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1. Can we use past perfect in the first part of the sentence and past simple in the second one? To show that 1st action was started before the 2nd? Or why there is no need to complicate this sentence?

«She carried them with her as she started toward the house.»

2. Why is past perfect used here?

«She hadn’t had a new style in years, and she was tired of looking the same every day.»

3. Why is 'used to' is used with 'had gotten'?

«She had gotten used to waking up to the smell of brewing coffee in the morning, and she missed having another adult presence in the apartment.»

4. Why is passive voice used here?

«She had been used to having another person around, just to talk to or listen.»

5. Why 'gone by' not 'went by'?

«Now, with three years gone by, she honestly didn’t know if she would ever love someone again the way she had loved David. »

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anyauserthere is no need to complicate this sentence

Because the actions are simultaneous ("as") and their time sequence is not ambiguous.

She carried them with her as she started toward the house.
anyauser2. Why is past perfect used here?
She hadn’t had a new style in years, and she was tired of looking the same every day.

It is necessary. It is the only tense that works to express a period of time earlier than a point of time in the past.
Compare the present perfect with the past perfect.

Present:

(at a restaurant) I haven't had a chocolate éclair in years, so I will order one for dessert.

Past: (the next day)

I hadn't had a chocolate éclair in years, so I ordered one for dessert last night.
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anyauser

1. Can we use past perfect in the first part of the sentence and past simple in the second one? To show that 1st action was started before the 2nd? Or why there is no need to complicate this sentence?

«She carried them with her as she started toward the house.»

'as' indicates 'at the same time', so it seems to me that you would change the meaning (or obscure it) if you changed 'carried' to 'had carried'.

anyauser

2. Why is past perfect used here?

«She hadn’t had a new style in years, and she was tired of looking the same every day.»

It's the past of

She hasn't had a new style in years, and she is tired of looking the same every day.

In both cases, her style stays the same for some period of time, and at the end of that period she's tired of it. With the "present version" the anchor time is the present moment (the time the sentence is uttered). With the "past version" (your example sentence) the anchor time is in the past. This could be something mentioned previously in the text or simply the point in time when she got tired of that style.

anyauser

3. Why is 'used to' is used with 'had gotten'?

«She had gotten used to waking up to the smell of brewing coffee in the morning, and she missed having another adult presence in the apartment.»

I'm not sure what you mean. We can suppose that those words were used together because that's the meaning the writer wanted to convey.

to be used to ~ to be accustomed to
to get used to ~ to become accustomed to

'had gotten used to' is the past perfect of 'to get used to'. It means 'had become accustomed to'.

anyauser

4. Why is passive voice used here?

«She had been used to having another person around, just to talk to or listen.»

It's not a passive construction. 'had been' is simply the past perfect of 'to be'. Thus, 'had been used to' is the past perfect of 'to be used to', just as 'was used to' is the past of the same idiom, and 'has been used to' is the present perfect.

anyauser

5. Why 'gone by' not 'went by'?

«Now, with three years gone by, she honestly didn’t know if she would ever love someone again the way she had loved David. »

'with X years gone by' can be considered an idiom. It's simply a fixed expression.

Also, "Three years went by" is a full sentence. Full sentences are not used after the preposition 'with'.

CJ

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anyauser3. Why is 'used to' is used with 'had gotten'?

https://www.thefreedictionary.com/used+to

"used to" is an idiom. It means, as an adjective, "accustomed to" or as a verb, some habitual action in the past.

She had gotten used to waking up to the smell of brewing coffee in the morning, and she missed having another adult presence in the apartment.

She had become accustomed to waking up to the smell of brewing coffee in the morning.

anyauser4. Why is passive voice used here?

It is not passive voice. It is the active voice.

anyauser5. Why 'gone by' not 'went by'?

«Now, with three years gone by, she honestly didn’t know if she would ever love someone again the way she had loved David. »

Because it is modifying the noun phrase "three years." The simple past form is never used as a noun modifier.

e.g.

With her chores done for the day, Jill could relax and watch TV.

Otherwise, you have to write a full clause, something like this:

«Three years went by like a flash and she honestly didn’t know if she would ever love someone again the way she had loved David. »

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