Changes in Command Line Tools for Xcode 7.3

After the most recent update (7.3) to the Command Line Tools for Xcode, OSX seems to have changed in some unexpected ways.

1.

After a reboot I can't sync my git repository without first opening the GitHub Desktop application.

$ git push  
Permission denied (publickey).  
fatal: Could not read from remote repository

Once I've opened (and closed) the desktop application, it works as
expected. Does this have to do with Git being updated to 2.7.4?

2.

I can't run latexmk without sudo. This wasn't required before the update.

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What has really changed in 7.3, and how can I fix my problems?

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