Correctly refresh file when computing input_files_id and a file is set as refresh_input

When debugging an issue with the .deb file, I noticed that var/build_id for linux-packages changed over time.

After looking at input_file_need_dl, I think we don't correctly refresh a file marked as refresh_input when computing its input_file_id (although we correctly refresh it before starting the build). So if a file already exists from a previous build, the old file will be used to compute input_file_id.