docs: clarify desktop vs kubo config paths

README.md

@@ -233,16 +233,25 @@ $ ipfs-desktop --no-sandbox
 
 ### Where are my IPFS configuration and log files?
 
-You can open these files from the IPFS logo menu by selecting `Open Logs Directory` or `Open Configuration File` from the `Advanced` submenu. Or, find them in your OS as follows:
+> [!IMPORTANT]
+> IPFS Desktop app configuration is separate from the configuration and repository of Kubo IPFS node.
+
+You can open Desktop app and log files from the IPFS logo menu by selecting `Open Logs Directory` or `Open Configuration File` from the `Advanced` submenu. Or, find them in your OS as follows:
 - **Mac:** `~/Library/Application Support/IPFS Desktop/`
 - **Windows:** `%appdata%/IPFS Desktop/`
 - **Linux:** `~/.config/IPFS Desktop/`
 
 ### How does IPFS Desktop select the IPFS repo location?
 
-IPFS Desktop uses [ipfsd-ctl](https://github.com/ipfs/js-ipfsd-ctl), which, by default, checks the `IPFS_PATH` environment variable. If that isn't set, it falls back to `$HOME/.ipfs`. As soon as the first run has succeeded, repository location info is saved in the configuration file, which becomes the source of truth.
+> [!IMPORTANT]
+> IPFS Desktop uses [Kubo](https://github.com/ipfs/kubo) implementation of IPFS node, which has its own configuration and repository, separate from the Desktop app.
+
+IPFS Desktop uses [ipfsd-ctl](https://github.com/ipfs/js-ipfsd-ctl) to locate Kubo repository.
+
+1. First, it checks the `IPFS_PATH` environment variable.
+2. If that isn't set, it falls back to `$HOME/.ipfs`. As soon as the first run has succeeded, repository location info is saved in the configuration file, which becomes the source of truth.
 
-To open your repo directory from the IPFS logo menu, select `Open Repository Directory` from the `Advanced` submenu.
+To open your Kubo repo directory from the IPFS logo menu, select `Open Repository Directory` from the `Advanced` submenu.
 
 ### Which version of IPFS does IPFS Desktop use?