Disable unwanted default applications and clean up related scripts

Remove `enable-default-apps.ts` script, add `disable-deprecated-apps.ts`, update seeding logic in `seed.ts` to set `isActive` to false for documents, and modify `DOCKER.md` and `scripts/package.json` accordingly.

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scripts/package.json

@@ -7,7 +7,7 @@
     "hello": "tsx ./src/hello.ts",
     "seed": "tsx ./src/seed.ts",
     "remove-chat": "tsx ./src/remove-chat.ts",
-    "enable-default-apps": "tsx ./src/enable-default-apps.ts",
+    "disable-deprecated-apps": "tsx ./src/disable-deprecated-apps.ts",
     "typecheck": "tsc -p tsconfig.json --noEmit",
     "test": "node --test 'tests/**/*.test.mjs'"
   },