Dry run exits before layers etc. create files

[peteschultz]

This pull request moves up the check for the dry run flag to before the RegisterData stage, when many files are first created. With this pull request, the only files created when the dry run flag is set are:

• the outputPath directory (if not already present)
• the checkpointWriteDir (if not already present and checkpointWrite is true)
• The generated .params and .params.lua files in the outputPath directory

This means that when the DryRun flag is set, output from a previous run should not be clobbered, except for the generated .params and .params.lua files.