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I have an HDD which doesn't boot (details) but when mounted into USB enclosure, all files are completely readable. I have a spare larger clean HDD which I can clean install / repair to.

What is the best way to recover data, programs and settings to a new HDD?

The original HDD has Mountain Lion OS X and dual-partition Windows 7 (system + data), installed via this scheme.

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13 hours ago you said all your partitions are readable in Wnidows. You can recover the data easy enough. Your programs likely should just be reinstalled. – Ramhound Oct 15 '13 at 11:00
@Ramhound Manually copying files is an obvious solution. The question is whether there's a way to also reliably recover programs installed and their settings--and to avoid manual reinstall. – yurkennis Oct 15 '13 at 11:46
You can create a image of the partition then restore the partition on a new hdd after you have setup a working boot sector. – Ramhound Oct 15 '13 at 11:48
@Ramhound Could you detail how is it better to do that: which way to create a partition, to setup a working boot sector, to properly restore the image to new HDD? – yurkennis Oct 15 '13 at 12:05

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