Suggest parallelly::availableCores() in mc.cores docs

[ms609-agent]

Prose code blocks that suggest options(mc.cores = parallel::detectCores()) now suggest parallelly::availableCores() instead. detectCores() reports the hardware count. availableCores() respects Slurm/PBS/cgroup allocations, R CMD check's core limit and MC_CORES, so "use all cores" doesn't oversubscribe a shared machine or HPC job.

These are documentation snippets, not run examples, so no Suggests entry is needed. The single-threaded default (getOption("mc.cores", 1L)) is unchanged. R sources and Rd were edited in step: one line per snippet, plus realigning the neighbouring comment.

🤖 Generated with Claude Code

[github-actions]

Performance benchmark results

Call	Status	Change	Time (ms)
ClusteringInfoDistance(tr280)	⚪ NSD	0.29%	9.38, 9.45 → 9.37, 9.4
ClusteringInfoDistance(tr50)	⚪ NSD	-0.79%	6.75, 6.74 → 6.72, 6.84
LAPJV(test2000)	⚪ NSD	0.84%	96.5, 96.5 → 95.4, 96.4
LAPJV(test40)	⚪ NSD	1.63%	0.0184, 0.0185 → 0.0182, 0.018
LAPJV(test400)	⚪ NSD	0.99%	3.26, 3.29 → 3.25, 3.25
MutualClusteringInfo(tr280)	⚪ NSD	2.63%	19.4, 19 → 19.1, 18.1
MutualClusteringInfo(tr50)	⚪ NSD	2.23%	18.4, 18.2 → 18.1, 17.7
NNIMaxStep(2000, normalize = TRUE)	⚪ NSD	0.06%	0.215, 0.214 → 0.215, 0.215
NNIMaxStep(300, normalize = TRUE)	⚪ NSD	0.19%	0.0317, 0.0317 → 0.0317, 0.0317
NNIMaxStep(300)	⚪ NSD	0.89%	0.009, 0.00901 → 0.00891, 0.00896
PathDist(postTrees)	⚪ NSD	-0.13%	2.38, 2.4 → 2.38, 2.4
PhylogeneticInfoDistance(tr180)	⚪ NSD	0.08%	58.3, 58.9 → 58.4, 59.3
PhylogeneticInfoDistance(tr50)	⚪ NSD	-0.41%	43.8, 44 → 44, 44.2
RobinsonFoulds(tr280)	⚪ NSD	-0.33%	4.77, 4.76 → 4.75, 4.81
RobinsonFoulds(tr280)	⚪ NSD	-0.7%	4.58, 4.59 → 4.58, 4.65
RobinsonFoulds(tr50)	⚪ NSD	-1.03%	4.56, 4.55 → 4.56, 4.62

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.57%. Comparing base (5c9e9eb) to head (68eca2d).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #218   +/-   ##
=======================================
  Coverage   97.57%   97.57%           
=======================================
  Files          60       60           
  Lines        6065     6065           
=======================================
  Hits         5918     5918           
  Misses        147      147           

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