We now have separate leaprc files for proteins, DNA, RNA, water+ions, lipids and carbohydrates. Please consult Chapter 3 in the Amber 2016 Reference Manual for complete details, including our recommendations for each category. The leaprc.water.* files include suggested parameters for monatomic ions that are appropriate for the given water model. To accomplish this, some filenames for ion parameters have been changed--see the Manual, or examine the headers of the frcmod.ions* files, if you need more fine-grained control of ion parameters.
The leaprc.ff14SB has been moved to the oldff subdirectory, but is unchanged from AmberTools15. This means that it can still be used for workflows that benefit from having a "generic" leaprc file, but note that oldff/leaprc.ff14SB does not have the currently-recommended parameters for DNA, and will not be updated as other parts of force fields evolve. Users should make plans to transition away from use of files in the "oldff" subdirectory.