[r] Replace SOMAArray read and write calls with ManagedQuery

[nguyenv]

Issue and/or context:

Part of work for #2054

Changes:

• Change C++ ManagedQuery constructor to take in SOMAArray instead of std::unique_ptr<SOMAArray>. Pybind11 by default holds a unique_ptr (shared_ptr can be used, but there are known issues which prevents us from using it) whereas Rcpp holds a shared_ptr - to easily support both, pass by value rather than smart pointer
• Refactor tiledbsoma-r to use ManagedQuery for read and write queries
• Rename sr_{setup,next,etc} to mq_{setup,next,etc} where mq_setup now returns a ManagedQuery (rather than SOMAArray) that can be iterated through with sr_next
• Update apply_dim_{points,ranges} utility functions to take in a ManagedQuery

Notes for Reviewer:

Planned next steps:

1. Remove read, write, etc. from SOMAArray in C++ API.
2. Currently ManagedQuery::submit_write always calls submit and finalize. Rename ManagedQuery::submit_read to ManagedQuery::submit which both read and write path can use. Create a separate ManagedQuery::finalize.
3. Refactor the tiledbsoma-py write paths so that we only finalize once at the end, even with multiple submits.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.33%. Comparing base (4bcda05) to head (88fc315).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3678      +/-   ##
==========================================
+ Coverage   86.29%   86.33%   +0.04%     
==========================================
  Files          55       55              
  Lines        6390     6390              
==========================================
+ Hits         5514     5517       +3     
+ Misses        876      873       -3     

Flag	Coverage Δ
python	86.33% <ø> (+0.04%)	⬆️

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Components	Coverage Δ
python_api	86.33% <ø> (+0.04%)	⬆️
libtiledbsoma	∅ <ø> (∅)

[mojaveazure]

LGTM; can you bump the develop version (as of now, should bump to 1.16.99.3) https://github.com/single-cell-data/TileDB-SOMA/blob/viviannguyen/r-use-managedquery/apis/r/DESCRIPTION#L9 and add an item to the changelog https://github.com/single-cell-data/TileDB-SOMA/blob/viviannguyen/r-use-managedquery/apis/r/NEWS.md?