Fix Hombrew problems after upgrading Mac OS X from Mavericks to El Capitan, skipping Yosemite

I have been sticking with Mavericks (OS X 10.9.x) since released and now skip Yosemite and directly upgrade to the solid build of El Capitan (OS X 10.11). It's just a direct upgrade and things seem to be working after a couple of reboots.

Well, we all know installed packages may not work at all. For instance, Developer tools like Homebrew seems broken again.

As seen on the Github, people have started collaborating with each others to resolve this.

https://github.com/Homebrew/homebrew/issues/40519

First thing to fix broken Homebrew directory is the permission issue. Error like this for brew update command:

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Stashing your changes:
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Error: Failure while executing: git stash save --include-untracked --quiet

So, try the following command first:

sudo chown $(whoami):admin /usr/local && sudo chown -R $(whoami):admin /usr/local

Second trial of brew update, another error appeared while doing brew update as follows:

Error: Failure while executing: git pull -q origin refs/heads/master:refs/remotes/origin/master.

Since major upgrade, we need to install recent release of Xcode Command Line Tools. An easy way is to install Xcode 7.0.1 from AppStore and then open Xcode to agree the terms and conditions.

Within CXcode, click menu item:

[Xcode]->[Open Developer Tool]-> [More Developer Tools...]

It helps to open Apple's download website for Developer Tools.

Click to download and install the following package :

Command Line Tools OS X 10.10 for Xcode 7

Reopen Terminal again and then try brew update, once again another error message shows up. But this time it looks like things get fixed by the second call of brew update command. So, issue the update command twice to get itself fixed and ready:

$brew update
#Error message...
$brew update
#It works this time...