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I thought this had been resolved at some point after the discussion on bug 33912, but the Mac installer for the Mono framework, as of "4.6 Service Release 1 (126.96.36.199)", does not seem to check for and create /usr/local/ and /usr/local/bin/ if they do not exist. The 'mono' command ends up being unavailable from the command line because the shortcuts to the actual framework are not created anywhere within reach of bash's $PATH. These two directories do not exist by default in macOS.
P.S.: Is the install script anywhere on GitHub? I'm currently inspecting it as part of the actual .pkg I downloaded because I can't find it on the repo.
This is an intended change, see http://www.mono-project.com/docs/about-mono/releases/4.4.1/#changes-in-the-osx-installation-package
We no longer install anything into /usr/local/bin, but instead use /etc/paths.d/mono-commands for adding the "/Library/Frameworks/Mono.framework/Versions/Current/Commands" path to PATH (which should get run automatically by your shell).
Depending on how you start your shell/script this might not get executed, in those cases you can either run the eval() script mentioned in the link I posted above or modify PATH manually.
The (post)install script is available here: https://github.com/mono/mono/blob/master/packaging/MacSDK/packaging/resources/postinstall