I'm still having issues with opening links from other programs; using Waterfox 15.0, and also the pinned menu items being default icons and not working.
I've dug around in the registry, and I've found (I think) a smoking gun:
has it's default value set to:
"C:\Program Files\Waterfox\firefox.exe" -requestPending -osint -url "%1"
This would, on the face of it appear to be a bit of a problem. I don't have a firefox.exe in that folder. However, if I create a symbolic link to waterfox.exe from firefox.exe, everything starts working correctly.
I think that although the Waterfox branding inside the executable itself is good, it seems that there's a string substitution missing in the installer, making it point to firefox.exe instead of the (correct) waterfox.exe.
If I change the text "firefox.exe" in this registry entry to "waterfox.exe" then URLs clicked from other applications start working again.
The only way I can get the jumplist from the taskbar working correctly is by creating the aforementioned symlink from firefox.exe to waterfox.exe in the porgram's install directory.
I'll assume (but haven't dug for yet - as I'm unsure how they work) that the jumplists are likewise a little wrong, thanks to the installer.
Other keys I've found which reference firefox (I don't have firefox installed on my computer) are:
Similarly, all these values in HKEY_CURRENT_USER.
HKEY_CURRENT_USER\Software\Clients\StartMenuInternet has a Default value of "FIREFOX.EXE"
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\App Paths\firefox.exe has a default value containing "c:\Program Files\Waterfox\firefox.exe"
HKEY_LOCAL_MACHINE\SOFTWARE\Mozilla\Waterfox\13.0 (en-US)\Main has a value "PathToExe" which contains "c:\Program Files\Waterfox\firefox.exe"
HKEY_LOCAL_MACHINE\SOFTWARE\Mozilla\Waterfox\13.0\bin has a value "PathToExe" which contains "c:\Program Files\Waterfox\firefox.exe"
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Clients\StartMenuInternet\FIREFOX.EXE\Capabilities has a value "ApplicationIcon" with the value: "C:\Program Files\Waterfox\firefox.exe,0"
There are a fair number of places where the string "C:\Program Files\Waterfox\Firefox.exe" appears; too many to list here, but I give you this list as an indication that something seems to have gone wrong with the installer somewhere.