Originally posted by teuben
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Do you mean that many applications override the default settings provided by the OS? Maybe you could provide a few instances (and maybe file a bug)?
Re. "... adding common apps once I find the settings file."
My guess is that there's no one common settings file. I think applications store their application-specific shortcuts internally and perhaps each application has its own way of storing its shortcuts. Whether this information is accessible to the user via an application-specific GUI, or in a simple text file or in some sort of database would depend on the application.
One possible way to ferret out which file of an application stores user-set shortcuts (and possibly the default ones as well), is this:
Close as many open applications, especially browsers, as possible but keep a terminal window open at $HOME.
Open the application of interest.
Don't do anything for a minute.
Now set or modify a shortcut in your application.
Save and exit the application.
Immediately switch to the terminal and run
find -newermt "1 min ago" -ls
This command may take a while but will recursively list files altered in the last minute and, with a little luck, you should be able to identify the relevant file.
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