Alcatraz - Xcode Command Line Tools are not currently installed

Question

I'm managing Xcode plug-ins via Alcatraz.

Everything was alright until I installed and then uninstalled Git following instruction in the uninstalled.sh file in official git.zip file:

sudo rm -rf /usr/local/git/   (in my case it's /usr/local/git/bin/git)
sudo rm /etc/paths.d/git   
sudo rm /etc/manpaths.d/git

I have no idea what I've done with git would affect Alcatraz.

Once I click Package Manager in Xcode I get this error:

I found nothing to download in the Preference Download section, and I did try to install the Command Line Tool following Xcode Command Line Tool tutorial

Here's how I verified it:

myMacBook-Air:~ me$ xcode-select -p 
/Applications/Xcode.app/Contents/Developer

And even:

myMacBook-Air:~ me$ gcc --version    
Configured with:--prefix=/Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1   
Apple LLVM version 7.0.0 (clang-700.0.72) Target: x86_64-apple-darwin14.5.0   
Thread model: posix

The warning still pops up.

Did I fail to install the command line tool?

(or maybe it's not about the git but has something related to the Xcode 7 upgrade?)

How could I fix this?

Answer 1

This answer actually works,

looks like Alcatraz has something to do with git.