[fix] Follow the file permission mode in the patch

[uilianries]

Description of your Pull Request

• Add a test to validate the reported issue [bug] the file mode is ignorred when applying patches #23
• Add logic to run chmod according to the file permission mode listed in the patch file
• Only regular files are changed; no operation will be done for folders or symlinks
• In case an error occurs when doing chdmod, it will be ignored to keep backward compatibility
• In case we are not able to obtain the file mode from the patch file, it will be ignored too.
• It only applies to a git patch-style file
• On Windows it should have minimal effect as Python's chmod can only change the read-only status.

fixes #23

• Refer to the issue that supports this Pull Request.
• If the issue has missing info, explain the purpose/use case/pain/need that covers this Pull Request.
• I've tested locally that my code works.
• I've added relevant tests to verify that my code works.