chore(deps): Upgrade to Zod v4

package.json

@@ -102,7 +102,7 @@
     "tinypool": "^2.0.0",
     "tree-sitter-wasms": "^0.1.13",
     "web-tree-sitter": "^0.25.10",
-    "zod": "^3.25.76"
+    "zod": "^4.1.12"
   },
   "devDependencies": {
     "@biomejs/biome": "^2.2.6",

src/config/configLoad.ts

@@ -157,26 +157,33 @@ export const mergeConfigs = (
 
   const baseConfig = defaultConfig;
 
-  // If the output file path is not provided in the config file or CLI, use the default file path for the style
-  if (cliConfig.output?.filePath == null && fileConfig.output?.filePath == null) {
-    const style = cliConfig.output?.style || fileConfig.output?.style || baseConfig.output.style;
-    baseConfig.output.filePath = defaultFilePathMap[style];
-
-    logger.trace('Default output file path is set to:', baseConfig.output.filePath);
-  }
-
   const mergedConfig = {
     cwd,
     input: {
       ...baseConfig.input,
       ...fileConfig.input,
       ...cliConfig.input,
     },
-    output: {
-      ...baseConfig.output,
-      ...fileConfig.output,
-      ...cliConfig.output,
-    },
+    output: (() => {
+      const mergedOutput = {
+        ...baseConfig.output,
+        ...fileConfig.output,
+        ...cliConfig.output,
+        git: {
+          ...baseConfig.output.git,
+          ...fileConfig.output?.git,
+          ...cliConfig.output?.git,
+        },
+      };
+
+      if (mergedOutput.filePath == null) {
+        const style = mergedOutput.style ?? baseConfig.output.style;
+        mergedOutput.filePath = defaultFilePathMap[style];
+        logger.trace('Default output file path is set to:', mergedOutput.filePath);
+      }
+
+      return mergedOutput;
+    })(),
     include: [...(baseConfig.include || []), ...(fileConfig.include || []), ...(cliConfig.include || [])],
     ignore: {
       ...baseConfig.ignore,
@@ -193,6 +200,11 @@ export const mergeConfigs = (
       ...fileConfig.security,
       ...cliConfig.security,
     },
+    tokenCount: {
+      ...baseConfig.tokenCount,
+      ...fileConfig.tokenCount,
+      ...cliConfig.tokenCount,
+    },
   };
 
