diff --git a/config.sample.py b/config.sample.py
index 85c17d50..0231625b 100644
--- a/config.sample.py
+++ b/config.sample.py
@@ -85,9 +85,15 @@ keyaliases['com.example.app'] = 'example'
 #the @ prefix.
 keyaliases['com.example.another.plugin'] = '@com.example.another'
 
-#The ssh path to the server's public web root directory. This is used for
-#uploading data, etc.
-serverwebroot = 'user@example:/var/www/repo'
+# The full path to the root of the repository.  It must be specified in
+# rsync/ssh format for a remote host/path. This is used for syncing a locally
+# generated repo to the server that is it hosted on.  It must end in the
+# standard public repo name of "/fdroid", but can be in up to three levels of
+# sub-directories (i.e. /var/www/packagerepos/fdroid).
+serverwebroot = 'user@example:/var/www/fdroid'
+
+# If you want to force 'fdroid server' to use a non-standard serverwebroot
+#nonstandardwebroot = True
 
 #Wiki details
 wiki_protocol = "http"
diff --git a/fdroidserver/init.py b/fdroidserver/init.py
index 09125551..26bc897d 100644
--- a/fdroidserver/init.py
+++ b/fdroidserver/init.py
@@ -102,12 +102,12 @@ def main():
         prefix = tmp
         examplesdir = prefix
 
-    repodir = os.getcwd()
+    fdroiddir = os.getcwd()
 
     if not os.path.exists('config.py') and not os.path.exists('repo'):
         # 'metadata' and 'tmp' are created in fdroid
         os.mkdir('repo')
-        shutil.copy(os.path.join(examplesdir, 'fdroid-icon.png'), repodir)
+        shutil.copy(os.path.join(examplesdir, 'fdroid-icon.png'), fdroiddir)
         shutil.copyfile(os.path.join(examplesdir, 'config.sample.py'), 'config.py')
         os.chmod('config.py', 0o0600)
     else:
@@ -206,13 +206,14 @@ def main():
             write_to_config('keydname', keydname)
         genkey(keystore, repo_keyalias, password, keydname)
 
-    print('Built repo in "' + repodir + '" with this config:')
+    print('Built repo based in "' + fdroiddir + '"')
+    print('with this config:')
     print('  Android SDK:\t\t\t' + sdk_path)
     print('  Android SDK Build Tools:\t' + os.path.dirname(aapt))
     print('  Android NDK (optional):\t' + ndk_path)
     print('  Keystore for signing key:\t' + keystore)
     print('\nTo complete the setup, add your APKs to "' +
-          os.path.join(repodir, 'repo') + '"' +
+          os.path.join(fdroiddir, 'repo') + '"' +
 '''
 then run "fdroid update -c; fdroid update".  You might also want to edit
 "config.py" to set the URL, repo name, and more.  You should also set up
diff --git a/fdroidserver/server.py b/fdroidserver/server.py
index 5a6cc61d..43ea05fd 100644
--- a/fdroidserver/server.py
+++ b/fdroidserver/server.py
@@ -26,6 +26,7 @@ import common
 config = None
 options = None
 
+
 def main():
 
     global config, options
@@ -42,8 +43,22 @@ def main():
         print "Specify a single command"
         sys.exit(1)
 
-    if args[0] != 'update':
-        print "The only command currently supported is 'update'"
+    if args[0] != 'init' and args[0] != 'update':
+        print "The only commands currently supported are 'init' and 'update'"
+        sys.exit(1)
+
+    serverwebroot = config['serverwebroot'].rstrip('/').replace('//', '/')
+    host, fdroiddir = serverwebroot.split(':')
+    serverrepobase = os.path.basename(fdroiddir)
+    if 'nonstandardwebroot' in config and config['nonstandardwebroot'] == True:
+        standardwebroot = False
+    else:
+        standardwebroot = True
+    if serverrepobase != 'fdroid' and standardwebroot:
+        print('ERROR: serverwebroot does not end with "fdroid", '
+              + 'perhaps you meant one of these:\n\t'
+              + serverwebroot.rstrip('/') + '/fdroid\n\t'
+              + serverwebroot.rstrip('/').rstrip(serverrepobase) + 'fdroid')
         sys.exit(1)
 
     repodirs = ['repo']
@@ -51,21 +66,27 @@ def main():
         repodirs.append('archive')
 
     for repodir in repodirs:
-        index = os.path.join(repodir, 'index.xml')
-        indexjar = os.path.join(repodir, 'index.jar')
-        if subprocess.call(['rsync', '-u', '-v', '-r', '--delete',
-                '--exclude', index, '--exclude', indexjar, repodir, config['serverwebroot']]) != 0:
-            sys.exit(1)
-        if subprocess.call(['rsync', '-u', '-v', '-r', '--delete',
-                index, config['serverwebroot'] + '/' + repodir]) != 0:
-            sys.exit(1)
-        if subprocess.call(['rsync', '-u', '-v', '-r', '--delete',
-                indexjar, config['serverwebroot'] + '/' + repodir]) != 0:
-            sys.exit(1)
+        if args[0] == 'init':
+            if subprocess.call(['ssh', '-v', host,
+                                'mkdir -p', fdroiddir + '/' + repodir]) != 0:
+                sys.exit(1)
+        elif args[0] == 'update':
+            index = os.path.join(repodir, 'index.xml')
+            indexjar = os.path.join(repodir, 'index.jar')
+            if subprocess.call(['rsync', '-u', '-v', '-r', '--delete',
+                                '--exclude', index, '--exclude', indexjar,
+                                repodir, config['serverwebroot']]) != 0:
+                sys.exit(1)
+            if subprocess.call(['rsync', '-u', '-v', '-r', '--delete',
+                                index,
+                                config['serverwebroot'] + '/' + repodir]) != 0:
+                sys.exit(1)
+            if subprocess.call(['rsync', '-u', '-v', '-r', '--delete',
+                                indexjar,
+                                config['serverwebroot'] + '/' + repodir]) != 0:
+                sys.exit(1)
 
     sys.exit(0)
 
 if __name__ == "__main__":
     main()
-
-