feat: use gitpython for git stuff

[NicolasIRAGNE]

Closes #412

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[Copilot]

Pull Request Overview

This PR refactors the codebase to use GitPython for Git operations instead of directly executing Git commands through subprocess calls. This change improves code maintainability, error handling, and provides better Git integration.

• Replaces direct git command execution with GitPython library calls
• Updates authentication mechanism to use GitPython's configuration system
• Refactors test suite to mock GitPython instead of subprocess calls

Reviewed Changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
pyproject.toml	Adds GitPython dependency
src/gitingest/utils/git_utils.py	Core refactor from subprocess to GitPython API
src/gitingest/clone.py	Updates clone operations to use GitPython
tests/test_git_utils.py	Refactors tests to mock GitPython instead of subprocess
tests/test_clone.py	Updates clone tests for GitPython integration
tests/conftest.py	Adds GitPython mocking infrastructure
src/server/query_processor.py	Minor string formatting change
Dockerfile	Updates pip install to include mcp extra
.pre-commit-config.yaml	Adds GitPython to pre-commit dependencies

Comments suppressed due to low confidence (2)

src/gitingest/utils/git_utils.py:311

• This line appears to be in the wrong file. The IngestErrorResponse import and usage belongs in src/server/query_processor.py, not in git_utils.py.

        msg = f"Invalid GitHub URL: {url!r}"