   try {

src/config/configSchema.ts

@@ -74,67 +74,55 @@ export const repomixConfigBaseSchema = z.object({
 
 // Default config schema with default values
 export const repomixConfigDefaultSchema = z.object({
-  input: z
-    .object({
-      maxFileSize: z
-        .number()
-        .int()
-        .min(1)
-        .default(50 * 1024 * 1024), // Default: 50MB
-    })
-    .default({}),
-  output: z
-    .object({
-      filePath: z.string().default(defaultFilePathMap.xml),
-      style: repomixOutputStyleSchema.default('xml'),
-      parsableStyle: z.boolean().default(false),
-      headerText: z.string().optional(),
-      instructionFilePath: z.string().optional(),
-      fileSummary: z.boolean().default(true),
-      directoryStructure: z.boolean().default(true),
-      files: z.boolean().default(true),
-      removeComments: z.boolean().default(false),
-      removeEmptyLines: z.boolean().default(false),
-      compress: z.boolean().default(false),
-      topFilesLength: z.number().int().min(0).default(5),
-      showLineNumbers: z.boolean().default(false),
-      truncateBase64: z.boolean().default(false),
-      copyToClipboard: z.boolean().default(false),
-      includeEmptyDirectories: z.boolean().optional(),
-      includeFullDirectoryStructure: z.boolean().default(false),
-      tokenCountTree: z.union([z.boolean(), z.number(), z.string()]).default(false),
-      git: z
-        .object({
-          sortByChanges: z.boolean().default(true),
-          sortByChangesMaxCommits: z.number().int().min(1).default(100),
-          includeDiffs: z.boolean().default(false),
-          includeLogs: z.boolean().default(false),
-          includeLogsCount: z.number().int().min(1).default(50),
-        })
-        .default({}),
-    })
-    .default({}),
+  input: z.object({
+    maxFileSize: z
+      .number()
+      .int()
+      .min(1)
+      .default(50 * 1024 * 1024), // Default: 50MB
+  }),
+  output: z.object({
+    filePath: z.string().default(defaultFilePathMap.xml),
+    style: repomixOutputStyleSchema.default('xml'),
+    parsableStyle: z.boolean().default(false),
+    headerText: z.string().optional(),
+    instructionFilePath: z.string().optional(),
+    fileSummary: z.boolean().default(true),
+    directoryStructure: z.boolean().default(true),
+    files: z.boolean().default(true),
+    removeComments: z.boolean().default(false),
+    removeEmptyLines: z.boolean().default(false),
+    compress: z.boolean().default(false),
+    topFilesLength: z.number().int().min(0).default(5),
+    showLineNumbers: z.boolean().default(false),
+    truncateBase64: z.boolean().default(false),
+    copyToClipboard: z.boolean().default(false),
+    includeEmptyDirectories: z.boolean().optional(),
+    includeFullDirectoryStructure: z.boolean().default(false),
+    tokenCountTree: z.union([z.boolean(), z.number(), z.string()]).default(false),
+    git: z.object({
+      sortByChanges: z.boolean().default(true),
+      sortByChangesMaxCommits: z.number().int().min(1).default(100),
+      includeDiffs: z.boolean().default(false),
+      includeLogs: z.boolean().default(false),
+      includeLogsCount: z.number().int().min(1).default(50),
+    }),
+  }),
   include: z.array(z.string()).default([]),
-  ignore: z
-    .object({
-      useGitignore: z.boolean().default(true),
-      useDefaultPatterns: z.boolean().default(true),
-      customPatterns: z.array(z.string()).default([]),
-    })
-    .default({}),
-  security: z
-    .object({
-      enableSecurityCheck: z.boolean().default(true),
-    })
-    .default({}),
-  tokenCount: z
-    .object({
-      encoding: z
-        .string()
-        .default('o200k_base')
-        .transform((val) => val as TiktokenEncoding),
-    })
-    .default({}),
+  ignore: z.object({
+    useGitignore: z.boolean().default(true),
+    useDefaultPatterns: z.boolean().default(true),
+    customPatterns: z.array(z.string()).default([]),
+  }),
+  security: z.object({
+    enableSecurityCheck: z.boolean().default(true),
+  }),
+  tokenCount: z.object({
+    encoding: z
+      .string()
+      .default('o200k_base')
+      .transform((val) => val as TiktokenEncoding),
+  }),
 });
 
 // File-specific schema. Add options for file path and style
@@ -166,7 +154,17 @@ export type RepomixConfigFile = z.infer<typeof repomixConfigFileSchema>;
 export type RepomixConfigCli = z.infer<typeof repomixConfigCliSchema>;
 export type RepomixConfigMerged = z.infer<typeof repomixConfigMergedSchema>;
 
-export const defaultConfig = repomixConfigDefaultSchema.parse({});
+// Pass empty objects to let Zod apply all default values
+// Zod v4 requires explicit nested objects since we removed outer .default({})
+export const defaultConfig = repomixConfigDefaultSchema.parse({
+  input: {},
+  output: {
+    git: {},
+  },
+  ignore: {},
+  security: {},
+  tokenCount: {},
+});
 
 // Helper function for type-safe config definition
 export const defineConfig = (config: RepomixConfigFile): RepomixConfigFile => config;

src/mcp/prompts/packRemoteRepositoryPrompts.ts

@@ -1,5 +1,9 @@
+// @ts-nocheck - Zod v3 compatibility for MCP SDK (imported by mcpAction.ts)
+// Note: @ts-expect-error would be preferable, but the type incompatibility extends
+// beyond .shape to the entire handler function signature, causing 9+ type errors per file.
+// This will be resolved when MCP SDK supports Zod v4.
 import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
-import { z } from 'zod';
+import { z } from 'zod/v3';
 
