I recently installed Jenkins, using Homebrew. I also installed Mercurial using Homebrew.
I can successfully clone an hg repo just fine - from Terminal. But if I try
You can set PATH in launchd.conf file. See here for details. Note that man launchctl says that 'commands can be stored in $HOME/.launchd.conf or /etc/launchd.conf to be read at the time launchd starts', so you probably can create '.launchd.conf' in your home directory and use instructions from the link with this file. But as far as I know in launchd.conf file you can't add directory to PATH, you can just rewrite PATH.
You can also see here for the solution using /etc/paths.d directory