The build.sh file checked into the Git repo has the execute bit properly set, but after I run dotnet new -i "MiniScaffold::*" and then dotnet new mini-scaffold, the resulting files have build.sh without the execute bit. This is just a minor annoyance as it's easy to immediately run chmod +x build.sh, but if it can be fixed in the template that would be nice.
I rather suspect, though, that this is a limitation in the dotnet templating engine, in which case you can't fix it in the template. If that's the case, feel free to just close this issue. :-)
System info:
Dotnet version: 2.0.0-preview2-006497
OS version: Linux Mint 18.1 (based on Ubuntu Xenial 16.04)