Steps to reproduce the issue

1. Install Joomla on a webspace where html_public folder is named "html". There are some shared hosters, even those who claim their hosting packages "Joomla ready"
2. Try to create an layout override for any module/component/layout

Expected result

Successful copy attempt.

Actual result

Copy attempt failes with a list of warnings and an COM_TEMPLATES_OVERRIDE_FAILED error

JFile: :copy(/html/components/[...].php, /html/templates/[...].php): copy(/html//templates/[...].php): failed to open stream: No such file or directory

Please note the double slash between "html" and "templates" on the "output" side.

System information (as much as possible)

Additional comments

JStream::_getFilename (line 1391 and str_1401) does a simple str_replace on $filename to eliminate JPATH_ROOT thus removing all parts of $filename which resemble JPATH_ROOT.

$filename = str_replace(JPATH_ROOT, '', $filename);

should be replaced with something like this:

$pos = strpos($filename, JPATH_ROOT);
if ($pos !== false) {
   $filename = substr_replace($filename, '', $pos, strlen(JPATH_ROOT));
}

so that only the first occurrence gets replaced. This error probably affects any file system operation such as module updates, too.