Add flatpak permissions command. Requires reboot.

Wabbajack-on-Steam-Deck-Linux-via-Bottles.md

@@ -15,7 +15,7 @@ This guide covers how to run Wabbajack in a Bottles environment. The process is
 
 Thanks to advancements with Wine, it now appears that running Wabbajack on Linux is a viable option - though please understand that there won't be any guarantee of 100% compatibility. As it stands, it's 'good enough' to be able to install a Wabbajack modlist. Starting with Wine v9.15, it seems that only a few steps are required to successfully run the Wabbajack application, login to Nexusmods via the GUI, then download and install a modlist. Wabbajack on Linux requires a version of Wine newer than 9.15 and this isn't really possible on Steam Deck without disabling the OS protection. However, we can use an application called Bottles to run a Wine environment with the required version.
 
-The following must be run in Desktop mode if you are carrying out these steps on Steam Deck. 
+The following must be run in Desktop mode if you are carrying out these steps on Steam Deck.
 
 
 ---
@@ -120,7 +120,11 @@ Wabbajack needs a couple of additional things installed into the Wine prefix - M
 
 Scroll down and click the Download arrow next to both Gecko and Mono, allowing each to download and install. This can take a little time.
 
+Install Gecko:
+
 <img src="https://github.com/Omni-guides/Wabbajack-Modlist-Linux/blob/main/images/WabbajackBottles/WabbajackBottles_Gecko.png" width="600">
+  
+Then install Mono:
 
 <img src="https://github.com/Omni-guides/Wabbajack-Modlist-Linux/blob/main/images/WabbajackBottles/WabbajackBottles_Mono.png" width="600">
 
@@ -172,7 +176,22 @@ Finally, click the back arrow in the top left to return to the main Bottles wind
 ---
 
 
-### Step 9 - Add and configure Wabbajack as an application
+### Step 9 - Set flatpak permissions for Bottles, and reboot
+
+If you are running the flatpak version of bottles, you will need to set permissions for the flatpak Bottles app to have access to your home directory, and the Wabbajack directory. If you have used a different path, or are running the flatpak version of Bottles on a general Linux system, you will need to adapt the following command to suit:
+
+```
+flatpak override --user com.usebottles.bottles --filesystem=/home/deck
+```
+
+**Unfortunately, the only way I have been able to get these permissions to be re-read, is to _reboot the deck_, then switch back to Desktop mode after the reboot, and continue with the remaining steps.** The same may be required on general Linux systems using flatpak Bottles, at least until I find a way to re-read the flatpak permissions.
+
+
+---
+
+
+### Step 10 - Add and configure Wabbajack as an application
+
 
 Even though the Bottle environment must be set as Windows 7 for the Nexus Login page to work, the rest of the Wabbajack application needs to run as Windows 10. To do this we must add Wabbajack.exe as an application, and then set it to be Windows 10.
 
@@ -196,7 +215,7 @@ Lastly, we need to set Wabbajack to use the Windows 10 version. Click Wabbajack.
 ---
 
 
-### Step 10 - Symlink Steam Library
+### Step 11 - Symlink Steam Library
 
 TO get Wabbajack to detect games as being installed, we must link our Linux Steam Library from Linux into the Bottles prefix. If you have been following the steps exactly, the prefix will exist at `/home/deck/Wabbajack/Wabbajack`, so the command to link the Steam Library will be (on internal storage):
 
@@ -214,7 +233,7 @@ ln -s /run/media/mmcblk0p1/SteamLibrary "$HOME/Wabbajack/Wabbajack/drive_c/Progr
 ---
 
 
-### Step 11 - Add shortcut for Wabbajack.exe
+### Step 12 - Add shortcut for Wabbajack.exe
 
 To make it easier to start Wabbajack, we can add it as a shortcut. From the main Bottles window, click the Add "Shortcuts..." button.
 
@@ -229,7 +248,7 @@ Browse to the location of Wabbajack.exe downloaded in Step 1, which for me is `/
 ---
 
 
-### Step 12 - Run Wabbajack
+### Step 13 - Run Wabbajack
 
 At last, we can finally run the Wabbajack application. Click the Play button next to the new Wabbajack shortcut: