Don't encode URL's in [code] blocks.
An example:
[code]
% git clone https://github.com/pallets/werkzeug.git
[/code]
Will be rendered like this:
% git clone [url=https://github.com/pallets/werkzeug.git]https://github.com/pallets/werkzeug.git[/url]
While the expected result would be:
% git clone https://github.com/pallets/werkzeug.git