If the project explorer shows the hidden files in from your revision control system (.hg or .svn directory), or there are too many files from Altera Quatrus or Xilinx ISE that clutter the project explorer, you can hide those files from view:

Select the View Menu (small triangle pointing down) > Customize View > Filters.
Customize View

Now you can filter out hidden files (`.* resources`) or `All non VHDL Files`.