now possible to clone/create repository in a given external directory.

*issues*:
  - not possible to switch between external/local directory without closing the app. (PasswordRepository is a singleton, has to be cleaned when a change is made)

app/src/main/AndroidManifest.xml

@@ -1,7 +1,9 @@
 <?xml version="1.0" encoding="utf-8"?>
 <manifest xmlns:android="http://schemas.android.com/apk/res/android"
 	package="com.zeapo.pwdstore">
-
+    <uses-permission android:name="android.permission.INTERNET" />
+    <uses-permission android:name="android.permission.READ_EXTERNAL_STORAGE"/>
+    <uses-permission android:name="android.permission.WRITE_EXTERNAL_STORAGE"/>
 	<application android:allowBackup="true" android:icon="@drawable/ic_launcher"
 		android:label="@string/app_name" android:theme="@style/AppTheme">
 		<activity android:name=".PasswordStore" android:label="@string/app_name">
@@ -34,8 +36,4 @@
         <activity android:name="net.rdrei.android.dirchooser.DirectoryChooserActivity" />
 	</application>
 
-	<uses-permission android:name="android.permission.INTERNET" />
-    <uses-permission android:name="android.permission.READ_EXTERNAL_STORAGE"/>
-    <uses-permission android:name="android.permission.WRITE_EXTERNAL_STORAGE" />
-
 </manifest>

app/src/main/java/com/zeapo/pwdstore/PasswordStore.java

@@ -47,9 +47,31 @@ public class PasswordStore extends ActionBarActivity  {
     @Override
     public void onResume(){
         super.onResume();
-        // create the repository static variable in PasswordRepository
-        PasswordRepository.getRepository(new File(getFilesDir() + this.getResources().getString(R.string.store_git)));
+        File dir = null;
 
+        if (settings.getBoolean("git_external", false)) {
+            if (settings.getString("git_external_repo", null) == null)
+            {
+                // todo: show the main screen
+            } else {
+                dir = new File(settings.getString("git_external_repo", null));
+            }
+        } else {
+            dir = new File(getFilesDir() + "/store");
+        }
+        assert dir != null;
+
+        // uninitialize the repo if the dir does not exist or is absolutely empty
+        if (!dir.exists() || !dir.isDirectory()) {
+            settings.edit().putBoolean("repository_initialized", false).apply();
+        }
+
+        if (!PasswordRepository.getPasswords(dir).isEmpty()) {
+            settings.edit().putBoolean("repository_initialized", true).apply();
+        }
+
+        // create the repository static variable in PasswordRepository
+        PasswordRepository.getRepository(new File(dir.getAbsolutePath() + "/.git"));
         checkLocalRepository();
     }
 
@@ -192,7 +214,8 @@ public class PasswordStore extends ActionBarActivity  {
     private void createRepository() {
 //        final String keyId = settings.getString("openpgp_key_ids", "");
 
-        File localDir = new File(getFilesDir() + "/store/");
+        File localDir = PasswordRepository.getWorkTree();
+
         localDir.mkdir();
         try {
             PasswordRepository.createRepository(localDir);
@@ -239,8 +262,7 @@ public class PasswordStore extends ActionBarActivity  {
         FragmentManager fragmentManager = getFragmentManager();
         FragmentTransaction fragmentTransaction = fragmentManager.beginTransaction();
 
-        // TODO: Remove the getpaswords() as it is a temporary fix until every user has the repository_initialized set
-        if (settings.getBoolean("repository_initialized", false) || PasswordRepository.getPasswords(localDir).size() > 0) {
+        if (settings.getBoolean("repository_initialized", false)) {
             // do not push the fragment if we already have it
             if (fragmentManager.findFragmentByTag("PasswordsList") == null) {
 
@@ -249,7 +271,6 @@ public class PasswordStore extends ActionBarActivity  {
                     fragmentManager.popBackStack();
                 }
 
-                PasswordRepository.setInitialized(true);
                 plist = new PasswordFragment();
                 Bundle args = new Bundle();
                 args.putString("Path", PasswordRepository.getWorkTree().getAbsolutePath());

app/src/main/java/com/zeapo/pwdstore/git/GitActivity.java

@@ -432,8 +432,7 @@ public class GitActivity extends ActionBarActivity {
      * @param view
      */
     public void cloneRepository(View view) {
-        localDir = new File(getApplicationContext().getFilesDir().getAbsoluteFile() + "/store");
-
+        localDir = PasswordRepository.getWorkTree();
         hostname = ((EditText) findViewById(R.id.clone_uri)).getText().toString();
         port = ((EditText) findViewById(R.id.server_port)).getText().toString();
         // don't ask the user, take off the protocol that he puts in

app/src/main/java/com/zeapo/pwdstore/utils/PasswordRepository.java

@@ -5,8 +5,8 @@ import android.util.Log;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.filefilter.FileFilterUtils;
 import org.eclipse.jgit.api.Git;
-import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.transport.RefSpec;
 import org.eclipse.jgit.transport.RemoteConfig;
@@ -49,11 +49,7 @@ public class PasswordRepository {
     }
 
     public static boolean isInitialized() {
-        return initialized;
-    }
-
-    public static void setInitialized(boolean v) {
-        initialized = v;
+        return repository != null;
     }
 
     public static void createRepository(File localDir) throws Exception{
@@ -112,6 +108,7 @@ public class PasswordRepository {
 
     public static void closeRepository() {
         repository.close();
+        repository = null;
     }
 
     public static ArrayList<File> getFilesList(){
@@ -130,15 +127,6 @@ public class PasswordRepository {
         return repository.getWorkTree();
     }
 
-    /**
-     * Gets a file from the working tree
-     * @param name the relative path of the file
-     * @return the file in the repository
-     */
-    public static File getFile(String name) {
-        return new File(repository.getWorkTree() + "/" + name);
-    }
-
     /**
      * Gets the .gpg files in a directory
      * @param path the directory path