 /**
  * Register Repomix-related prompts to the MCP server

src/mcp/tools/attachPackedOutputTool.ts

@@ -1,8 +1,12 @@
+// @ts-nocheck - Zod v3 compatibility for MCP SDK (imported by mcpAction.ts)
+// Note: @ts-expect-error would be preferable, but the type incompatibility extends
+// beyond .shape to the entire handler function signature, causing 9+ type errors per file.
+// This will be resolved when MCP SDK supports Zod v4.
 import fs from 'node:fs/promises';
 import path from 'node:path';
 import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
 import type { CallToolResult } from '@modelcontextprotocol/sdk/types.js';
-import { z } from 'zod';
+import { z } from 'zod/v3';
 import { defaultFilePathMap } from '../../config/configSchema.js';
 import type { ProcessedFile } from '../../core/file/fileTypes.js';
 import {
@@ -255,8 +259,10 @@ This tool accepts either a directory containing a repomix output file or a direc
 Supports multiple formats: XML (structured with <file> tags), Markdown (human-readable with ## headers and code blocks), JSON (machine-readable with files as key-value pairs), and Plain text (simple format with separators).
 Calling the tool again with the same file path will refresh the content if the file has been updated.
 It will return in that case a new output ID and the updated content.`,
-      inputSchema: attachPackedOutputInputSchema.shape,
-      outputSchema: attachPackedOutputOutputSchema.shape,
+      // biome-ignore lint/suspicious/noExplicitAny: Zod v3 compatibility for MCP SDK
+      inputSchema: attachPackedOutputInputSchema.shape as any,
+      // biome-ignore lint/suspicious/noExplicitAny: Zod v3 compatibility for MCP SDK
+      outputSchema: attachPackedOutputOutputSchema.shape as any,
       annotations: {
         readOnlyHint: true,
         destructiveHint: false,

src/mcp/tools/fileSystemReadDirectoryTool.ts

@@ -1,8 +1,12 @@
+// @ts-nocheck - Zod v3 compatibility for MCP SDK (imported by mcpAction.ts)
+// Note: @ts-expect-error would be preferable, but the type incompatibility extends
+// beyond .shape to the entire handler function signature, causing 9+ type errors per file.
+// This will be resolved when MCP SDK supports Zod v4.
 import fs from 'node:fs/promises';
 import path from 'node:path';
 import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
 import type { CallToolResult } from '@modelcontextprotocol/sdk/types.js';
-import { z } from 'zod';
+import { z } from 'zod/v3';
 import { logger } from '../../shared/logger.js';
 import { buildMcpToolErrorResponse, buildMcpToolSuccessResponse } from './mcpToolRuntime.js';
 
@@ -28,8 +32,10 @@ export const registerFileSystemReadDirectoryTool = (mcpServer: McpServer) => {
       title: 'Read Directory',
       description:
         'List the contents of a directory using an absolute path. Returns a formatted list showing files and subdirectories with clear [FILE]/[DIR] indicators. Useful for exploring project structure and understanding codebase organization.',
-      inputSchema: fileSystemReadDirectoryInputSchema.shape,
-      outputSchema: fileSystemReadDirectoryOutputSchema.shape,
+      // biome-ignore lint/suspicious/noExplicitAny: Zod v3 compatibility for MCP SDK
+      inputSchema: fileSystemReadDirectoryInputSchema.shape as any,
+      // biome-ignore lint/suspicious/noExplicitAny: Zod v3 compatibility for MCP SDK
+      outputSchema: fileSystemReadDirectoryOutputSchema.shape as any,
       annotations: {
         readOnlyHint: true,
         destructiveHint: false,