`code_setup.sh` > support deleted files

[mmathieum]

Sometime a previously present file needs to be deleted from the repositories (like shared-overwrite/.github/actions/setup/action.yml that was deleted in #667).

Add support for MT.DELETE.<filename> files in /shared-overwrite/** in code_setup.sh so a file named shared-overwrite/.github/actions/setup/MT.DELETE.action.yml would have for consequence the deleting of .github/actions/setup/action.yml in the repositories.

[copilot-swe-agent]

The agent encountered an error and was unable to start working on this issue: This may be caused by a repository ruleset violation. See granting bypass permissions for the agent, or please contact support if the issue persists. (Request id: E6E0:3057A8:47D4EA:63388C:69DF806C)