Not only do we have the account from what the French troops did, we have more about what the French troops left behind. Hunger, orphans roaming the countryside, decomposing bodies of men and beast, bringing epidemics.
As for others crimes, between contending armies (or when the French had to confront people with actual guns) we have the episode of Wellington trying to convince Massena that the Ordenanças were part of the Portuguese military establishment. After trading correspondence, Wellington finally wrote Massena, that if he wouldn't stop executions he couldn't be held accountable for what the Portuguese troops reaction might be in the future. Only after this, he confides to Forjaz in a letter, does Wellington stop hearing about any retaliations against the captured Ordenanças. How many Ordenanças were then executed, contrary to the laws of war?
Now, I'm using expressions of today to talk about the past, but then again, we are here in the present and talking about the most desastrous period in Portugal since the Earthquake in 1755. It kind of still hurts collectively.
Jorge