.relativeFilePath,
-      fileContent: JSON.stringify(newJson, null, 2),
+      fileContent: JSON.stringify({ mcpServers: {} }, null, 2),
       validate,
       global,
     });
@@ -85,6 +136,9 @@ export class ClaudecodeMcp extends ToolMcp {
 
     const mcpJson = { ...json, mcpServers: rulesyncMcp.getMcpServers() };
 
+    // The legacy path `~/.claude/.claude.json` is intentionally not touched
+    // here — see the LEGACY_GLOBAL_* docstring above for the rationale.
+
     return new ClaudecodeMcp({
       outputRoot,
       relativeDirPath: paths.relativeDirPath,
@@ -97,7 +151,7 @@ export class ClaudecodeMcp extends ToolMcp {
 
   toRulesyncMcp(): RulesyncMcp {
     return this.toRulesyncMcpDefault({
-      fileContent: JSON.stringify({ mcpServers: this.json.mcpServers }, null, 2),
+      fileContent: JSON.stringify({ mcpServers: this.json.mcpServers ?? {} }, null, 2),
     });
   }
 
diff --git a/src/features/mcp/mcp-processor.test.ts b/src/features/mcp/mcp-processor.test.ts
index e5c3fd621..4cafe033c 100644
--- a/src/features/mcp/mcp-processor.test.ts
+++ b/src/features/mcp/mcp-processor.test.ts
@@ -221,6 +221,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: false,
+          logger: expect.any(Object),
         });
       });
 
@@ -248,6 +249,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: false,
+          logger: expect.any(Object),
         });
       });
 
@@ -276,6 +278,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: true,
+          logger: expect.any(Object),
         });
       });
     });
@@ -305,6 +308,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: false,
+          logger: expect.any(Object),
         });
       });
     });
@@ -334,6 +338,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: false,
+          logger: expect.any(Object),
         });
       });
     });
@@ -363,6 +368,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: false,
+          logger: expect.any(Object),
         });
       });
 
@@ -391,6 +397,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: true,
+          logger: expect.any(Object),
         });
       });
     });
@@ -420,6 +427,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: false,
+          logger: expect.any(Object),
         });
       });
     });
@@ -449,6 +457,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: false,
+          logger: expect.any(Object),
         });
       });
 
@@ -477,6 +486,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: true,
+          logger: expect.any(Object),
         });
       });
     });
@@ -505,6 +515,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: true,
+          logger: expect.any(Object),
         });
       });
 
@@ -551,6 +562,7 @@ describe("McpProcessor", () => {
           outputRoot: testDir,
           validate: true,
           global: false,
+          logger: expect.any(Object),
         });
       });
     });
diff --git a/src/features/mcp/mcp-processor.ts b/src/features/mcp/mcp-processor.ts
index aec200c78..1ed920ae6 100644
--- a/src/features/mcp/mcp-processor.ts
+++ b/src/features/mcp/mcp-processor.ts
@@ -390,6 +390,7 @@ export class McpProcessor extends FeatureProcessor {
           outputRoot: this.outputRoot,
           validate: true,
           global: this.global,
+          logger: this.logger,
         }),
       ];
       this.logger.debug(`Successfully loaded ${toolMcps.length} ${this.toolTarget} MCP files`);
diff --git a/src/features/mcp/tool-mcp.ts b/src/features/mcp/tool-mcp.ts
index 76a6a9117..5467b5411 100644
--- a/src/features/mcp/tool-mcp.ts
+++ b/src/features/mcp/tool-mcp.ts
@@ -5,6 +5,7 @@ import {
 } from "../../constants/rulesync-paths.js";
 import { AiFileFromFileParams, AiFileParams } from "../../types/ai-file.js";
 import { ToolFile } from "../../types/tool-file.js";
+import type { Logger } from "../../utils/logger.js";
 import { RulesyncMcp } from "./rulesync-mcp.js";
 
 export type ToolMcpParams = AiFileParams;
@@ -19,7 +20,9 @@ export type ToolMcpFromRulesyncMcpParams = Omit<
 export type ToolMcpFromFileParams = Pick<
   AiFileFromFileParams,
   "outputRoot" | "validate" | "global"
->;
+> & {
+  logger?: Logger;
+};
 
 export type ToolMcpForDeletionParams = {
   outputRoot?: string;
@@ -37,7 +40,7 @@ export abstract class ToolMcp extends ToolFile {
   constructor({ ...rest }: ToolMcpParams) {
     super({
       ...rest,
-      validate: true, // Skip validation during construction
+      validate: true, // ToolMcp runs subclass validation below when requested
     });
 
     // Validate after setting patterns, if validation was requested