Refactoring the ParquetTools read/write APIs

[deephaven-internal]

This issue was auto-generated

PR: https://github.com/deephaven/deephaven-core/pull/5358 Author: malhotrashivam

Original PR Body

Marked a number of parquet read/write APIs as @deprecated. These include methods that accept java File objects, and will be replaced by methods accepting String instead.

Also, added a few new ParquetInstruction to replace some APIs:

• Methods which accept a TableDefinition have been deprecated and will be replaced by setting a new instruction for the definition.
• Similarly, a new instruction for Parquet file layout has been added, which will replace APIs inside ParquetTools which had layout names in the method name (Ex. readSingleFileTable will be replaced by readTable with layout set as single file).
• Added a new instruction for providing index columns for writing. This will be the new default approach and older APIs have been deleted since those were not released yet.

Also, moved some public utility methods outside of ParquetTools, to prevent internal methods being exposed as APIs.

Initial work for this change was started as part of #5206, and has now been moved over to this PR.

[margaretkennedy]

This needs to be rolled into the already ongoing Parquet updates (#21 #45 #22 #48 )