Such characters are supposed to be encoded for usage in URLs (known as percent-encoding or URL encoding). Browsers like Firefox show the URL in human readable form in the address bar, though when you copy it to the clipboard it is still encoded. There must be something wrong with either where you are getting the links from or plowshare needs a feature to convert and process those links correctly, like similar applications have.
In case of wget proper usage would look like this:
However putting link in single or double qoutes work, as well as escaping the characters in question with
The latter one is the most time-consuming solution, as you have to know which characters to escape and it gets very messy pretty fast.
Of course I was searching for the mesh network routing protocol.