Split settings out from syntax into proper files and add missing settings

Takes several non-syntax settings out of the syntax file and puts them in their standard files so vim will behave properly (e.g., users with filetype indent disabled will not have their indent settings overridden, and any users with syntax disabled would still have other settings applied).

Also adds standard guards for `b:did_ftplugin` and `b:did_indent`, and overrides a few previously-missing settings that ever ftplugin should override (formatoptions-=t, comments, commentstring).