Custom php.ini / my.cnf / nginx.conf files?

Considering 100% of the target audience are developers, I don't think you have to worry too much about scaring us with config files or right clicking a bundle file

That being said, for PHP and MySQL specifically, it might make sense to have a simple textarea where we can dump extra config directives. I'm not 100% sure about MySQL, but I know PHP won't complain about a directive being overridden by a later area.

You would then dump the contents of the textarea into php_A969/etc/php/conf.d/zzzz-override.ini and using this compile-time variable to tell PHP to load additional ini files from that directory: https://www.php.net/manual/en/configuration.file.php#configuration.file.scan

That way, you don't have to ask us to override the entire php.ini file

For Nginx, you already have the /conf/conf.d/*.conf; and /conf/sites-enabled/*; include directives, which means you only have to add a general textarea (to go into /conf/conf.d/zzzz-override.conf;) and a per-site textarea. The per-site textarea needs to default to

    root "/<userpath>/.indigo/welcome";
    index index.php index.html;

    location / {
        try_files $uri $uri/ /index.php?$query_string;
    }

(with a "Reset to default" button) and allow us to completely rewrite this block.

The reason why we need to be able to completely rewrite this block is that different sites may have different URL rewrite requirements. Here's an example of a /conf/sites-enabled/site.conf block for a XenForo 2 devboard:

location /devboards/xf22/ {
    try_files $uri $uri/ /devboards/xf22/index.php?$uri&$args;
    index index.php index.html;
}

location /devboards/xf22/install/data/ {
    internal;
}
location /devboards/xf22/install/templates/ {
    internal;
}
location /devboards/xf22/internal_data/ {
    internal;
}
location /devboards/xf22/library/ { #legacy
    internal;
}
location /devboards/xf22/src/ {
    internal;
}

(This goes above the location ~ \.php$ { part in the sites-enabled config.)

Indigo I'd say removing existing config shouldn't be necessary for anything other than nginx as you noted, because (at least in php.ini) you can always just do some_config_directive= and if that's the "latest" value (i.e. stored in php_A969/etc/php/conf.d/zzzz-override.ini), it should effectively "delete" the existing config.

I would imagine the same kind of "override with blank value" exists in my.cnf for MySQL.

If someone needs even more advanced-er editing than this feature would offer, they can always revert back to the "full config file override" method you detailed above

Sounds good, once this + the XDebug thing is done, I can begin testing in earnest

Indigo Saving the zzz-override.ini via the GUI doesn't cleanly shut down the system stack, giving us the "Port is already in use" error.