With the ever-increasing adoption of machine learning for data analytics, maintaining a machine learning pipeline is becoming more complex as both the datasets and trained models evolve with time. In a collaborative environment, the changes and updates due to pipeline evolution often cause cumbersome coordination and maintenance work, raising the costs and making it hard to use. Existing solutions, unfortunately, do not address the version evolution problem, especially in a collaborative environment where non-linear version control semantics are necessary to isolate operations made by different user roles. The lack of version control semantics also incurs unnecessary storage consumption and lowers efficiency due to data duplication and repeated data pre-processing, which are avoidable. In this paper, we identify two main challenges that arise during the deployment of machine learning pipelines, and address them with the design of versioning for an end-to-end analytics system MLCask. The system supports multiple user roles with the ability to perform Git-like branching and merging operations in the context of the machine learning pipelines. We define and accelerate the metric-driven merge operation by pruning the pipeline search tree using reusable history records and pipeline compatibility information. Further, we design and implement the prioritized pipeline search, which gives preference to the pipelines that probably yield better performance. The effectiveness of MLCask is evaluated through an extensive study over several real-world deployment cases. The performance evaluation shows that the proposed merge operation is up to 7.8x faster and saves up to 11.9x storage space than the baseline method that does not utilize history records.