Alcatraz - Xcode command line tools are not currently installed 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/   
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: 



Even re-install the Alcatraz it's still there.

Update

I did install the Command Line Tool following Xcode Command Line Tool tutorial

Here's the message I got:

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.

How could I fix this?
After installing git-2.5.3-intel-universal-mavericks you have at least three git executables on your Mac: 


/Applications/Xcode.app/Contents/Developer/usr/bin/git (v2.3.8 (Apple Git-58))
/usr/local/git/bin/git (v2.5.3)
/usr/bin/git (which is a stub only)


If you've followed the instructions in the README.txt inside the git-2.5.3-intel-universal-mavericks.dmg you probably renamed the original git stub:

sudo mv /usr/bin/git /usr/bin/git-system


Renaming or removing the stub already breaks Alcatraz.

You may now whether rename git-system:

sudo mv /usr/bin/git-system /usr/bin/git


or reinstall git-2.5.3-intel-universal-mavericks and link the GIT-git to /usr/bin:

sudo ln -s /usr/local/git/bin/git /usr/bin


to fix your issue.