This is my first bug report ever. I have made an honest attempt to find similar bug reports in the "product: Tomboy" category. I am guessing this has come up and I was just unable to find it. The "bug" is of a type that is difficult to describe. It is at the intersection of common usage and a specific feature of Tomboy that leads to a catastrophic User failure. The program functions correctly, but ends up doing something that makes the data useless. An example might illustrate best.

An example:

Let us say that in a note we have a link titled "the effects of carbon dioxide on echinoderms". The user knows that the title isn't quite perfect, so he goes to edit it, hoping to replace it with something superior. Knowing the final phrase will start with "the", the user erases everything but "the". Some time passes while the user is thinking of the new link title, or the User goes off looking at his email, or whatever. And in that time Tomboy does its magic and changes every instance of "the" in every note to a link to the page titled "the" that used to be "the effects of carbon dioxide on echinoderms".

The user finally thinks of it, and changes "the" to "the effects of atmospheric saturation of CO2 on echinoderm physiology" and closes the note. The user then opens another note, only to find that every instance of "the" in every note has been changed to a link to "the effects of atmospheric saturation of CO2 on echinoderm physiology".

Now, of course, the simple solution to this is to retitle the note "the effects of CO2..." as "the" copy its contents to a new, untitled note, wait for Tomboy to change everything back to "the", and then erase the note titled "the". But if the problem is a common phrase or a date or a year, the User may NOT want to change every instance, and the only solution is a manual re-edit. And since the user is editing the links while simultaneously editing what will become non-links, the potential for catastrophic spreading of more link titles becomes possible.

Perhaps a User-set warning would be appropriate: 

"Warning: changing this link title will make 6,512 changes to your notes. Should I continue?"

Something like that?