Why shouldn’t I modify the files in the system runtime directory?
Just be careful about modifying files under $VIMRUNTIME, which usually is /usr/share/vim/vimXX (Unix) or C:\Program Files\vim\vimXX (Windows) and XX being the version for which it applies, e.g. 73 for Vim 7.3. One should generally avoid modifying those files because they may be replaced during an upgrade of your Vim installation and your changes will be lost. Also, if you upgrade to a new major or minor revision of Vim (e.g., from 7.3 to 7.4), the new version of Vim will use a different $VIMRUNTIME directory and while your changes won’t be lost, they will be ignored. Consequently, take a look at filetypes for an explanation of several ways to modify Vim’s response to different filetypes and where to put those modifications so that they will not be overwritten.