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Now I'd like to map the Green ,Blue, Red and Yellow keys to directly launch applications whilst using the remote buddy activity, can this be done and how.
Sure, this can be done. If you want these buttons to only do one thing - launch these apps - then:
1) Go to Prefs > Mapping > Global mapping
2) Select the respective action "Behaviour > Activate [name of app] Behaviour" for the respective buttons
BTW I have also paired the Harmony bluetooth keyboard which also needs re-mapping, it works but the trackpad is not active. but to get it to work i had to add either a device as Plex or a device as Apple computer. I'm a little lost how to get both working smoothly with Remote buddy.
Due to the design of the OS X Bluetooth stack, you're likely to run into issues when trying to pair the same Harmony Hub with two different identities (PS3 Remote, Keyboard, ..) to the same Mac. For details, please see "4. soft keyboard pairing" in this FAQ:
https://www.iospirit.com/support/faqs/remotebuddy/category/23/Hardware-Harmony-Smart-Control/entry/261/Nothing-happens-when-I-press-a-button-on-the-Smart-Control-/
Cheers,
Felix