Document backwards incompatible changes, like --chain -> --keep-chain

[speleo3]

I just noticed that the PROPKA 2.1 --chain argument is now --keep-chain (changed in 6f733072be5ee6dfdbe841eb0a8ab7bb7c9b9d24), and --chain now takes an argument and has a different meaning (is handled by PROPKA). This is neither mentioned in https://github.com/Electrostatics/pdb2pqr/blob/master/ChangeLog.md nor in https://github.com/Electrostatics/pdb2pqr/blob/master/docs/releases.rst

[sobolevnrm]

I agree. I will make the change when I have the time... unless anyone else beats me to it. :)

Thanks!