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Question:
How do I change the default link colors from green to red? Also, how do I remove the logo?

Answer:
Unlike other components, the front end of Project Fork uses the templates of the admin. So, you need to open administrator > components > com_projectfork > themes > default > css > projectfork.css.

Edit:

.pf_navigation td.btn_section a.pf_button
{
color:#YOURCOLOR !important;

Or, you could create a custom theme as described in the documentation of Project Fork.

To remove the logo you can open and edit administrator > components > com_projectfork > themes > default > index.php

Around line 75 change

<div id="theme_logo"><?php $pf_theme->loadPanels('theme_logo'); ?></div>

to...

<div id="theme_logo"><?php //$pf_theme->loadPanels('theme_logo'); ?></div>

Or, remove the line all together.

Another way to just open the logo image resave as a transparent png. You can find it here:

administrator > components > com_projectfork > themes > default > images > logo.png