How can I configure firefox to open links in the same window, but requests from external applications in a new window?
GoTo about:config and change
Browser.link.open_external = 2 or 3
to 1 instead of 2 or 3.
It worked for me on Firefox 64 (Linux Mint 19.1).
In the config menu, set browser.link.open_external to 2.
MozillaZine documentation
EDIT: The above method only works for pre-3.5 versions of Firefox, and for SeaMonkey. See also:
advanced.system.supportDDEExec
Make Firefox open URLs passed from external applications in new tabs
Bug 172962 - Options for where to open URLs from other applications (reuse tab, new tab, new window)