chore(version): bump version to 0.9.31 and update package references

- Updated version to `0.9.31` in `README.md`, `cli-package/package.json`, and `src/utils/version.ts`.
- Synced `@soulcraft/brainy` dependency version to `0.9.31` in the CLI package for consistency.
- Updated npm version badge in `README.md` to reflect the new version.

This update ensures consistent versioning across the project and aligns references between main and CLI packages.

cli-package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@soulcraft/brainy-cli",
-  "version": "0.9.30",
+  "version": "0.9.31",
   "description": "Command-line interface for the Brainy vector graph database",
   "type": "module",
   "bin": {
@@ -40,7 +40,7 @@
     "url": "git+https://github.com/soulcraft-research/brainy.git"
   },
   "dependencies": {
-    "@soulcraft/brainy": "0.9.30",
+    "@soulcraft/brainy": "0.9.31",
     "commander": "^14.0.0",
     "omelette": "^0.4.17"
   },