refactor: cleanup the refresh_dir code, update tests (#494)

* feat: take Ignore List into consideration when refreshing directory

* undo the extension check in refresh_dir

.github/workflows/mypy.yaml

@@ -23,8 +23,9 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install -r requirements.txt
-          pip install mypy==1.11.2
+          python -m pip install --upgrade uv
+          uv pip install --system -r requirements.txt
+          uv pip install --system mypy==1.11.2
           mkdir tagstudio/.mypy_cache
 
       - uses: tsuyoshicho/action-mypy@v4