Reopened Pull request 

Double checked, the current master branch for 10.1.0 has not included these fixes.

so, during my testing, I found that using:
include($extra_config);
does APPEAR to be slower than using the original
exec('php .....');

I think, maybe using the change that i've made that uses include instead gives a more real time representation of an install/upgrade/remove using the zppy client. Scripts execute line by line right? So, include will literally copy and paste the lines into the currently executing script (so any lines after in the zppy client will be executed after), whereas exec(''); would create a new process?

The other file change is just a modification to those file management functions that I added to the file handler. They're fully safe,clean and compatible now :)