fix: prevent duplicate pre-commit hook execution

- Add explicit stages: [pre-commit] to all hooks except gitlint
- Keep gitlint on stages: [commit-msg] for commit message validation
- Prevents hooks from running on both pre-commit and commit-msg stages
- Each hook now runs exactly once on the appropriate stage

This resolves the issue where some hooks were executing twice during
commits, improving performance and reducing redundant output.

.pre-commit-config.yaml

@@ -8,14 +8,22 @@ repos:
     rev: v4.6.0
     hooks:
       - id: trailing-whitespace
+        stages: [pre-commit]
       - id: end-of-file-fixer
+        stages: [pre-commit]
       - id: check-yaml
+        stages: [pre-commit]
       - id: check-added-large-files
+        stages: [pre-commit]
       - id: check-merge-conflict
+        stages: [pre-commit]
       - id: check-json
+        stages: [pre-commit]
       - id: check-toml
+        stages: [pre-commit]
       - id: mixed-line-ending
         args: ["--fix=lf"]
+        stages: [pre-commit]
 
   # Python code formatting and linting
   - repo: https://github.com/astral-sh/ruff-pre-commit
@@ -23,7 +31,9 @@ repos:
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
+        stages: [pre-commit]
       - id: ruff-format
+        stages: [pre-commit]
 
   # Git commit message linting with gitlint
   - repo: https://github.com/jorisroovers/gitlint
@@ -39,6 +49,7 @@ repos:
       - id: bandit
         args: ["-c", "pyproject.toml"]
         additional_dependencies: ["bandit[toml]"]
+        stages: [pre-commit]
 
 # Configuration for specific hooks
 ci: