Clinical-Genomics / cg / 15907280448

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fix completed at before started at in analysis table (#4455)(major)

## Description
Part of #4454 
### Summary of changes
1. Makes the fetching of Housekeeper versions for each analysis (in upload and generation of delivery reports) dependent on the version entry id instead of the equality between `analysis.completed_at` date and version date. 
2. Makes the analysis `completed_at` date be `datetime.now()` when called through the `cg workflow store` command, and not dependent on the deliverables file timestamp.

### Added

- Main method to get versions in the `HousekeeperAPI` gets version entry id as parameter, not bundle name and date
- Remove optional parameter `analysis_completed_at` from `generate_delivery_report` CLI command

### Changed

- Make the `AnalysisAPI.create_housekeeper_bundle` method return a tuple of Housekeeper bundle and version (instead of returning None)
- Make several delivery report API methods receive for parameter an Analysis object instead of the `analysis.completed_at date`

### Fixed

- Cleans unused functions and tests

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