You can check files with correct permissions into Git to be able to run them on the continuous integration server right after checkout. Setting the right properties in the git-index will force Git to checkout the file and set the right file permissions. Set the core.fileMode in the git configuration to false. The means: Do not ignore the file mode. Then update the git-index with --chmod for your file, commit and push the file to the repository.

See: git-update-index