The tools package's information states that there should be a lot of packages included, e.g. tabularx. After installing and looking in the package, only amsmath files are found, but no other files. The version from 04/04/2016 contains only 30 files.
Packaged on: 4/4/2016 7:15:30 PM
Number of files: 30
Size on disk: 2.66 MB
As the tools package contains a lot of basic packages (e.g. array, calc, longtable) this should be corrected as soon as possible.
Possible workaround: install tools source from CTAN and run pdflatex tools.ins to create the files; copy missing .sty files in MiKTeX installation directory (make a new tools directory) and refresh FNDB.
An easier work-around is to get the tds.zip (http://mirrors.ctan.org/install/macros/latex/required/latex-tools.tds.zip), unpack it somewhere outside miktex and then register it in miktex settings as a new root.
And amsmath package should not be in the tools package...