Fix errors causing intermittent failures of ServerInModuleDeploymentTestCase

After some in-depth investigation a number of issues have been identified as causing the intermittent failures to the ServerInModuleDeploymentTestCase test case.

1 - The in-memory cached modified time for a deployment can be corrupted if the .deployed marker is deleted after it is written but before the modified time is cached.
2 - Multiple calls after a deployment can cause a .deployed marker to be written, however external processes waiting for the presence of this file so that it can be deleted can delete
it after the first of these calls but before the subsequent call. The end result is that the process thinks it has deleted the file but in some circumstances it is just written again!
3 - The test was written before zipped archives were automatically deployed but not updated - the test case should test the correct behaviour for automatic zip
deployment and deployment based on marker files.

In addition to this modifications to the test revealed that once a deployment scanner has been removed there is an error if there is an attempt to add a new deployment scanner using a name used previously.