Fix err with mr notes and deleted files

https://internal-tracker.builder.ai/#/projects/3651?storyId=1978123

https://internal-tracker.builder.ai/#/projects/3651?storyId=1976134

Project where the changes have been tested: https://gitlab.builder.ai/builder/builder-bx/Bx/assembler_projects/stg/autobxengpro06043183-178150-ruby/-/merge_requests

Changes to post MR notes:

The shell script has been converted to a python script and tests have been added to verify the working of the python script.

Failures in the following cases have been fixed with these changes:

1. When a protected file is deleted in the branch , the code-validator should flag this as an error appropriately.
2. When a non-protected file is present only in the clean repository (code-engine or approved branch), the code-validator should not flag this as an error.

Changes to remove empty files from the clean repository (In case of protected mode, these will be files that do not have protected markers and hence are empty after the files are sanitised. In case of customised mode, these will be files that are fully customisable