This is common error on NuttX, but unfortunately the build system is not clear to explain to the user about it.
$ git clone https://github.com/apache/incubator-nuttx $ cd incubator-nuttx $ ./tools/configure.sh esp32-core:nsh ... This program built for x86_64-pc-linux-gnu Report bugs to bug-make@gnu.org make: *** [tools/Makefile.unix:319: dirlinks] Error 2 ERROR: failed to refresh
This problem happens because you missed to clone the apps/ repository:
$ cd ..
$ git clone https://github.com/apache/incubator-nuttx-apps apps
Now you can configure it correctly:
$ cd incubator-nuttx $ ./tools/configure.sh esp32-core:nsh ... # # configuration written to .config #
Alan C. Assis 
Thanks. I haven’t built NuttX in a while but I’ve saved this link for next time.
You are welcome Celem! I hope you test it soon, it is evolving fast and the new documentation is making things easier: https://nuttx.apache.org/docs/latest/index.html