[query] reduce uses of fs.open with compression

[ehigham]

Change Description

This PR refactors stream handling in the codebase by introducing buffering and byte tracking utilities as extension methods. It adds RichCodeInputStream and RichCodeOutputStream classes with methods like buffer and trackBytes to simplify stream creation and management.

The changes remove direct instantiation of BufferedInputStream, BufferedOutputStream, and ByteTrackingOutputStream throughout the codebase, replacing them with the new extension methods. This standardizes stream handling and makes the code more consistent.

The PR also updates various file operations in EmitClassBuilder, MatrixWriter, TableWriter, and other classes to use these new utilities, ensuring consistent stream handling across the codebase.

Security Assessment

This change cannot impact the Hail Batch instance as deployed by Broad Institute in GCP

[ehigham]

Warning

This pull request is not mergeable via GitHub because a downstack PR is open. Once all requirements are satisfied, merge this PR as a stack on Graphite.
Learn more

• [query] reduce uses of fs.open with compression #15196 👈 (View in Graphite)
• [query] remove non-primitives from scala fs #15178
• [query] clean-up unused fs methods #15177
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