Use AddJsLink to set and add a JS Link file.

var scriptLinksEnumerable = scriptLinks as string[] ?? scriptLinks.ToArray();
if (scriptLinksEnumerable.Length == 1)
{
    var scriptSrc = scriptLinksEnumerable[0];
    if (!scriptSrc.StartsWith("http", StringComparison.InvariantCultureIgnoreCase))
    {
        var serverUri = new Uri(site.Context.Url);
        if (scriptSrc.StartsWith("/"))
        {
            scriptSrc = $"{serverUri.Scheme}://{serverUri.Authority}{scriptSrc}";
        }
        else
        {
            var serverRelativeUrl = string.Empty;
            if (site is Web)
            {
                serverRelativeUrl = ((Web)site).EnsureProperty(w => w.ServerRelativeUrl);
            }
            else
            {
                serverRelativeUrl = ((Site)site).RootWeb.EnsureProperty(w => w.ServerRelativeUrl);
            }
            scriptSrc = $"{serverUri.Scheme}://{serverUri.Authority}{serverRelativeUrl}/{scriptSrc}";
        }
    }

    var customAction = new CustomActionEntity
    {
        Name = key,
        ScriptSrc = scriptSrc,
        Location = SCRIPT_LOCATION,
        Sequence = sequence
    };
    ret = ((Site)site).AddCustomAction(customAction);
}
else
{
    var scripts = new StringBuilder(@" var headID = document.getElementsByTagName('head')[0];
var scripts = document.getElementsByTagName('script');
var scriptsSrc = [];
for(var i = 0; i < scripts.length; i++) {
if(scripts[i].type === 'text/javascript'){
scriptsSrc.push(scripts[i].src);
}
}
");
    foreach (var link in scriptLinksEnumerable)
    {
        if (!string.IsNullOrEmpty(link))
        {
            scripts.Append(@"
if (scriptsSrc.indexOf('{1}') === -1)  {  
var newScript = document.createElement('script');
newScript.id = '{0}';
newScript.type = 'text/javascript';
newScript.src = '{1}';
headID.appendChild(newScript);
scriptsSrc.push('{1}');
}".Replace("{0}", key).Replace("{1}", link));
        }

    }

    ret = AddJsBlockImplementation(site, key, scripts.ToString(), sequence);
}

var scripts = new StringBuilder(@" var headID = document.getElementsByTagName('head')[0];
var scripts = document.getElementsByTagName('script');
var scriptsSrc = [];
for(var i = 0; i < scripts.length; i++) {
    if(scripts[i].type === 'text/javascript'){
        scriptsSrc.push(scripts[i].src);
    }
}");

foreach (var link in scriptLinksEnumerable)
{
    if (!string.IsNullOrEmpty(link))
    {
        scripts.Append(@"
if (scriptsSrc.indexOf('{1}') === -1)  {  
    var newScript = document.createElement('script');
    newScript.id = '{0}';
    newScript.type = 'text/javascript';
    newScript.src = '{1}';
    headID.appendChild(newScript);
    scriptsSrc.push('{1}');
}".Replace("{0}", key).Replace("{1}", link));
    }

}

var jsAction = new CustomActionEntity()
{
    Name = key,
    Location = "ScriptLink",
    ScriptBlock = scripts.ToString(),
    Sequence = sequence
};
AddCustomAction(site, jsAction);

// Example becomes too long

site.AddJsLink(site, key, scriptLinks, 0)