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fix: avoid deprecation logs for calling cli stages (#5770)
Avoid deprecating command line calls to cloud-init boot stages. When cloud-init's boot stages are invoked directly on the command line it is typically an attempt to add supplemental configuration to a system after initial boot has completed. Although direct calls to cloud-init boot stages could lead to misconfiguration if boot stages are called out of sequence or customized /etc/cloud/cloud.cfg alters which config modules are run during the boot stage, the support of such uses or custom environments is out of scope for this feature. It remains a simple tool to apply additional configuration via user-data onto an existing system after initial boot. At some point in the future, a new sub-command may be provided by cloud-init tooling to allow for supplemental configuration of user-data post-boot, in that event this --file feature will become deprecated in favor of a cleaner/simpler alternative. Fixes GH-5726
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