This question is based on a Linux install, but I’ll add here for posterity that it works for Windows as well.
I like to install apps in particular directories (not the Windows default), and I was struggling to get PyCharm CE to show up as a pane in navigator. This post provided the clue I needed. I reinstalled, let the system put PyCharm in the default location, and it popped right up on Navigator.
This is dumb and frustrating - the Anaconda team needs to fix this (so that the app can be installed anywhere and still work), or update documentation to indicate that Anaconda is looking in the default locations.