Fix local Git source branch preparation

[ramblezhang]

Summary

• Treat local::... sources that are exact Git repositories or worktrees as branch-aware Git sources.
• Reclone invalid or polluted local Git workspaces when the workspace root or origin does not match the expected target.
• Pass per-process safe.directory configuration through local clone/fetch upload-pack calls.
• Fetch the resolved source branch ref explicitly before checkout and validate the target commit exists in the workspace.
• Normalize legacy local-directory snapshot baselines only for exact local Git sources, while preserving normal incremental tasks for real Git commit changes.

Validation

• dotnet test tests/OpenDeepWiki.Tests/OpenDeepWiki.Tests.csproj --filter "FullyQualifiedName~RepositoryAnalyzerSourceTests|FullyQualifiedName~IncrementalUpdateWorkerTests"
• dotnet build OpenDeepWiki.sln --no-restore
• git diff --check origin/main..HEAD

Follow-up correctness fix for merged PR #375.