Reduce file and folder permissions across subo

[danielledeleo]

I went through Subo and adjusted the file permissions according to the following rules:

• directories are all 0755
• locally cached and temporary files are 0644
• runnable source files are 0600

Fixes #171

[cohix]

@jagger27 I like @denopink 's suggestion :) Let's do that, and then this looks good!