feat: support latest Zod

[ryansuhartanto]

Support both Zod version 3 and 4 in non-breaking way.

Motivation and Context

Simple PR to support latest Zod version (v4.1.12) that kept the older version.
This is achieved by bumping the minor version 3 to the latest maintained version (v3.25.76).

Note

This PR does not provide support for Zod v4 schema.

Users are required to import zod/v3 (instead of zod) when using Zod version ^4.
Existing codebases that depend on Zod version ^3 are unaffected.

How Has This Been Tested?

From running npm run test, the result are the same with the current main branch.

Summary of all failing tests
 FAIL  src/integration-tests/taskResumability.test.ts (17.241 s)
  ● Transport resumability › should resume long-running notifications with lastEventId

    expect(received).toBeGreaterThan(expected)

    Expected: > 0
    Received:   0

      198 |
      199 |         // Verify we received some notifications and lastEventId was updated
    > 200 |         expect(notifications.length).toBeGreaterThan(0);
          |                                      ^
      201 |         expect(notifications.length).toBeLessThan(4);
      202 |         expect(onLastEventIdUpdate).toHaveBeenCalled();
      203 |         expect(lastEventId).toBeDefined();

      at Object.<anonymous> (src/integration-tests/taskResumability.test.ts:200:38)


Test Suites: 1 failed, 39 passed, 40 total
Tests:       1 failed, 824 passed, 825 total
Snapshots:   0 total
Time:        34.156 s
Ran all test suites.

Breaking Changes

None.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update

Checklist

• I have read the MCP Documentation
• My code follows the repository's style guidelines
• New and existing tests pass locally
• I have added appropriate error handling
• I have added or updated documentation as needed

Additional context

I just replaced from 'zod' into from 'zod/v3' in the entire codebase.
zod/v3 export does exist in Zod version ^3.25:
https://github.com/colinhacks/zod/blob/v3.25.76/packages/zod/package.json#L34

Serve as the same purpose as #1102.
Does NOT provide Zod v4 support in #555.

[ryansuhartanto]

Blocked by either:

• Support "zod/v3" from zod@4 StefanTerdell/zod-to-json-schema#179
• chore: allow zod 4 peer StefanTerdell/zod-to-json-schema#180