By definition, what you add to a copylefted piece of free software must be distributed under the same free software license. So anybody can read what was added (freedom 1) and that would be completely fool for a company to add a malware. Just imagine its reputation once someone discovers it (by simply reading the source code).

With permissive licenses (such as the Apache license), you can redistribute the whole under a proprietary license. With no access to the source code. That is what t3g is promoting. And in this situation, you simply cannot tell what was added. It may be a spyware, a backdoor, etc. Only the developer knows and ends up with an unethical power over the users, who are those who achieve their work through the software.

That said, it is indeed safer to stick to what the repositories offer. Small unknown free applications have usually been only read by their authors. That is why there is a risk. Far smaller than in the case of proprietary software. But a risk anyway.

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