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Consider this part of paragraph:

The elements of the page get highlighted as the mouse moves over them to make it easy for the user to detect the boundary of each element. Then, the user specifies several anchors by selecting elements of the page. For each anchor, a dialogue opens in which the user can select or define distinguishing features of an anchor based on its attributes (e.g. id, class), text or a pattern in its text (Figure 2).

what is your suggestion to avoid repeating "the user"? somehow I think using "he" or "she" is not neutral

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    Since nobody wants to get into the he/she controversy, I think you have to stick with "user". I don't see the repetition as being a problem since they are in separate sentences, and you are writing instructions, not a novel. Possibly you could use some synonym for "user", but mixing them in your example will just add confusion. Any reason why repetition is a problem? – user3169 Jun 27 '15 at 18:08
  • @user3169 I think in the third sentence I can use a "passive" sentence. it seems in the case above "the user" is not annoying, but I would like to know the opinion of a native speaker. – Ahmad Jun 27 '15 at 18:34
  • Why are you not inclined to use the singular they? There's nothing wrong with your sentences though. – M.A.R. ಠ_ಠ Jun 27 '15 at 19:34
  • @M.A.Ramezani I use "the user". Is it acceptable to use "they" in the next sentence? – Ahmad Jun 27 '15 at 19:51
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I can't think of a better way to write "the user" in your sentences, only to reword them so you don't need to use it as often. Whoever is reading the sentence understands that "a user" will be using the software and doing the actions, without needing to explicitly say so.

To me, it stands out more that you reference the elements so often, and that you talk about the user "detecting" the boundary instead of the user "seeing" it, or the software "making it visible".

"Highlight" already means "to draw attention to something", so it might be redundant to explain why there is a highlight, depending on how important the element boundaries are.

And the phrasing "the x of the y" is more common in other languages than English; you write "elements of the page, boundary of each element, elements of the page, features of an anchor". It is clear and understandable, but it feels like hard work. "Elements of the page" can become "page elements", and after you have written "elements of the page" once, you don't need to refer to them as "elements of the page" again, instead of just "elements" (unless the context makes it easy to confuse them with other elements).

e.g. I might write:

Page elements are highlighted as the mouse moves over them, and the user specifies anchors by selecting one or more elements. For each anchor, a dialogue allows selecting or defining anchor features by text value, text patterns or attributes (e.g. id, class). (Figure 2).

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I am a native speaker. I think that the passive voice would work well for the third sentence:

"For each anchor, a dialogue opens in which distinguishing features of an anchor can be selected or defined based on its attributes (e.g. id, class), text or a pattern in its text (Figure 2)."

or

"For each anchor, [the application name] displays a dialogue in which distinguishing features of an anchor can be selected or defined based on its attributes (e.g. id, class), text or a pattern in its text (Figure 2)."

I personally do not like the "singular" plural pronoun they; it still sounds somewhat uneducated and ideologically forced to my ear, however, it has become steadily more acceptable over the last few decades to most people, so you could use they; only a few of us would be annoyed.

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