I'm using the latest binary built from $ go get -u github.com/arduino/arduino-cli.

There seems to be a version conflict between the cores used by Arduino-CLI and the built-in cores in the Arduino IDE.

• IDE 1.8.6 and 1.8.7 come bundled with AVR core 1.6.22/1.6.23 (respectively)
• $ arduino-cli core install arduino:avr installs AVR core 1.6.21, since AVR core 1.6.22/1.6.23 have not been released (don't know why)
• this causes IDE 1.8.6/1.8.7 to revert back to AVR 1.6.21
• now, use the IDE Board Manager to upgrade to AVR 1.6.22/1.6.23
• this causes $HOME/.arduino15/packages/arduino/hardware/avr/1.6.21 to be removed
• which causes $ arduino-cli core list to return an empty list

Possibly related to Issue #28.

(Edited: clarify that IDE 1.8.6 comes bundled with AVR 1.6.22, and IDE 1.8.7 comes with AVR 1.6.23).