Defaults: re-score every 10 generations, drop bad hosts, wait 8 h for cores

[eliotmcintire]

Three settings that FireSense runs have always set by hand now take those values by default: DEoptim re-scores its surviving population periodically, a host that fails checks is left out instead of stopping the job, and a job waits for busy cores instead of failing. In the FireSense comparison, re-scoring converged in about half the generations and reached the best scores without lucky draws.

Affects: DEoptim runs that never set clusters.deoptimRescoreEvery now re-score every 10 generations, builds that never set clusters.onBadHost drop failing hosts, and builds that never set clusters.waitForCores wait up to 8 hours for cores.

Technical details

The defaults were hard-coded where read: R/DEoptim.R:253-254 (unset meant 0), R/estimateCluster.R:293 ("stop"), R/allocateWhenAvailable.R:41, R/estimateCluster.R:369 and R/reserveCapacity.R:55 (0). They now come from one list, .optionDefaults in R/optionDefaults.R, read with .clustersOption(); explicit settings, including 0, still win. New tests: tests/testthat/test-optionDefaults.R and the default-10 test in test-DEoptimRescore.R (both fail on development). The test setup sets clusters.waitForCores = 0 so tests that expect an immediate shortfall error do not wait 8 hours. R CMD check on the branch: 0 errors, 0 warnings, 3 existing notes, all tests pass.

Also fixed the two devtools::document() errors: in R/clusters.R the @export/@importFrom tags sat inside \dontrun{} (so plotMachine() and testMachine() were never exported and are now), and R/reservations.R had an @inheritParams for freeCoresLessReserved() that inherited nothing, now removed.

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 74.09%. Comparing base (a095faa) to head (ffd06c8).

Files with missing lines	Patch %	Lines
R/estimateCluster.R	50.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff              @@
##           development      #53   +/-   ##
============================================
  Coverage        74.09%   74.09%           
============================================
  Files               21       22    +1     
  Lines             2061     2061           
============================================
  Hits              1527     1527           
  Misses             534      534           

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