Deprecations, documentation and clean up in preparation for 5.0

[palday]

Release TODO

• add entry in NEWS.md
• after opening this PR, add a reference and run docs/NEWS-update.jl to update the cross-references.
• I've bumped the version appropriately

Changes

• deprecated use_threads has been removed (closes Drop multithreading in bootstrap #675)
• deprecated hide_progress has been removed (closes Consistency in progress options #567)
• Optsummary.lowerbd has been removed (remove lowerbd field from OptSummary #849)
• restoreoptsum! tests have been ... restored
• fitlog logic has been simplified (always keep, final is just final fitlog value) (replace fitlog with a column table, always populate it #850)
• nesting syntax in fixed effects is removed (remove local definitions of fulldummy and nesting operator #855)
• README has been updated
• Section on optimization in docs has been updated optimization info/backend updates #853
• Choice of backend and optimizer is abstracted away (allowing us to change the default backend more easily) optimization info/backend updates #853
• dataset and datasets has been removed (remove dataset and datasets #854)
• one-argument GLMM predict supports the type kwarg. (allow specifying type argument in GLMM predict on original data #856)
• likelihoodratiotest has been consolidated with lrtest (rework likelihoodratio test to be just a pretty-printing wrapper around lrtest #858)

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.45%. Comparing base (718af55) to head (908fb5a).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #848      +/-   ##
==========================================
- Coverage   95.51%   95.45%   -0.07%     
==========================================
  Files          38       38              
  Lines        3683     3675       -8     
==========================================
- Hits         3518     3508      -10     
- Misses        165      167       +2     

Flag	Coverage Δ
current	95.15% <ø> (-0.07%)	⬇️
minimum	95.45% <ø> (-0.07%)	⬇️

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