diff --git a/.github/workflows/generate-builds.yml b/.github/workflows/generate-builds.yml
index 40c63424bc..2148ce3f53 100644
--- a/.github/workflows/generate-builds.yml
+++ b/.github/workflows/generate-builds.yml
@@ -165,7 +165,6 @@ jobs:
         cmake --build build-cmake --config Release -j4
         (cd build-cmake && cpack -G External)
 
-        mv README.md readme.txt
         mv build-cmake/*.appimage soh.appimage
       env:
         CC: gcc-12
@@ -174,9 +173,7 @@ jobs:
       uses: actions/upload-artifact@v7
       with:
         name: soh-linux
-        path: |
-          soh.appimage
-          readme.txt
+        path: soh.appimage
     - name: Save Cache deps folder
       if: ${{ github.ref_name == github.event.repository.default_branch }}
       uses: actions/cache/save@v5
diff --git a/README.md b/README.md
index 4dd7f0315b..70a4fafb0d 100644
--- a/README.md
+++ b/README.md
@@ -21,27 +21,14 @@ You can verify you have dumped a supported copy of the game by using the compati
 * Launch `soh.exe`
 
 #### Linux
-* Place your supported copy of the game in the same folder as the appimage.
 * Execute `soh.appimage`.  You may have to `chmod +x` the appimage via terminal.
+* When prompted, select your supported copy of the game.
+* Saves, settings and `oot.o2r` are stored in `~/.local/share/soh/`. If the folder you launch from already has `shipofharkinian.json`, `oot.o2r` or `oot-mq.o2r`, that folder is used instead. Set `SHIP_HOME` to choose another folder.
 
 #### macOS
 * Run `soh.app`. When prompted, select your supported copy of the game.
 * You should see a notification saying `Processing OTR`, then, once the process is complete, you should get a notification saying `OTR Successfully Generated`, then the game should start.
 
-#### Nintendo Switch
-* Run one of the PC releases to generate an `oot.o2r` and/or `oot-mq.o2r` file. After launching the game on PC, you will be able to find these files in the same directory as `soh.exe` or `soh.appimage`. On macOS, these files can be found in `/Users/<username>/Library/Application Support/com.shipofharkinian.soh/`
-* Copy the files to your sd card
-```
-sdcard
-└── switch
-    └── soh
-        ├── oot-mq.o2r
-        ├── oot.o2r
-        ├── soh.nro
-        └── soh.o2r
-```
-* Launch via Atmosphere's `Game+R` launcher method.
-
 ### 4. Play!
 
 Congratulations, you are now sailing with the Ship of Harkinian! Have fun!
diff --git a/soh/soh/Extractor/Extract.cpp b/soh/soh/Extractor/Extract.cpp
index b4c98f3927..4e6e26b768 100644
--- a/soh/soh/Extractor/Extract.cpp
+++ b/soh/soh/Extractor/Extract.cpp
@@ -257,15 +257,15 @@ void Extractor::GetRoms(std::vector<std::string>& roms) {
         // Go through each file in the directory
         while ((dir = readdir(d)) != NULL) {
             struct stat path;
+            std::string fullPath = mSearchPath + "/" + dir->d_name;
 
             // Check if current entry is not folder
-            stat(dir->d_name, &path);
-            if (S_ISREG(path.st_mode)) {
+            if (stat(fullPath.c_str(), &path) == 0 && S_ISREG(path.st_mode)) {
 
                 // Get the position of the extension character.
                 char* ext = strrchr(dir->d_name, '.');
                 if (ext != NULL && (strcmp(ext, ".z64") == 0 || strcmp(ext, ".n64") == 0 || strcmp(ext, ".v64") == 0)) {
-                    roms.push_back(dir->d_name);
+                    roms.push_back(fullPath);
                 }
             }
         }
diff --git a/soh/soh/OTRGlobals.cpp b/soh/soh/OTRGlobals.cpp
index 30b7dcd910..0341e4f366 100644
--- a/soh/soh/OTRGlobals.cpp
+++ b/soh/soh/OTRGlobals.cpp
@@ -2,6 +2,7 @@
 #include "OTRAudio.h"
 #include <algorithm>
 #include <atomic>
+#include <cstdlib>
 #include <filesystem>
 #include <fstream>
 #include <vector>
@@ -1545,7 +1546,44 @@ bool VerifyArchiveVersion(OTRVersion version) {
     return version.major != INT16_MAX && version.major != gBuildVersionMajor;
 }
 
+#ifdef __linux__
+// When run as an AppImage, keep user data in ~/.local/share/soh instead of the launch folder.
+// Keep using the launch folder if it already has data from older versions.
+static void SetAppImageHome() {
+    if (getenv("APPIMAGE") == nullptr || getenv("SHIP_HOME") != nullptr) {
+        return;
+    }
+
+    for (const char* file : { "shipofharkinian.json", "oot.o2r", "oot-mq.o2r" }) {
+        if (std::filesystem::exists(file)) {
+            return;
+        }
+    }
+
+    std::filesystem::path home;
+    const char* dataHome = getenv("XDG_DATA_HOME");
+    const char* userHome = getenv("HOME");
+    if (dataHome != nullptr && std::filesystem::path(dataHome).is_absolute()) {
+        home = dataHome;
+    } else if (userHome != nullptr && userHome[0] != '\0') {
+        home = std::filesystem::path(userHome) / ".local" / "share";
+    } else {
+        return;
+    }
+    home /= appShortName;
+
+    std::error_code ec;
+    std::filesystem::create_directories(home, ec);
+    if (!ec) {
+        setenv("SHIP_HOME", home.c_str(), 0);
+    }
+}
+#endif
+
 extern "C" void InitOTR(int argc, char* argv[]) {
+#ifdef __linux__
+    SetAppImageHome();
+#endif
     OTRGlobals::Instance = new OTRGlobals();
     OTRGlobals::Instance->RunExtract(argc, argv);