Right, you definitely don't want to make a font with ligatures for every combination of characters. Not only would the font be huge, there are usually more than two characters in a row that may need the same special treatment.

The trick is to write a contextual alternates ("calt") feature. There's more than one way to do it, so you need to plan it out first and then implement it in feature code. One way to do it goes something like this:

The default \r will be designed to accept the usual connecting stroke coming from the glyph that precedes it. In the absence of such a glyph, you need to substitute an alternate \r that doesn't connect. The code would look something like this:

feature calt {
ignore sub @glyphsthatconnectontheright r' ;
sub r' by r.alt ;
} calt ;

where \r.alt is the non-connecting version of the \r. The ignore line basically says, "if the \r follows a glyph that connects, skip the next part". If it's some other glyph, then it will substitute the alternate \r. (The apostrophe marks the glyph that you want to potentially substitute.)

That's the basic idea. There are other approaches. You could for instance make the default \r one that doesn't connect and substitute a connecting alternate when it follows glyphs that connect. Or, your connection scheme may be more complex to get a more natural appearance (more than one possible connecting stroke, for instance, low, medium, high, none).