refactor: replace JSON Schema + AJV with Zod-first architecture

Zod schemas are now the single source of truth for input/output
validation, MCP tool definitions, REST route schemas, and OpenAPI
spec derivation. All artefacts are built at runtime from Zod schemas
using z.toJSONSchema() and safeParse(), eliminating the need for
a pre-build code generation step.

Changes:
- Add zod@4.3.6 as dependency
- Add src/schemas/ with Zod schemas, validators, MCP tools,
  API routes, and OpenAPI spec builder
- Remove src/generated/ and src/generated-stubs/ (all generated code)
- Remove scripts/generate-schemas.js and its test
- Remove ajv and ts-json-schema-generator dependencies
- Remove generate:schemas from build pipeline and CI workflows
- Update mcp-server.ts and api-server.ts imports to src/schemas/
- Update test imports from generated/ to schemas/
- Update tsconfig: module/moduleResolution to NodeNext/nodenext,
  add types: ["node"], fix missing comma
- Update CI workflows: remove generate:schemas steps
- Pin vitest@3.2.3 (update broke mock compatibility)

Author: Mearman

.github/workflows/cross-platform-tests.yml

@@ -154,9 +154,6 @@ jobs:
           ls -la test-data/cross-platform/
         shell: bash
 
-      - name: Generate schemas (required for TypeScript compilation)
-        run: pnpm run generate:schemas
-        
       - name: Build project
         run: pnpm run build
 

.github/workflows/main.yml

@@ -130,13 +130,6 @@ jobs:
             git push
           fi
         
-      # Generate required files before quality checks
-      - name: Generate schemas (required for TypeScript compilation)
-        run: pnpm run generate:schemas
-        
-      - name: Format generated files
-        run: pnpm run format
-        
       # Quality checks (must pass for all further steps)
       - name: Run lint (fast fail)
         run: pnpm run lint

package.json

@@ -19,10 +19,8 @@
     "./package.json": "./package.json"
   },
   "scripts": {
-    "build": "npm run generate:schemas && tsc",
-    "dev": "npm run generate:schemas && tsc --watch",
-    "generate:schemas": "node scripts/generate-schemas.js",
-    "generate:schemas:watch": "nodemon --watch src/index.ts --watch src/commands/ --ext ts --exec \"npm run generate:schemas\"",
+    "build": "tsc",
+    "dev": "tsc --watch",
     "start": "node dist/cli.js",
     "mcp-server": "node dist/mcp-server.js",
     "api-server": "node dist/api-server.js",
@@ -72,50 +70,48 @@
   "author": "Joe Mearman",
   "license": "CC-BY-NC-SA-4.0",
   "devDependencies": {
-    "@amanda-mitchell/semantic-release-npm-multiple": "^3.15.0",
-    "@commitlint/cli": "^19.8.1",
-    "@commitlint/config-conventional": "^19.8.1",
-    "@eslint/js": "^9.28.0",
+    "@amanda-mitchell/semantic-release-npm-multiple": "^3.17.0",
+    "@commitlint/cli": "^20.5.0",
+    "@commitlint/config-conventional": "^20.5.0",
+    "@eslint/js": "^10.0.1",
     "@semantic-release/changelog": "^6.0.3",
     "@semantic-release/exec": "^7.1.0",
     "@semantic-release/git": "^10.0.1",
     "@types/mdast": "^4.0.4",
-    "@types/node": "^24.0.1",
-    "@types/unist": "^3.0.0",
-    "@typescript-eslint/eslint-plugin": "^8.34.0",
-    "@typescript-eslint/parser": "^8.34.0",
+    "@types/node": "^25.6.0",
+    "@types/unist": "^3.0.3",
+    "@typescript-eslint/eslint-plugin": "^8.59.0",
+    "@typescript-eslint/parser": "^8.59.0",
     "@vitest/coverage-v8": "^3.2.3",
-    "ajv": "^8.17.1",
     "commitizen": "^4.3.1",
-    "conventional-changelog-conventionalcommits": "^9.0.0",
+    "conventional-changelog-conventionalcommits": "^9.3.1",
     "cz-conventional-changelog": "^3.3.0",
-    "eslint": "^9.28.0",
-    "eslint-config-prettier": "^10.1.5",
-    "eslint-plugin-prettier": "^5.4.1",
-    "jiti": "^2.4.2",
-    "prettier": "^3.5.3",
-    "prettier-plugin-jsdoc": "^1.3.2",
-    "semantic-release": "^24.2.5",
-    "ts-json-schema-generator": "^2.4.0",
-    "tsx": "^4.19.4",
-    "typedoc": "^0.28.5",
-    "typedoc-material-theme": "^1.4.0",
-    "typedoc-plugin-coverage": "^4.0.1",
-    "typedoc-plugin-markdown": "^4.6.4",
-    "typedoc-plugin-missing-exports": "^4.0.0",
-    "typescript": "^5.0.0",
-    "typescript-eslint": "^8.34.0",
+    "eslint": "^10.2.1",
+    "eslint-config-prettier": "^10.1.8",
+    "eslint-plugin-prettier": "^5.5.5",
+    "jiti": "^2.6.1",
+    "prettier": "^3.8.3",
+    "prettier-plugin-jsdoc": "^1.8.0",
+    "semantic-release": "^25.0.3",
+    "tsx": "^4.21.0",
+    "typedoc": "^0.28.19",
+    "typedoc-material-theme": "^1.4.1",
+    "typedoc-plugin-coverage": "^4.0.3",
+    "typedoc-plugin-markdown": "^4.11.0",
+    "typedoc-plugin-missing-exports": "^4.1.3",
+    "typescript": "^6.0.3",
+    "typescript-eslint": "^8.59.0",
     "vitest": "^3.2.3"
   },
   "dependencies": {
-    "@modelcontextprotocol/sdk": "^1.12.3",
-    "commander": "^14.0.0",
-    "glob": "^11.0.3",
-    "remark": "^15.0.0",
+    "@modelcontextprotocol/sdk": "^1.29.0",
+    "commander": "^14.0.3",
+    "glob": "^13.0.6",
+    "remark": "^15.0.1",
     "remark-parse": "^11.0.0",
     "remark-stringify": "^11.0.0",
-    "unified": "^11.0.0",
-    "unist-util-visit": "^5.0.0",
+    "unified": "^11.0.5",
+    "unist-util-visit": "^5.1.0",
     "zod": "4.3.6"
   },
   "engines": {