Apple Mail frequently hangs for minutes, fails to save account changes, autonomously modifies your settings. Too clever by half, feels like they only tested it for Cloud based mail.

Moved ~/Library/Containers/com.apple.mail to backup directory.
Moved to using [https://www.postbox-inc.com/ Postbox] which may not be sexy but is solid (what I want
in a Mail client). I then moved to using my iPad for mail instead.
X11 needs to be installed for applications like ImageMagick.
[https://support.apple.com/en-gb/HT201341 Apple Support] guides one to [https://www.xquartz.org/ XQuartz].
SSH failed to my website after domain moved to new server, complaining about possible spoofing.
Simplest answer is to remove the ''known_hosts'' file in the user's .ssh folder.
AppStore always gives "This item is temporarily unavailable. Try again later." messages.
See threads like [https://discussions.apple.com/thread/6622317 Xcode 6.1 unavailable].
Cleaning the Darwin user cache for the AppStore by:

rm -rf "$(getconf DARWIN_USER_CACHE_DIR)/com.apple.appstore"

may help. Multiple causes.