I have projects set up that rely on symlinks (e.g. where multiple applications depend on the same library as a symlinked folder)

It'd be better to have this as a .phan/config.php setting such as 'ignore_symlinks' defaulting to false (see src/Phan/Config.php)

@TysonAndre well my only problem was that phan crashed when encountering the link. i actually wouldn't mind if phan would follow the link instead of ignoring it.

assuming nobody actually need links to be ignored, do you think we could just do a

                    while ($file_info->isLink()) {
                        // follow links
                        $file_info = new SplFileInfo($file_info->getLinkTarget());
                    }

? perhaps with a max-follow-link thing to protect against infinite link-to-link loop, which would cause the code above to hang - sounds like an extremely rare edge-case, but still, perhaps

                    $link_counter=0;
                    while ($file_info->isLink()) {
                        // follow links
                        $file_info = new SplFileInfo($file_info->getLinkTarget());
                        if(++$link_counter >= 100) {
                            throw new \RuntimeException("infinite link loop");
                        }
                    }

edit: the code above might be incorrect, seems one should use SplFileInfo::getRealPath instead of SplFileInfo::getLinkTarget