chore: update package overrides and dependencies in package.json and pnpm-lock.yaml

- Added new overrides for hono, minimatch, tar, and ajv to ensure compatibility with specific versions.
- Updated hono to version 4.12.1 and minimatch to version 10.2.2 in pnpm-lock.yaml.
- Removed deprecated dependencies and ensured all packages align with the latest version requirements.

Author: PatrickSys

package.json

@@ -160,7 +160,11 @@
       "sharp"
     ],
     "overrides": {
-      "@modelcontextprotocol/sdk>ajv": "8.18.0"
+      "@modelcontextprotocol/sdk>ajv": "8.18.0",
+      "hono@<4.11.10": ">=4.11.10",
+      "minimatch@<10.2.1": ">=10.2.1",
+      "tar@<7.5.8": ">=7.5.8",
+      "ajv@<6.14.0": ">=6.14.0"
     }
   }
 }