there are some ways to deal with it.
1. augeas, but it depends on what application are you using. augeas only works 
when template available. the most common config files are built-in supported 
like sysctl.conf, iptables, httpd.conf. you have to write your own augeas 
template if you are using own apps.
2. template, i think erb template is a good idea. copy config file and add 
variables or ruby codes. as you say, you don't want to use it because you just 
need modify a few part of a big file. so, consider way 3 and 4.
3. erb template can insert any ruby code you want, so save the static part to a 
file, and read it at top of erb template can let you include other file.  but 
template is compiled in master, so the static file must in master and may not 
what you wanted.
4. like sysctl, httpd most apps in linux already have include functions, my 
suggestion is try to find if your app config can include another config file or 
not. if not, can you add it?

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