Add an 'upgrading' note about the plugin re-layout

docs/UPGRADING.md

@@ -13,6 +13,7 @@ If any of this does not make sense to you, or you have trouble updating your .in
     - [Bidirectional communication for plugins](#bidirectional-communication-for-plugins)
     - [Consistent timing](#consistent-timing)
   + [Breaking changes](#breaking-changes)
+    - [git checkouts aren't compatible with Arduino IDE (GUI)]([#repository-rearchitecture)
     - [Layer system switched to activation-order](#layer-system-switched-to-activation-order)
     - [The `RxCy` macros and peeking into the keyswitch state](#the-rxcy-macros-and-peeking-into-the-keyswitch-state)
     - [HostOS](#hostos)
@@ -323,6 +324,14 @@ As a developer, one can continue using `millis()`, but migrating to `Kaleidoscop
 
 ## Breaking changes
 
+### Repository rearchitecture
+
+To improve build times and to better highlight Kaleidoscope's many plugins, plugins have been move into directories inside the Kaleidoscope directory. 
+
+The "breaking change" part of this is that git checkouts of Kaleidoscope are no longer directly compatible with the Arduino IDE, since plugins aren't in a directory the IDE looks in. They are, of course, visible to tools using our commandline build infrastructure / Makefiles.
+
+When we build releases, those plugins are moved into directories inside the arduino platform packages for each architecture to make them visible to the Arduino IDE.
+
 ### Layer system switched to activation order
 
 The layer system used to be index-ordered, meaning that we'd look keys up on