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I am thinking along the lines of "normalize" -- something like proper-ize.

-- UPDATE --

In one of my comments, I presented an example...

a disorganized mess (for example, a cluttered desk) that I want to "make proper" by organizing things "properly"

Take the above example figuratively NOT literally. An answer like "tidy up" is not what I'm looking for.

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Proper has many different meanings. Which one are you referring to? Proper grammar? Proper manners? Proper as in societally acceptable? – onomatomaniak Nov 21 '11 at 12:06
Pretty much in any context, where there's something "improper" that can be "made proper". In my case, it is disorganized mess (for example, a cluttered desk) that I want to "make proper" by organizing things "properly". – treecoder Nov 21 '11 at 12:11
You could say rectify, although this only works for some meanings of proper. – Peter Shor Nov 21 '11 at 13:23
I don't think you have shown why "tidy up" is not what you are looking for ("tidy up" can be used figuratively and literally; even literally it can mean to bring things into order; also yes, you can 'tidy up' an improperly aligned things) – Unreason Nov 21 '11 at 13:52
Why must one word suit all these varied contexts? This seems like manufactured problem to me. – onomatomaniak Nov 22 '11 at 18:09

You might consider using organize or systematize.

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You can tidy up a cluttered desk.

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But I can't tidy up an improperly aligned sewing that I might want to "make proper" – treecoder Nov 21 '11 at 12:55
I don't think there is one word to apply in all cases. For the improperly aligned sewing the word "rectify" came to my mind, as Peter Shor writes above. It would help if you explained the exact context of the word you are looking for. – Irene Nov 21 '11 at 13:26
My exact context is programming. I need to sanitize some HTML content, but it is NOT typical HTML sanitization, I just want to make changes to the HTML to "make it proper" according to a set of conditions -- i.e. make it adhere to those conditions. – treecoder Nov 21 '11 at 13:33
Then why isn't Raku's answer good enough for you? It explains exactly what you want, it just isn't a single word. – Irene Nov 21 '11 at 13:41
Note that tidy is well known package that tidies up html. – Unreason Nov 21 '11 at 13:47

Would fix work? Unlike repair, it doesn't always carry a connotation of something being broken, i.e. it can be used if something is merely not quite right.

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How about "to clean something up"?

In an IT context, you can use something like "make something adhere to a standard".

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Maybe you're looking for conform (which you can also use figuratively):

conform: to give the same shape, outline, or contour to : bring into harmony or accord conform furrows to the slope of the land

(Source: M-W)

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