While using OS X El Capitan 10.11.x, is it safe to disable System Integrity Protection? There are all these additional apps that modify folders and the dock that I want to install but you have to disable rootless first.
Good idea or bad idea?
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If you disable SIP you'll get the same level of protection as you had with OS X versions before El Capitan. Whether this is enough for your needs it something only you can decide.
OTOH it's not that much trouble to disable SIP briefly to chance a protected part of the system. If you want to be on the safe side, disconnect from any networks while you do this.
I felt like it had a negative impact on the battery life of my macbook pro(around 300 cycle counts but not more than 300).After I disabled SIP, I was hardly getting five hours of battery. Few days ago, I enabled it, and it's back to normal.
About the safety issue of the core system file :If you know what you're doing, you should be fine. The following link should help you more about the SIP. http://www.imore.com/el-capitan-system-integrity-protection-helps-keep-malware-away
It is not safe to disable SIP. It is there to keep external apps from modifying system files, and once it has been disabled nothing short of a reinstall of the whole OS from external media can rectify this.
Once system files have been modified, even once, an attacker could have corrupted and infected your whole system, and turning it back on will not change this, as the damage has been done.
To be fair, Windows essentially allows the same thing every time you click yes to install any program(grants admin access to all files), but this doesn't make it more ok. That being said, I have installed dozens of programs from the internet on Windows and I have been (as far as I know) fine.
SIP is essentially a level of privilege above sudo. If you need to disable it, do so, but don't fool yourself: it is not secure.