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I have installed mathools package from MikTeX packahe manager (both normal and admin). However, MikTeX still tries to find it in the mh bundle and does not find it as a separate package.

How do I tell MikTeX that this package is now not part of the mh bundle?

Not duplicate: Many people asked how to install mathtools after it was moved out of mh in August 2014. The answer is to use MikTeX package manager. I did it.

Now the package is installed and the package manager (both normal and admin versions). The MikTeX package manager shows that the package is present under texmf\tex\latex\mathtools.

However, when I try to compile a tex file, I got the error message saying that tex\latex\mh\mathtools.sty is missing. Note that it tried to find it in a wrong location.

I did run Settings (both normal and Admin) - Refresh FNDB and Update Formats, to no avail. What should I do?

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    Isn't there an old auxiliary file that still mentions this path? Try deleting all auxiliary files from your editor. I can't imagine another reason. – Bernard Aug 15 '15 at 7:34
  • Does kpsewhich mathtools.sty give tex\latex\mh\mathtools.sty still in the mh directory? Does the mh folder still contain anything (on my machine it does not). Try deleting the mh folder if empty. Make sure you don't have the mh package in your local version either. Then uninstall both mathtools and re-install it, but not in both User and Admin mode but only one of the two. Recreate the FNDB. – moewe Aug 15 '15 at 11:32
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    Update the FNDB with miktex settings and miktex settings (admin). Also synchronize in both package managers the repositories (menu repositories). – Ulrike Fischer Aug 15 '15 at 11:46
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I'm not a developer of MiKTeX nor TeXnicCenter but I'm a teacher how to use MikTeX (and TeXnicCenter). Some of my students have problems with their installation and asked me how to solve that. BTW are that usually students not following my installation hints ...

MiKTeX has a separate update system and a separate package system. To have a well working system you should syncronize your MiKTeX system as described in the documentation or on several answers here on the page.

MiKTeX had some problems with the two packages mh and mathtools. With a current version of MiKTeX theese problems are gone.

Conclusion from your remarks: You have a version problem. Wild guess: two installed versions, portable and basic/complete?

The best way to get a running system with MiKTeX and TeXnicCenter is to install first the current MiKTeX (I prefere the complete version). After you have installed MiKTeX install TeXnicCenter. Now TeXnicCenter is able to recognize that MiKTeX is installed and is able to configurate itself.

Conclusion: If you installed a new MiKTeX for easy life install TeXnicCenter new. If not you have to check each entry in your TeXnicCenter for correct pathes to the new MiKTeX distribution!

That was the reason for my comment: "For me it sounds that you have a problem with different versions you are using. How did you install MiKTeX?"

Your last comment mentioned you had two versions of MiKTeX on your computer. That is not a good idea. MiKTeX is build to give you the possibility to update your system on the fly (if you want), but then you can only use one version on your computer. Or how could MiKTeX be able to syncronize the updating system and the package management system?

Best and securest way to use two different version of MiKTeX is to use two virtual maschines, one for each version.

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