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This is only one of hundreds of such questions about usage that all teeter
on the question of reader anticipation. That is, if the reader isn't misled
by dropping the "that," then usual practice is to eliminate unnecessary
words. The hard part is anticipating the user expectations. Purists will
mumble and diagram the sentence to prove that you need the preposition. As
an English major, I see that point. As a writer, it's utter bosh. Usually
the "that" is implied and can be safely left off. But sometimes it can't,
just because its absence leaves a speed bump the reader feels as he passes
over the space. Here we're returning to the old and sorry but true phrase of
"know thy audience...and keep in touch." If you need a rule of thumb, I'm
personally of the "ultra-precise default" camp; when in doubt, add a word to
preserve clarity and precision. In my view, we're not in business for style,
but for meticulous transmission of concepts. And if you're heading for
translation, it's vitally important that you be clear, because many
translators aren't native English speakers and you're actually writing for
the translator, not the end user.
On another level, the overuse of "that" is often a sign of unnecessary
wording. For example, "This section assumes that you have a basic
understanding of..." isn't as easy to read as "You should have a basic
understanding of..." In strict terms, the section doesn't assume
anything...the writer does. Here at our company, we've used second person
extensively to overcome wordiness and it's usually acceptable to the client.