Google Apps has an "Google Apps Email Settings API" which allows to create a new mail filter via an API call.
Is there any (perhaps undocumented) way to get the list of current filters and update them?
A Filter object was added to the API that allows for filter processing, including retrieval, creation and deletion.
https://developers.google.com/gmail/api/guides/filter_settings
Specifically:
Listing Filters
GET https://www.googleapis.com/gmail/v1/users/userId/settings/filters
Returns a JSON list of Filter objects
Retrieving a specific Filter
GET https://www.googleapis.com/gmail/v1/users/userId/settings/filters/id
Returns a single JSON Filter object
Deleting a specific Filter
DELETE https://www.googleapis.com/gmail/v1/users/userId/settings/filters/id
Creating a Filter
POST https://www.googleapis.com/gmail/v1/users/userId/settings/filters
With a JSON encoded Filter in the request body.
While the REST URLs have v1 in the address, they are linked from the current documentation. Also note, GMail API migration is currently in progress, and the deprecated API will cease to function as of July 2016. Keep this in mind, as the API may change.