Move graph and bean validation to utils

• Moved graph database initialization and validation to GraphUtils.java.
• Moved bean validation functions to BeanUtils.java.
• Made functions accessible without class initialization.
• Made all Utils classes final with a private empty constructor (no subclassing, no instantiation).
• Moved sub-command specific graph validation to cli for validation package.
• Made input parameters in variation package buissiness logic classes immutable.

requested review from @worku005

assigned to @worku005

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• 1852a2b7 - GraphUtils.createGraphDatabaseService now resolves the database directory to...

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• b300d210 - Fixed Pantools.setPangenomeGraph using the wrong directory, removed instantiation of ConsoleUtils
• 3dd6fe62 - Added private constructor to all utils classes to avoid instantiation.

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marked this merge request as ready

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• 263956de - Updated documentation comments

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• ed205c0a - 1 commit from branch include_variation
• e7ceaa50 - Merge branch 'include_variation' into move_graph_and_bean_validation_to_utils

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• ee1d1f1d - Revert "Merge branch 'include_variation' into move_graph_and_bean_validation_to_utils"

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• fc7e83a1 - Made input parameters in business logic classes immutable in variation package.

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