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Looking for a tool that would verify integrity of ALL files on a Windows 7 x64 NTFS disk reliably?

This is for testing of experimental defrag software, so it really needs to be secure and foolproof. I know it will take a long time, there's millions of files on the disk, but safety just cannot be compromised in a situation like this. Freeware solution much preferred.

Can be either Windows software (=inducing pitfalls about files changing due to booting Windows) or a stand alone boot (for example linux boot cd + usb key for storing chksum/metadata).

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I'd go with a combination of chkdsk, which does a good job of checking the metadata logs and directory entries, and checksum software, like md5deep. I would use a good hash like SHA 256.

I should also probably ask, are you writing your own APIs? I hope not. . .

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"md5deep can accept a list of known hashes and compare them to a set of input files" --yes thank you, this is exactly what i'm looking for. –  kilves76 Jul 18 '11 at 6:10
    
Sorry i don't have enough reputation yet to vote your answer up. –  kilves76 Jul 18 '11 at 8:19
    
You are the OP. You are suppose to accept it :) –  surfasb Jul 18 '11 at 8:24
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Chkdsk ignores all switches other than the first (except for /v which only applies to FAT file systems). Therefore, there is no functional command chkdsk /f /v /r. /f and /r are never used together in the same command line. The correct syntax, if you really want a full scan with surface test is:

chkdsk <drive:> /r /v

But that only tests the integrity of the file system, not the files' validity. Only system files can be scanned to be certain that their digital signatures and content are valid. For other files, there is no way to test because there is nothing to compare them to.

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"there is nothing to compare them to" --Yes exactly that's why i'm looking for a program that will do it, i'm sorry but you only re-paraphrased my question. –  kilves76 Jul 18 '11 at 6:07
    
Besides i think you are flat out wrong, there is significant difference in running time between chkdsk /f /v /x and chkdsk /f /v /x /b -- the previous will run in a quarter, while the latter will take several hours. –  kilves76 Jul 18 '11 at 6:15
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