[core/gitstore] refactor Manager methods to use Option pattern

[dungdm93]

Description

• Move authentication token in gitstore.Manager.Fetch into FetchOption (WithToken).
• Merge File and Read methods into a single Read method using ReadOption (WithSubpath, WithFile).
• Separate readFile and readArchive internal helper methods in manager.go.
• Return an error if both file and subpath are specified in ReadOption.
• Update all callers and unit tests to match the new API.