For instance, Google Chrome stores most of its data in sqlite3 databases in the profile directory. When I started at $current_employer I had a tendency to type calendar.google.com rather than the relevant calendar.example.com to get to my work calendar. After a couple of mistakes, this became self-reinforcing, because the auto-complete would preferentially show the most common completion of "calendar" as I typed that, which would be the wrong completion.
% cd Library/Application\ Support/Google/Chrome/Default
% sqlite3 History
sqlite> select count(*) from visits left join urls on visits.url = urls.id where urls.url like '%calendar.google%';
sqlite> delete from visits where url in (select id from urls where url like '%calendar.google.com/');
sqlite> delete from urls where url like '%calendar.google.com/'
Exit sqlite3, start Chrome back up, and hey presto, when I start typing "calendar" only the correct instance is left.
Trying to do this when your higher-level systems are built on non-standard components would be rather harder and would involve much coding.
This principle can be applied at many levels.
-The Grumpy Troll