How to change server cfg on modified server

I'm trying to host a server that I've modified from the gitlabs repo, and though I know you run it using ./all run dedicated how do I specify my server config? I've tried changing the server.cfg that's in the server folder, and I've tried moving it to data as you would with a regular server. 
What's the normal process for doing this?

./all run dedicated expects server config in the same directory as release or autobuild (~/.xonotic/data/server.cfg on linux). It's generally not a good idea to change config files inside the source directory (data/xonotic-data.pk3dir).

I'm trying to host a server that I've modified from the gitlabs repo, and though I know you run it using ./all run dedicated how do I specify my server config? I've tried changing the server.cfg that's in the server folder, and I've tried moving it to data as you would with a regular server. 
What's the normal process for doing this?

You can assign your data folder with "-game data_directory". Mine looks somewhat like this:

Code:

./all run dedicated -sessionid bfgfun -game /home/xonotic/.xonotic/data.bfgfun -game /home/xonotic/additional_maps

So my /home/xonotic/.xonotic looks like this:

Code:

.xonotic/lock.bfgfun
.xonotic/data.bfgfun
.xonotic/data.bfgfun/data/
.xonotic/data.bfgfun/data/........... omit .......
.xonotic/data.bfgfun/curl_urls.txt
.xonotic/data.bfgfun/post-config.cfg
.xonotic/data.bfgfun/server.cfg
.xonotic/data.bfgfun/cvars_servername.txt
.xonotic/data.bfgfun/darkplaces_history.txt
.xonotic/key_0-public-fp.bfgfun.txt
.xonotic/key_0.d0si.bfgfun

My actual setup is a bit more complicated since I run more than one server (one public, one for testing and private games), but with the "-game" option, you can easily assign which folder to find your cfg files.

Thanks for taking the time to help me out!
Right now I'm keeping my server.cfg file in ~/.xonotic/data. When I ran

Code:

./all run dedicated -game ~/.xonotic/data

I got the error 

Code:

Quake Error: Nasty -game name rejected: /home/veecho/.xonotic/data 

Any clue what that means? I've tried changing the directory but it always pops up. Is there some sort of preferred location/naming scheme?

Thanks for taking the time to help me out!
Right now I'm keeping my server.cfg file in ~/.xonotic/data. When I ran

Code:

./all run dedicated -game ~/.xonotic/data

I got the error 

Code:

Quake Error: Nasty -game name rejected: /home/veecho/.xonotic/data 

Any clue what that means? I've tried changing the directory but it always pops up. Is there some sort of preferred location/naming scheme?

Sorry -- I wrote that from my memory. The game directories should be under ~/.xonotic and you only give relative path, i.e. in your case:

Code:

./all run dedicated -game data

~/.xonotic is the default parent folder, and is assumed. I believe you can change it but I never bothered with changing it.