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If you insist upon using MettleCI to manage them, the deployment of these files must be controlled in their entirety by a single DataStage project and MettleCI repository that deploys them (as if they were the exclusive owner) for all other projects to use. In that case, they could be treated as if the they were Exclusive to that MettleCI repository.
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In the case where the directory and .apt files contained within are owned by the DataStage project (Scenario 2), use the MettleCI Properties Configuration facility to instruct the deploy script of the location of the directory, by adding a variable into each var.* file in your repository:
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Some projects may involve exclusive .apt files in a shared directory without project-specific prefixes. This too is possible by removing the line to delete selected pre-existing .apt files, but does not provide MettleCI with a way to identify and delete .apt files that are no longer in use.