The default behavior of TeXShop can be modified in two ways: by making Preference changes, and by editing files in ~/Library/TeXShop. Here ~/Library is the Library folder in your home directory.

New versions of TeXShop generally do not change these user modifications because users don't like changes made behind their backs. But sometimes, new features require a few modifications. These modifications are explained in the document "About This Release" in the TeXShop Help menu. This document is rewritten for each TeXShop release. TeXShop still works fine if changes explained in "About This Release" aren't made, but then some new features may not work as advertised.

Although TeXShop does not usually upgrade items in ~/Library/TeXShop, there are three exceptions. The folders bin, Engines/Inactive, and Scripts are updated with each new release. Extra files added to those folders by users are left unchanged, but default TeXShop files are replaced by new versions and new default TeXShop files are added. Note that active Engine files are not changed because they live in Engines, but not in the Inactives subfolder.

The advantage of this design is that some engines put support files in the bin and scripts directories. Upgrades of TeXShop can automatically update these support files without user intervention. Similarly, new engines are sometimes added to the Engines/Inactive directory; users obtain them automatically without doing anything.

Each new TeXShop upgrade rewrites the folder ~/Library/TeXShop/New. This folder contains new items which a user might like to add to their other configuration folders. For example, new templates will appear in ~/Library/TeXShop/New. Users who want these new templates should move them to ~/Library/TeXShop/Templates and edit them as appropriate. Files in ~/Library/TeXShop/New are always described in "About This Release", so it is not necessary to examine ~/Library/TeXShop/New unless directed to do so.

It is useful to understand one technical detail of this design. A hidden file in ~/Library/TeXShop/New lists the version number of TeXShop which wrote that folder. The location ~/Library/TeXShop is only updated if the version number of TeXShop is higher than the version number listed in that hidden file. Consequently, ~/Library/TeXShop is not updated every time TeXShop runs, and older versions of TeXShop can safely be run without modifying ~/Library/TeXShop.

In rare cases, a user may wish to obtain the latest default files for a folder in ~/Library/TeXShop. If that folder is moved to the desktop, then the next time TeXShop runs it will recreate the folder from scratch. Then any modifications made can be merged in from the desktop copy. For instance, if the Templates folder from ~/Library/TeXShop is moved to the desktop, then the next TeXShop run will produce the latest default Templates folder. This drastic action, luckily, is seldom required.

How do I configure TeXShop?
Obtaining New Library Items