It is expected behaviour that any changes made to a core file will be lost
when an upgrade is performed.

On 9 November 2015 at 11:34, haya1300 notifications@github.com wrote:

Steps to reproduce the issue

Make a new site with custom.css made changes in de Protostar template
Make in the index.php the following changes:

// Add Stylesheets
$doc->addStyleSheet('templates/'.$this->template.'/css/template.css');

Just below these two lines, add the following:

$doc->addStyleSheet('templates/'.$this->template.'/css/custom.css');

Make in de css folder a new file named: custom.css and put there the new
css declarations
This is the way I have learned to make template overrides
Actual result

Then after upgrading to 3.5 all change are gone.
System information (as much as possible)

Database versie 5.6.21
PHP versie 5.6.3
Webserver Apache/2.4.10 (Win32) OpenSSL/1.0.1i PHP/5.6.3
WebServer naar PHP interface apache2handler
Joomla! versie Joomla! 3.5.0-beta Beta [ Ember ] 06-November-2015 24:00 GMT
Joomla! Platform versie Joomla Platform 13.1.0 Stable [ Curiosity ]
24-Apr-2013 00:00 GMT
Additional comments

To fix the problem go to the index.php file from the template and change
the user.css to custom.css (twice)
So I prefer to use custom.css instead user.css

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#8357.

Brian Teeman
Co-founder Joomla! and OpenSourceMatters Inc.
http://brian.teeman.net/

@haya1300

We have a user.css here: https://github.com/joomla/joomla-cms/blob/staging/templates/protostar/index.php#L48-L54 that dues the same as custom.css ;) We need to use the user.css and can't use the custom.css as there are places we use custom.css for changes to the TinyMCE as pointed out by @infograf768

Feel free to copy your template (there is a easy way in the Backend Template manger) and change everything you want. This copy is also not affected by any future update. (so a update will never change anything you changed)

Docu can be found here: https://docs.joomla.org/J3.x:Modifying_a_Joomla!_Template#Copy_the_Template

Thanks for understanding I'm going to close this issue now as Expected Behavior