[r] Use libtiledbsoma handles for arrays

[johnkerl]

Already done for groups

#2406; [sc-55685].

Steps:

• Status quo is
  • There is a private$.tiledb_array with connection to self$object
    • This is set on construction/open, and closed on close
  • The libtiledbsoma handles are currently ephemeral
    • Every read / write / get_metadata etc which is libtiledbsoma-capable currently takes a uri and a ctx and does open/op/close
• Needing to be done:
  • Remove the last refrences to private$.tiledb_array with connection to self$object
    • [r] Remove last private$.tiledb_array and self$object from R classes [WIP] #3129
  • Glitch: while with 3129 we are removing the last references to self$object within R/*.R, there are hundreds of lines of uses of $object within tests/testthat -- tracked on [r] Remove TileDB-R accesses within tests/testthat #3124
  • Then set a libtiledbsoma handle on construction/open, and close it on close
  • Modify all the methods to not take uri+ctx but rather the open handle

To check:

• Currently the array set_metadata does not error out when the array is opened for read -- this is a bug.
  • This should be auto-fixed by this issue, but, it needs to be tested.

[johnkerl]

Blocked by #3051 since here
https://github.com/single-cell-data/TileDB-SOMA/blob/1.15.0rc2/apis/r/R/SOMADataFrame.R#L182
the self$object is used. Removing that private$.tiledb_array / self$object from the base class TileDBArray.R causes this query-condition logic to return empty results, in a way that makes unit-test cases fail in non-obvious ways.

We need to move the query-condition logic over from TileDB-R before we can continue here.

[johnkerl]

This is a duplicate of #3061