Set the HomeOrgs store url in the controller

Setting the HomeOrgs store proxy url in the controller is more
robust. The Config object might not be available when the
HomeOrgs store is included. Setting the url after the store is
instantiated is more robust and reliable.
Update cordova plugins to the last versions
Cordova File 1.0.1;switched to cdvfile:// protocol

The upgrade affected several parts of the app.
The new plugin distinguishes between the internal app storage
and the previous sdcard storage. The new protocol for accessing
files is cdvfile://.

All the files are now stored under: cdvfile://localhost/persistent

This commit adds a bunch of console.log statements because of the
transition to the new Cordova File plugin.

Here is a list of changes:

- Webservice: use fileEntry.toURL() instead of fileEntry.fullPath
- controller/Settings: use fileEntry.toURL() instead of fileEntry.fullPath
- controller/Scorm
  + use fileEntry.toURL() instead of fileEntry.fullPath
  + renamed getArchive to processArchive; better name
  + separated the downloading and parsing completely.
    After the archive has been downloaded the processArchive
    is called instead of the parseScorm. It is a better and more
    general approach.
  + adapted the code to work with the cdvfile://localhost/persistent
    paths.
- supsi/Filesystem:
  + use fileEntry.toURL() instead of fileEntry.fullPath
  + refactored getDirectory, it now uses the new function
    createDirectory
  + commented some leftover code that wasn't doing anything useful
  + refactored getFile function
- js/android/extensions: use fileEntry.toURL() instead of fileEntry.fullPath
- js/ios/extensions: use fileEntry.toURL() instead of fileEntry.fullPath