Fix isort deprecation warning by explicitly setting stages

- Add stages: [pre-commit] to isort hook configuration
- This overrides deprecated stage names from the repository
- Update documentation to explain the fix

Author: yaniv-golan

.pre-commit-config.yaml

@@ -33,6 +33,7 @@ repos:
       - id: isort
         args: [--profile=black]
         files: ^\.github/scripts/.*\.py$
+        stages: [pre-commit]  # Override deprecated stage names from repository
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.1.9

docs/development/PRE_COMMIT.md

@@ -107,6 +107,18 @@ git commit --no-verify -m "message"
 
 ## Troubleshooting
 
+### Deprecation Warnings
+
+If you see warnings about deprecated stage names, they have been addressed in our configuration by explicitly setting `stages: [pre-commit]` for hooks that have this issue. This overrides the deprecated stage names defined in the hook repositories themselves.
+
+If you still see warnings after updating hooks, run:
+
+```bash
+pre-commit autoupdate --repo https://github.com/pycqa/isort
+```
+
+This will update to the latest version that may have fixed the issue.
+
 ### Hooks are slow
 
 - First run downloads tools (one-time)