I am having exactly similar issue as https://github.com/appium/python-client/issues/121
I tried to find answer and I found suggestion to use desired_caps['autoAcceptAlerts'] = True
But this only works if user is in same app as it was launched. If user clicks on deeplink or any link which opens through browser and pops-up alert window it just hangs until timeout.
info: <-- POST /wd/hub/session/9b097c07-9527-4e5f-95a8-a99dba12d9af/element/3/click 200 1204.922 ms - 74 {"status":0,"value":"","sessionId":"9b097c07-9527-4e5f-95a8-a99dba12d9af"}
info: --> POST /wd/hub/session/9b097c07-9527-4e5f-95a8-a99dba12d9af/element {"using":"xpath","sessionId":"9b097c07-9527-4e5f-95a8-a99dba12d9af","value":"//UIAbutton[@name='Open']"}
info: [debug] Waiting up to 0ms for condition
info: [debug] Pushing command to appium work queue: "au.mainApp().getTreeForXML()"
info: [debug] Sending command to instruments: au.mainApp().getTreeForXML()
info: [debug] [INST] 2016-07-28 21:42:23 +0000 Debug: evaluation finished
info: [debug] [INST] 2016-07-28 21:42:23 +0000 Debug: responding with:
info: [debug] [INST] 2016-07-28 21:42:23 +0000 Debug: Running system command #15: /usr/local/Cellar/node/6.3.1/bin/node /usr/local/lib/node_modules/appium/node_modules/appium-uiauto/bin/command-proxy-client.js /tmp/instruments_sock 2,{"status":0,"value":""}...
Appium comes out of stuck situation if I manually go back to app.
As mentioned in above logs I tried to click on Alert window Open button using xpath as //UIAbutton[@name='Open']" but it just gets stuck and once I come back to app manually it fails with error [debug] Responding to client with error: {"status":7,"value":{"message":"An element could not be located on the page using the given search parameters."},"sessionId":"9b097c07-9527-4e5f-95a8-a99dba12d9af"}
I can communicate with alert windows in app but not when app goes in background as browser and browser alert window pops-up.