fix: improve JSON schema generation and publishing

- Refactor JSON schema generation to use zod-to-json-schema
- Publish manifest schema to schemas/ directory
- Update package.json exports for schema files
- Add WIP version 0.3 support
- Clean up schema generation scripts

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

yarn.lock

@@ -42,6 +42,7 @@ __metadata:
     ts-jest: "npm:^29.3.2"
     typescript: "npm:^5.6.3"
     zod: "npm:^3.25.67"
+    zod-to-json-schema: "npm:^3.24.6"
   bin:
     mcpb: dist/cli/cli.js
   languageName: unknown
@@ -6387,6 +6388,15 @@ __metadata:
   languageName: node
   linkType: hard
 
+"zod-to-json-schema@npm:^3.24.6":
+  version: 3.24.6
+  resolution: "zod-to-json-schema@npm:3.24.6"
+  peerDependencies:
+    zod: ^3.24.1
+  checksum: 10c0/b907ab6d057100bd25a37e5545bf5f0efa5902cd84d3c3ec05c2e51541431a47bd9bf1e5e151a244273409b45f5986d55b26e5d207f98abc5200702f733eb368
+  languageName: node
+  linkType: hard
+
 "zod@npm:^3.25.67":
   version: 3.25.67
   resolution: "zod@npm:3.25.67"