This may be repeated information, but here is how I got my old Harmony One working with my new FireTV. This required no command line configuration, and no copying anything to the FireTV. It seems like the new Flirc firmware addressed many of these things, so most of the help I was looking for in setting it up were out of date.
I got the FireTV mainly to use Kodi, so my setup was centered on that use case.
I had no idea that you could use the Flirc Windows GUI to set up multiple, co-existing profiles on the Flirc - I read that here on these forums, and it made setup easier for me.
I have the latest firmware loaded into the Flirc, the latest update to the FireTV, and the current downloadable version of Kodi as of August 7, 2015.
With that latest configuration, setup was actually quite straightforward...here are the steps I took
1) Add the Flirc device to the Harmony remote.
Using the Harmony desktop software for my ancient Harmony One, I was able to add the Flirc as a Windows Media Center device (Add Device -> Device Type = Windows Media Center, Manufacturer = Flirc, Model = Kodi
2) Create an activity for "FireTV"
I also modified the activity to send a "0" command to the FireTV when I switch to that activity. The "0" button doesn't seem to have any real effect other that waking it up. I didn't want to use "Select" because the One isn't very smart about not sending commands to devices that are already awake, and I didn't want switching to the FireTV from say the TiVo to execute a "Select" command not knowing what it may be selecting... :)
3) Use my WDLive SMP remote to add "learned" commands for "Menu", and "Home", and "Back", and assign them to the desired buttons on the Harmony.
The Flirc configuration for the One within the Harmony software didn't program these buttons to send any IR signal (I may have screwed up but nothing happened on the Flirc GUI when I pressed those buttons, so I assume that no signal was sent). Learning any old IR command from any other remote should work, but I happened to have a WDLive remote handy so I used it.
4) Update the Harmony One remote.
5) Plug the Flirc into the PC and set up the FireTV profile first (in the Flirc GUI).
For my case, I created a virtual button on the LCD of the One called "Home" and used it for "Home". I used the hard buttons "Previous" and "Menu" for "Back" and "Context Menu" respectively.
6) After configuring the FireTV in the Flirc GUI, set up the Kodi profile.
I did not reuse the buttons I used to program the FireTV profile with.
After that, I connected the Flirc to the FireTV using a USB extender I had lying around and everything worked (except for voice commands which I knew wouldn't work anyway). I used this configuration all last night and didn't encounter any repeated button presses, missed presses, or anything. The response was snappy, and it worked for navigating the FireTV's native UI as well as Kodi's UI.
Anyway, this little device is pretty sweet. Would have been sweeter if I got the FireTV first (I got a Fire Stick and returned it to get the FireTV) 'cuz when I had the Stick, the Flirc was on sale on Amazon for $14.99 . Oh well...it was still worth the $19.99 I paid for it!